| Package |
Latest Version |
Doc |
Dev |
License |
linux-64 | osx-64 | win-64 | noarch | Summary |
| 10x_bamtofastq |
1.4.1 |
|
|
MIT |
X | X | | | Tool for converting 10x BAMs produced by Cell Ranger, Space Ranger,... |
| 2pg_cartesian |
1.0.1 |
|
|
Apache |
X | | | | 2pg cartesian is a framework of optimization algorithms for protein... |
| 3d-dna |
201008 |
|
|
MIT |
| | | X | 3D de novo assembly (3D-DNA) pipeline. |
| 3seq |
1.8 |
|
|
CC-BY-NC-SA-4.0 |
X | X | | | 3SEQ tests all sequence triplets in an alignment for a mosaic... |
| a3partitioner |
0.1.0 |
doc |
|
MIT |
| | | X | A bioinformatics tool for creating APOBEC3 and non-APOBEC3 partitions |
| a5-miseq |
20160825 |
|
|
GPLv3 |
X | | | X | A5-miseq is a pipeline for assembling DNA sequence data generated on... |
| aacon |
1.1 |
|
dev |
Apache-2.0 |
| | | X | AACon: A Fast Amino Acid Conservation Calculation Service |
| abacas |
1.3.1 |
doc |
|
GPL-2.0-or-later |
| | | X | ABACAS is intended to rapidly contiguate (align, order, orientate),... |
| abacat |
0.0.4a |
|
|
MIT |
| | | X | abacat - A BActerial genome Curation and Annotation Toolkit |
| abawaca |
1.00 |
|
|
open |
X | X | | | abawaca is a binning program for metagenomics |
| abeona |
0.45.0 |
doc |
dev |
Apache |
X | X | | X | A simple transcriptome assembler based on kallisto and Cortex graphs. |
| abismal |
3.2.4 |
doc |
dev |
GPL-3.0-only |
X | X | | | abismal is a fast and memory-efficient mapper for short bisulfite... |
| abnumber |
0.4.3 |
|
|
MIT |
| | | X | AbNumber - Antibody numbering using ANARCI |
| abpoa |
1.5.3 |
|
|
MIT |
X | X | | | abPOA: fast SIMD-based partial order alignment using adaptive band |
| abra2 |
2.24 |
|
|
MIT |
X | | | | ABRA2 is an updated implementation of ABRA |
| abricate |
1.0.1 |
|
|
GPL-2.0-only |
X | X | | X | Mass screening of contigs for antibiotic resistance genes |
| abritamr |
1.0.19 |
|
dev |
GPL-3.0-only |
| | | X | Running AMRFinderPlus for MDU |
| abromics_galaxy_json_extractor |
0.8.3.6 |
doc |
dev |
GPLv3 |
| | | X | Tool to convert Galaxy AMR output to abromics project |
| abruijn |
2.1b |
|
|
BSD-3-Clause |
X | X | | | Long read assembly via A-Bruijn graph |
| absense |
1.0.1 |
|
|
GPL-3.0-or-later |
| | | X | abSENSE: a method to interpret undetected homologs |
| abundancebin |
1.0.1 |
|
|
copyright |
X | X | | | Abundance-based tool for binning metagenomic sequences |
| abyss |
2.3.10 |
doc |
dev |
GPL-3.0-only |
X | X | | | Assembly By Short Sequences - a de novo, parallel, paired-end short... |
| abyss-k128 |
2.0.2 |
|
|
GPL3 |
X | | | | Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler |
| ac |
1.1 |
|
|
GPL3 |
X | | | | A lossless compression tool for Amino Acid sequences |
| ac-diamond |
1.0 |
|
|
GNU |
X | | | | AC-DIAMOND is a DNA-protein alignment tool |
| acdc |
1.02 |
doc |
dev |
MIT |
X | | | | (a)utomated (c)ontamination (d)etection and (c)onfidence estimation for... |
| aci |
1.4.20240116 |
doc |
|
MIT |
| | | X | Visualizes coverage for amplicons |
| acms |
1.3.0 |
|
|
GPL-3.0-or-later |
X | | | | Ambivalent Covariance Models (aCMs) are our prototypic suggestion to... |
| actc |
0.6.0 |
|
|
BSD-3-Clause-Clear |
X | | | | PacBio utility to align clr to ccs reads |
| adam |
1.0.1 |
|
|
Apache-2.0 |
X | X | | X | Genomics analysis platform built on Apache Avro, Apache Spark, and... |
| adapt |
1.6.0 |
|
|
MIT |
| | | X | A package to efficiently design activity-informed nucleic acid... |
| adapterremoval |
2.3.4 |
|
|
GPL3 |
X | X | | | The AdapterRemoval v2 tool for merging and clipping reads. |
| adapterremovalfixprefix |
0.0.5 |
|
|
GPLv3 |
X | X | | X | Fixes adapter removal prefixes to make sure no clashing read names are... |
| adas |
0.1.3 |
|
|
MIT |
X | | | | adas is a sequence database search engine for long sequences. It is an... |
| addrg |
0.2.1 |
|
|
MIT |
X | X | | | Add read group to BAM files |
| admixtools |
7.0.2 |
|
|
Free |
X | X | | | ADMIXTOOLS (Patterson et al. 2012) is a software package that supports... |
| admixture |
1.3.0 |
|
|
Free |
X | X | | | ADMIXTURE is a software tool for maximum likelihood estimation of... |
| adpred |
1.3.1 |
|
|
MIT |
| | | X | python adpred module for prediction of Transcription activation domains... |
| advntr |
1.5.0 |
|
|
BSD |
X | X | | | A tool for genotyping Variable Number Tandem Repeats (VNTR) from sequence data |
| aegean |
0.16.0 |
|
|
ISC |
X | | | | The AEGeAn Toolkit provides a bundle of software tools for evaluating... |
| aenum |
2.0.8 |
|
|
BSD |
X | X | | | Advanced Enumerations (compatible with Python's stdlib Enum),... |
| aeon |
0.1.1 |
|
|
MIT |
X | X | | | Python/Rust library for symbolic manipulation of Boolean networks. |
| afpdb |
0.2.3 |
doc |
|
MIT |
| | | X | A Numpy-based PDB structure manipulation package |
| afplot |
0.2.1 |
|
|
MIT |
X | X | | X | Plot allele frequencies in VCF files |
| afragmenter |
0.0.3 |
|
|
MIT |
| | | X | Schema-free, tunable protein domain segmentation tool for AlphaFold structures |
| afterqc |
0.9.7 |
|
|
MIT |
X | X | | X | Automatic Filtering, Trimming, Error Removing and Quality Control for... |
| agat |
1.4.2 |
doc |
dev |
GPLv3 |
| | | X | Another Gff Analysis Toolkit (AGAT). Suite of tools to handle gene... |
| agc |
3.2 |
|
|
MIT |
X | X | | | Assembled Genomes Compressor (AGC) is a tool designed to compress... |
| age-metasv |
2015.01.29.3 |
|
|
CCPL |
X | X | | | optimal alignment of sequences with structural variants (SVs),... |
| agfusion |
1.252 |
|
|
MIT |
X | X | | X | Python package to annotate and visualize gene fusions. |
| agg |
0.3.6 |
|
|
GPL3 |
X | X | | | gvcf aggregation tool |
| agouti |
1.0.3 |
doc |
|
GNU |
| | | X | Annotation of Genomic and Transcriptomic Intervals |
| agrvate |
1.0.2 |
|
|
MIT |
| | | X | Rapid identification of Staphylococcus aureus agr locus type and agr... |
| airr |
1.5.1 |
|
|
CC |
| | | X | AIRR Community Data Representation Standard reference library for... |
| akt |
0.3.3 |
|
|
GPL3 |
X | X | | | Ancestry and Kinship Tools (AKT) |
| albatradis |
1.0.4 |
|
|
GNU |
X | X | | | Comparative TraDIS analysis |
| alcor |
1.9 |
|
|
GPL |
X | | | | Software for alignment-free simulation, mapping, and visualization of... |
| alder |
1.03 |
|
|
Custom |
X | X | | | The ALDER software computes the weighted linkage disequilibrium (LD)... |
| ale |
20180904 |
|
|
NCSA |
X | X | | | ALE: Assembly Likelihood Estimator |
| ale-core |
20220503 |
|
|
NCSA |
X | X | | | ALE: Assembly Likelihood Estimator. Core C implemented scoring... |
| alen |
0.3.1 |
|
|
MIT |
X | X | | | Simple terminal sequence alignment viewer |
| aletsch |
1.1.3 |
|
|
BSD-3-Clause |
X | X | | | Aletsch is an accurate, versatile assembler for multiple RNA-seq samples. |
| alevin-fry |
0.11.2 |
|
|
BSD |
X | X | | | alevin-fry is a tool for the efficient processing of single-cell data... |
| alfa |
1.1.1 |
|
|
MIT |
| | | X | A simple software to get a quick overview of features composing NGS dataset(s). |
| alfred |
0.3.2 |
|
|
BSD-3-Clause |
X | X | | | BAM alignment statistics, feature counting and feature annotation |
| align_it |
1.0.4 |
|
|
LGPL |
X | | | | Align-it is a tool to align molecules according to their... |
| aligncov |
0.0.2 |
|
|
MIT |
| | | X | Obtain tidy alignment coverage info from sorted BAM files |
| alignlib-lite |
0.3 |
doc |
dev |
GPL-2.0-or-later |
X | X | | | Simple wrapper around alignlib C++ library for sequence alignment. |
| alignment |
1.0.10 |
|
|
BSD |
| | | X | Native Python library for generic sequence alignment. |
| alignoth |
0.13.0 |
|
|
MIT |
X | | | | A tool for creating alignment plots from bam files |
| alignstats |
0.11 |
|
|
BSD-3-Clause |
X | X | | | Comprehensive alignment, whole-genome coverage, and capture coverage statistics. |
| aliview |
1.30 |
|
dev |
GPL-3.0-or-later |
| | | X | AliView is an intuitive and fast alignment viewer and editor for DNA... |
| allegro |
3 |
|
|
INDIVIDUAL |
X | X | | | A fast linkage and haplotype analysis utility making use of MTBDD to... |
| allhic |
0.9.14 |
|
dev |
BSD-3-Clause |
X | X | | | Genome scaffolding based on HiC data in heterozygous and high ploidy genomes |
| allo |
1.2.0 |
|
dev |
MIT |
| | | X | Multi-mapped read rescue strategy for gene regulatory analyses |
| altair-mf |
1.0.1 |
|
|
GPL |
X | | | | Software for alignment-free and spatial-temporal analysis of multi-FASTA data |
| altamisa |
0.3.0 |
|
|
MIT |
| | | X | Alternative Python API for accessing ISA-tab files. |
| alv |
1.7.2 |
|
|
GPL-3.0-only |
| | | X | A console-based sequence alignment viewer |
| amap |
2.2 |
|
dev |
GPL-2 |
X | X | | | AMAP is a multiple sequence alignment program based on sequence annealing. |
| amas |
1.0 |
|
|
GPL-3.0-or-later |
| | | X | Calculate various summary statistics on a multiple sequence alignment |
| amdirt |
1.6.5 |
|
dev |
GPL-3.0 |
| | | X | amdirt: AncientMetagenomeDir Toolkit |
| amiga |
3.0.3 |
|
|
GPL-3.0-or-later |
X | X | | | Analysis of Microbial Growth Assays |
| aminoextract |
0.3.1 |
|
dev |
MIT |
| | | X | AminoExtract is an application to extract aminoacid sequences from a... |
| amos |
3.1.0 |
|
|
Artistic |
X | | | | A Modular, Open-Source whole genome assembler |
| ampcombi |
2.0.1 |
doc |
dev |
MIT |
| | | X | A parsing tool to convert and summarise the outputs from multiple AMP... |
| ampd-up |
1.0.0 |
|
|
GPL-3 |
| | | X | De novo antimicrobial peptide sequence generation with recurrent neural networks |
| amplici |
2.2 |
|
dev |
BSD |
X | X | | | AmpliCI: Cluster amplicon sequences in a fastq file with or without UMIs. |
| amplicon_coverage_plot |
0.3.4 |
|
|
GPLv3 |
| | | X | Generate an amplicon coverage plot |
| ampliconclassifier |
0.4.14 |
|
dev |
BSD |
| | | X | AmpliconClassifier classifies the output of AmpliconArchitect to detect... |
| ampliconsuite |
1.3.5 |
|
|
BSD |
| | | X | An end-to-end wrapper for focal amplification analysis from... |
| amplicontyper |
0.1.29 |
|
|
GPL-3.0-only |
| | | X | Tool for training model and classifying reads from environmental ONT... |
| amplify |
2.0.1 |
|
|
GPL-3 |
| | | X | Attentive deep learning model for antimicrobial peptide prediction |
| ampligone |
1.3.1 |
doc |
dev |
GNU |
| | | X | Ampligone is a tool which accurately removes primer sequences from... |
| amplisim |
0.2.1 |
|
|
Apache |
X | | | | Plain simple amplicon sequence simulator for in-silico genomic... |
| amptk |
1.6.0 |
doc |
|
BSD-2-Clause |
X | X | | X | AMPtk: Amplicon tool kit for processing high throughput amplicon... |
| amused |
1.0 |
|
|
GPL-2.0 |
X | X | | X | Auditing Motifs Using Statistical Enrichment & Depletion |
| anadama2 |
0.10.0 |
doc |
|
MIT |
| | | X | AnADAMA2: Another Automated Data Analysis Management Application 2 |
| ananse |
0.5.1 |
|
|
MIT |
| | | X | ANANSE: ANalysis Algorithm for Networks Specified by Enhancers -... |
| anansescanpy |
1.0.0 |
|
|
Apache-2.0 |
| | | X | implementation of scANANSE for scanpy objects in Python |
| anansnake |
0.1.0 |
|
|
Apache-2.0 |
| | | X | Automated ANANSE analysis with seq2science & snakemake! |
| anarci |
2024.05.21 |
|
|
BSD-3-Clause |
| | | X | ANARCI: Antibody Numbering and Antigen Receptor ClassIfication |
| ancestry_hmm |
1.0.2 |
|
|
GPL3 |
X | X | | | Software for local ancestry inference |
| ancestry_hmm-s |
0.9.0.2 |
|
|
GPL3 |
X | X | | | Inferring adaptive introgression from genomic data using hidden Markov models |
| anchorwave |
1.2.5 |
|
dev |
MIT |
X | X | | | Sensitive alignment of genomes with high sequence diversity, extensive... |
| andi |
0.14 |
|
|
GPL-3.0-or-later |
X | X | | | Efficient Estimation of Evolutionary Distances |
| anglerfish |
0.7.0 |
|
|
MIT |
| | | X | Anglerfish, a tool to demultiplex Illumina libraries from ONT data |
| angsd |
0.940 |
|
|
GPLv3, |
X | | | | ANGSD: Analysis of next generation Sequencing Data |
| aniclustermap |
1.4.0 |
|
|
MIT |
| | | X | A tool for drawing ANI clustermap between all-vs-all microbial genomes |
| anise_basil |
1.2.0 |
|
|
BSD |
X | X | | | BASIL is a method to detect breakpoints for structural variants... |
| anndata |
0.6.22.post1 |
doc |
dev |
BSD-3-Clause |
| | | X | An annotated data matrix. |
| anndata2ri |
1.3.2 |
|
|
GPL-3 |
| | | X | Convert between AnnData and SingleCellExperiment |
| annembed |
0.2.2 |
|
|
MIT |
X | | | | annembed is an ultra-fast and scalable non-linear dimension... |
| annonars |
0.41.0 |
|
|
Apache-2.0 |
X | | | | Genome annotation based on Rust and RocksDB. |
| annosine2 |
2.0.8 |
doc |
dev |
MIT |
| | | X | AnnoSINE_v2 - SINE Annotation Tool for Plant and Animal Genomes. |
| annotsv |
3.4.4 |
|
|
GPL-3.0-only |
| | | X | Annotation and Ranking of Structural Variation |
| annotwg |
1.0 |
|
|
CeCILL |
| | | X | Tool for annotating large VCF files |
| anospp-analysis |
0.3.0 |
|
|
MIT |
| | | X | ANOSPP data analysis |
| ansible |
1.9.4 |
|
|
GPLv3 |
X | X | | | None |
| ant |
1.10.0 |
|
|
Apache |
X | X | | | Apache Ant is a Java library and command-line tool that help building software. |
| antarna |
2.0.1.2 |
|
|
The |
X | | | | antaRNA is a python based implementation of ant-colony optimization of... |
| antismash |
7.1.0 |
doc |
dev |
AGPL-3.0-or-later |
X | X | | X | antiSMASH - the antibiotics and Secondary Metabolite Analysis SHell |
| antismash-lite |
7.1.0 |
doc |
dev |
AGPL-3.0-or-later |
| | | X | antiSMASH - the antibiotics and Secondary Metabolite Analysis SHell |
| anvio |
7 |
|
dev |
GPL-3.0-or-later |
X | X | | X | A platform for integrated multi-omics |
| anvio-minimal |
8 |
doc |
dev |
GPL-3.0-or-later |
X | X | | X | An interactive analysis and visualization platform for omics data |
| any2fasta |
0.4.2 |
|
|
GPL-3.0 |
X | X | | X | Convert various sequence formats to FASTA |
| aodp |
2.5.0.2 |
|
|
GPL-3.0-only |
X | | | | Cluster oligonucleotide signatures for rapid identification by sequencing |
| aplanat |
0.5.6 |
doc |
dev |
Mozilla |
| | | X | Bokeh plotting API, with bio-focussed extras. |
| apoc |
1b16 |
|
|
This |
X | X | | | Large-scale structural comparison of protein pockets |
| apollo |
4.2.13 |
|
|
MIT |
| | | X | WebApollo API library |
| appspam |
1.03 |
doc |
|
GPL3 |
X | X | | | Alignment-free Phylogenetic Placement algorithm based on Spaced-word Matches |
| aprfinder |
1.5 |
|
|
MIT |
X | X | | | Tool for finding aphased repeats. |
| apscale |
2.0.4 |
|
dev |
MIT |
| | | X | Advanced Pipeline for Simple yet Comprehensive AnaLysEs of DNA... |
| apt-probeset-summarize |
2.10.0 |
|
|
GNU |
X | | | | From Affymetrix Power Tools package. apt-probeset-summarize is program... |
| aptardi |
1.4 |
|
|
MIT |
| | | X | aptardi is a tool that predicts polyA sites from RNA-Seq data and DNA sequence |
| apu-label-propagation |
1.2 |
|
|
MIT |
X | X | | | Adaptive Positive-Unlabelled label propagation |
| aquamis |
1.4.0 |
|
|
BSD-3 |
| | | X | AQUAMIS is a snakemake pipeline for routine assembly and quality... |
| aquila |
1.0.0 |
|
|
MIT |
| | | X | Diploid personal genome assembly and comprehensive variant detection... |
| aquila_stlfr |
1.2.11 |
|
|
MIT |
| | | X | Diploid assembly and variants calling for stLFR and hybrid assembler... |
| aquila_sv |
1.0 |
|
|
MIT |
| | | X | Diploid assembly and variants calling tool |
| aquila_umap |
1.0 |
|
|
MIT |
| | | X | This is a program to generate Umap for Aquila diploid assembly. |
| aquilasv |
1.5 |
|
|
MIT |
| | | X | A region-based diploid assembly and variants calling tool |
| aragorn |
1.2.41 |
|
|
GPLv3 |
X | X | | | ARAGORN, tRNA (and tmRNA) detection |
| arb-bio |
6.0.6 |
doc |
dev |
ARB |
X | X | | | ARB 6 Sequence Analysis Suite |
| arb-bio-devel |
6.0.6 |
doc |
dev |
ARB |
X | X | | | ARB 6 Sequence Analysis Suite |
| arb-bio-tools |
6.0.6 |
doc |
dev |
ARB |
X | X | | | ARB 6 Sequence Analysis Suite |
| arborator |
1.0.0 |
|
dev |
Apache-2.0 |
| | | X | Arborator: Simplifying operationalized pathogen surveillance and... |
| arboreto |
0.1.6 |
|
|
BSD |
| | | X | Scalable gene regulatory network inference using tree-based ensemble regressors |
| arcas-hla |
0.6.0 |
|
|
GPL-3.0-only |
| | | X | high-resolution HLA typing from RNA seq |
| archer |
0.1.1 |
|
|
MIT |
X | X | | | Pre-process amplicon data before running CLIMB workflows. |
| architeuthis |
0.3.1 |
|
dev |
Apache-2.0 |
X | X | | | Tool to analyze and summarize data for Kraken. |
| arcs |
1.2.8 |
|
|
GPL-3.0-or-later |
X | X | | | Scaffolding genome sequence assemblies using linked or long reads |
| arcsv |
1.0.2 |
|
|
GPL-3.0 |
| | | X | A pipeline to detect SV in archaic human |
| arem |
1.0.1 |
|
|
Artistic |
X | X | | X | Aligning Reads by Expectation-Maximization.\nBased on MACS (Model Based... |
| argh |
0.26.1 |
|
|
GNU |
X | X | | | None |
| argnorm |
0.7.0 |
doc |
|
MIT |
| | | X | Normalize antibiotic resistance genes (ARGs) abundance tables (e.g.,... |
| argo |
0.2.0 |
|
|
MIT |
| | | X | Argo: species-resolved profiling of antibiotic resistance genes in... |
| argparse |
1.4.0 |
|
|
Python |
X | X | | | Python command-line parsing library |
| argparse2tool |
0.5.2 |
doc |
dev |
Apache-2.0 |
| | | X | Instrument for forming Galaxy XML and CWL tool descriptions from... |
| args_oap |
3.2.4 |
|
|
MIT |
| | | X | ARGs-OAP: Online Analysis Pipeline for Antibiotic Resistance Genes... |
| argutils |
0.3.2 |
|
|
GNU |
X | X | | | Functions to build matched argument parsers and config files |
| aria2 |
1.34.0 |
|
dev |
GPL-2.0 |
X | X | | | aria2 is a lightweight multi-protocol & multi-source, cross... |
| ariba |
2.14.6 |
|
|
GNU |
X | X | | | ARIBA: Antibiotic Resistance Identification By Assembly |
| array-as-vcf |
1.1.0 |
doc |
dev |
MIT |
| | | X | Convert SNP array to VCF |
| arriba |
2.4.0 |
|
|
MIT |
X | X | | | Fast and accurate gene fusion detection from RNA-Seq data |
| art |
2016.06.05 |
|
|
GPL-3.0-only |
X | X | | | Illumina, 454 and Solid read simulator |
| artemis |
18.2.0 |
|
|
GPL-3.0 |
X | X | | X | A set of Java genome visualization tools including the Artemis genome... |
| artex |
0.2.0 |
|
|
GPL-3.0 |
X | | | | Artex - Artic pipeline extension |
| artic |
1.6.2 |
doc |
dev |
MIT |
| | | X | ARTIC pipeline - a bioinformatics pipeline for working with virus... |
| artic-porechop |
0.3.2pre |
|
|
GPL3 |
X | X | | | Adapter removal and demultiplexing of Oxford Nanopore reads (fork of... |
| artic-tools |
0.3.1 |
|
|
MIT |
X | X | | | A set of tools for working with the ARTIC bioinformatic pipeline. |
| arvados-cli |
0.1.20151207150126 |
|
|
Apache |
X | | | | None |
| arvados-cwl-runner |
2.7.0 |
|
|
Apache |
X | X | | X | Arvados Common Workflow Language runner |
| arvados-python-client |
3.0.0 |
|
|
Apache-2.0 |
X | X | | X | Python API for Arvados |
| ascat |
3.2.0 |
doc |
dev |
GPL-3.0-or-later |
X | X | | X | ASCAT is a method to derive copy number profiles of tumour cells,... |
| asciigenome |
1.18.0 |
doc |
|
MIT |
X | X | | X | Command-line genome browser running from terminal window and solely... |
| asgal |
1.1.8 |
|
|
GPL-3.0-or-later |
X | | | | A graph aligner |
| ashlar |
1.19.0 |
doc |
|
MIT |
| | | X | Alignment by Simultaneous Harmonization of Layer/Adjacency Registration |
| ashleys-qc |
0.2.1 |
|
|
MIT |
| | | X | Automated Selection of High quality Libraries for the Extensive... |
| askocli |
0.5 |
|
|
GNU |
X | X | | X | Command line interface for a distant AskOmics |
| asn2gb |
18.2 |
|
|
Public |
X | X | | | asn2gb converts ASN1 format sequence records to Genbank format |
| aspera-cli |
4.20.0 |
doc |
dev |
Apache-2.0 |
| | | X | Command Line Interface for IBM Aspera products. |
| asqcan |
0.4 |
|
|
GPL-3.0-only |
X | | | X | A combined pipeline for bacterial genome assembly, quality control and... |
| assemblerflow |
1.1.0.post3 |
doc |
dev |
GPL3 |
X | X | | X | A Nextflow pipeline assembler for genomics. Pick your modules. Assemble... |
| assembly-scan |
1.0.0 |
|
|
MIT |
X | X | | X | Assembly summary statistics in JSON format |
| assembly-stats |
1.0.1 |
|
|
GPL-3.0 |
X | X | | | Get assembly statistics from FASTA and FASTQ files |
| assembly_finder |
0.8.0 |
doc |
dev |
MIT |
| | | X | Snakemake-powered cli pipeline to download genomes with NCBI datasets |
| assemblycomparator2 |
2.7.1 |
doc |
dev |
GPL-3.0-or-later |
X | | | X | Assemblycomparator2: Genomes to report pipeline |
| assemblytics |
1.2.1 |
|
|
MIT |
| | | X | analyze a genome assembly by comparing it to a reference genome |
| assemblyutility |
20160209 |
|
|
MIT |
X | X | | | Tools for DBG2OLC genoome assembler |
| astalavista |
4.0 |
|
|
BSD |
X | X | | X | AStalavista is a computer program to extract alternative splicing (AS)... |
| aster |
1.19 |
|
|
AGPL-3.0-or-later |
X | X | | | Accurate Species Tree EstimatoR series; a family of optimation... |
| astral-tree |
5.7.8 |
|
|
Apache |
| | | X | ASTRAL is a tool for estimating an unrooted species tree given a set of... |
| atac |
2008 |
|
|
GPL |
X | X | | | ATAC is a computational process for comparative mapping between two... |
| atactk |
0.1.9 |
|
|
GPL-3.0-or-later |
X | | | X | A toolkit for working with ATAC-seq data. |
| ataqv |
1.3.1 |
doc |
dev |
GPL-3.0-only |
X | X | | | ataqv is a toolkit for measuring and comparing ATAC-seq results. It was... |
| athena_meta |
1.3 |
|
|
MIT |
X | | | X | Athena read cloud assembler for metagenomes |
| atlas |
2.0.0 |
|
|
MPL-2.0 |
X | X | | | ATLAS: Analysis Tools for Ancient and Low-depth Samples |
| atlas-data-import |
0.1.1 |
|
|
MIT |
| | | X | Scripts for extracting expression- and metadata from Single Cell... |
| atlas-fastq-provider |
0.4.7 |
|
|
GPL-3 |
| | | X | A package to provide FASTQs via download or file system linking. |
| atlas-gene-annotation-manipulation |
1.1.1 |
|
|
Apache-2.0 |
| | | X | Scripts for manipulating gene annotation |
| atlas-metadata-validator |
1.6.1 |
|
|
Apache |
| | | X | A MAGE-TAB validator for Expression Atlas and Single Cell Expression Atlas |
| atol-bpa-datamapper |
0.1.2 |
|
|
GPL-3.0-or-later |
| | | X | Map data from the BPA data portal for AToL's Genome Engine. |
| atropos |
1.1.32 |
doc |
|
CC0 |
X | X | | | trim adapters from high-throughput sequencing reads |
| attotree |
0.1.6 |
doc |
|
MIT |
| | | X | rapid estimation of phylogenetic trees using sketching |
| augur |
29.0.0 |
doc |
dev |
AGPL-3.0-only |
| | | X | Process pathogen genome data for the Nextstrain platform. |
| augustus |
3.5.0 |
doc |
dev |
Artistic |
X | X | | | AUGUSTUS is a gene prediction program for eukaryotes written by Mario... |
| auriclass |
0.5.4 |
|
dev |
GNU |
| | | X | AuriClass is a tool for quickly predicting the clade of a Candida auris genome. |
| auspice |
2.62.0 |
doc |
dev |
AGPL-3.0-only |
X | X | | | Auspice is an open-source interactive tool for visualising phylogenomic data |
| authentict |
1.0.1 |
|
|
GPL3 |
X | X | | | Estimates present-day DNA contamination in ancient DNA single-stranded... |
| autobigs-cli |
0.6.3 |
|
|
GPL-3.0-or-later |
| | | X | A CLI tool to rapidly fetch fetch MLST profiles given sequences for... |
| autobigs-engine |
0.13.0 |
|
dev |
GPL-3.0-or-later |
| | | X | A library to rapidly fetch fetch MLST profiles given sequences for... |
| autocycler |
0.2.1 |
doc |
dev |
GPL-3.0-or-later |
X | X | | | A tool for generating consensus long-read assemblies for bacterial genomes. |
| autodock |
4.2.6 |
|
|
GPL-2.0-only |
X | X | | | AutoDock is a suite of automated docking tools. |
| autodock-vina |
1.1.2 |
|
|
Apache |
X | X | | | AutoDock Vina is an open-source program for doing molecular docking |
| autogenes |
1.0.4 |
|
|
MIT |
| | | X | Automatic Gene Selection for Bulk Deconvolution. |
| autogrid |
4.2.6 |
|
|
GPL-2.0-only |
X | X | | | AutoDock is a suite of automated docking tools. |
| autolog |
0.2 |
|
|
GNU |
X | X | | X | quick and easy logging setup |
| automappa |
2.1.0 |
doc |
dev |
AGPL-3.0 |
| | | X | Automappa: An interactive interface for exploration of metagenomes |
| autometa |
2.2.3 |
doc |
dev |
AGPL-3.0 |
| | | X | Automated extraction of genomes from shotgun metagenomes |
| aviary |
0.11.1 |
doc |
dev |
GPL-3.0-or-later |
| | | X | End-to-end metagenomics hybrid assembly and binning pipeline. |
| avro |
1.8.0 |
|
|
Apache |
X | X | | | None |
| avro-cwl |
1.8.9 |
|
|
Apache |
X | X | | X | Avro is a serialization and RPC framework. This package is a fork of... |
| avro-python2 |
1.9.0 |
|
|
Apache |
X | X | | X | Avro is a serialization and RPC framework. |
| avro-python3 |
1.9.0 |
|
|
Apache |
X | X | | X | Avro is a serialization and RPC framework. |
| awscli |
1.8.3 |
|
|
Apache |
X | X | | | None |
| axiome |
2.0.4 |
|
|
MIT |
X | X | | X | AXIOME2: Automation Extension and Integration of Microbial Ecology |
| azure-cli |
0.10.3 |
|
|
Apache |
X | X | | | Microsoft Azure Cross Platform Command Line |
| b2b-utils |
0.019 |
|
dev |
GPL-3.0-or-later |
X | X | | | Genomics tools from BASE2BIO |
| b2btools |
3.0.7 |
doc |
dev |
GNU |
X | X | | X | The bio2Byte software suite to predict protein biophysical properties |
| bacgwasim |
2.1.1 |
|
|
MIT |
| | | X | BacGWASim is a simulator for Bacterial Machine learning and Genome-wide... |
| backports.csv |
1.0.1 |
|
|
UNKNOWN |
X | X | | | Backport of Python 3 csv module |
| backports.unittest_mock |
1.3 |
|
|
MIT |
X | X | | X | backports.unittest_mock |
| backspinpy |
0.2.1 |
|
|
MIT |
X | X | | X | backSPIN clustering algorythm |
| bacpage |
2024.03.08 |
doc |
dev |
GPL-3.0-or-later |
| | | X | An easy-to-use pipeline for the assembly and analysis of bacterial genomes |
| bacphlip |
0.9.6 |
|
|
MIT |
| | | X | A Random Forest classifier to predict bacteriophage lifestyle |
| bactopia |
3.1.0 |
|
dev |
MIT |
| | | X | Bactopia is a flexible pipeline for complete analysis of bacterial genomes. |
| bactopia-assembler |
1.0.4 |
|
dev |
MIT |
| | | X | The assembly process used by Bactopia. |
| bactopia-gather |
1.0.4 |
|
dev |
MIT |
| | | X | The methods used in Bactopia to gather all samples into one place |
| bactopia-py |
1.5.0 |
|
|
MIT |
| | | X | A Python package for working with Bactopia |
| bactopia-qc |
1.0.3 |
|
dev |
MIT |
| | | X | The methods used in Bactopia for read QC |
| bactopia-sketcher |
1.0.2 |
|
dev |
MIT |
| | | X | Methods used by Bactopia for minmer sketching |
| bactopia-teton |
1.1.1 |
|
dev |
MIT |
| | | X | Methods used by Bactopia for taxonomic classification |
| bactopia-variants |
1.0.2 |
|
dev |
MIT |
| | | X | Methods used by Bactopia for SNP and InDel analysis |
| baczy |
1.0.3 |
doc |
dev |
MIT |
| | | X | Bacterial toolkit |
| badread |
0.4.1 |
|
|
GNU |
| | | X | A long read simulator that can imitate many types of read problems |
| baitfisher |
1.0 |
|
|
GPL3 |
X | X | | | The BaitFisher-package is a software package for designing hybrid... |
| bakdrive |
1.0.4 |
|
|
MIT |
| | | X | Bakdrive finds a minimum set of driver species from real metagenomic... |
| bakta |
1.11.0 |
doc |
dev |
GPL-3.0-or-later |
| | | X | Rapid & standardized annotation of bacterial genomes, MAGs & plasmids. |
| bali-phy |
4.0 |
|
dev |
GPL2 |
X | X | | | Phylogenetics - Bayesian estimation of phylogenies and multiple... |
| balrog |
0.5.1 |
|
|
MIT |
X | X | | | Balrog: A universal protein model for prokaryotic gene prediction |
| baltic |
0.3.0 |
|
dev |
GPL-3.0-or-later |
| | | X | Lightweight package for analyzing, manipulating and visualizing... |
| bam-readcount |
1.0.1 |
doc |
dev |
MIT |
X | X | | | bam-readcount generates metrics at single nucleotide positions. |
| bam2fasta |
1.0.8 |
|
dev |
MIT |
| | | X | bam2fasta: cli tool to convert bam to fastas |
| bam2fastx |
3.0.0 |
|
|
BSD-3-Clause-Clear |
X | X | | | Converting and demultiplexing of PacBio BAM files into gzipped fasta... |
| bam2plot |
0.3.6 |
|
|
GPL-3.0-only |
| | | X | Plot of coverage from bam file |
| bamaddrg |
9baba65f88228e |
|
|
MIT |
X | | | | Add read group to BAM files |
| bamaligncleaner |
0.3 |
|
dev |
GPL-3.0-or-later |
| | | X | Removes unaligned references in BAM alignment file. |
| bambamc |
0.0.50 |
|
|
GPLv3 |
X | X | | | lightweight C implementation of name collating BAM file input and BAM... |
| bamclipper |
1.0.0 |
|
|
MIT |
X | X | | X | Remove primer sequence from BAM alignments by soft-clipping. |
| bamcmp |
2.2 |
|
|
GPL-3 |
X | X | | | Tools for deconvolving host and graft reads using full-length... |
| bamdash |
0.3.1 |
|
|
GPL-3.0-or-later |
| | | X | Aggregate pathogen NGS results into an interactive plot |
| bamhash |
1.1 |
|
|
GPL-3-0 |
X | X | | | Hash BAM and FASTQ files to verify data integrity |
| bamkit |
16.07.26 |
|
|
MIT |
| | | X | Tools for common BAM file manipulations |
| bamm |
1.7.3 |
|
|
LGPL-3.0 |
X | | | | Metagenomics-focused BAM file manipulation |
| bamr |
0.2.0 |
|
|
MIT |
| | | X | A lightweight Python3 bam reader library |
| bamread |
0.0.16 |
|
|
MIT |
X | X | | | Read bam files quickly into dataframes in Python |
| bamscale |
0.0.9 |
doc |
dev |
Public |
X | X | | | BAMscale is a one-step tool for either 1) quantifying and normalizing... |
| bamsnap |
0.2.19 |
|
|
MIT |
| | | X | A converter from .bam to .png for specific genomic region. |
| bamstats |
0.3.5 |
|
|
BSD-3-Clause |
X | X | | | A command line tool to compute mapping statistics from a BAM file |
| bamsurgeon |
1.4.1 |
|
|
MIT-license |
| | | X | Tools for adding genomic variants to BAM/SAM/CRAM files. Can be used to... |
| bamtocov |
2.7.0 |
|
|
MIT |
X | X | | | Extract coverage information from BAM files, supporting stranded and... |
| bamtools |
2.5.2 |
|
|
MIT |
X | X | | | C++ API & command-line toolkit for working with BAM data |
| bamutil |
1.0.15 |
|
|
GPLv3 |
X | X | | | Programs that perform operations on SAM/BAM files, all built into a... |
| bandage |
0.9.0 |
doc |
dev |
GPL-3.0-or-later |
X | X | | | Bandage - a Bioinformatics Application for Navigating De novo Assembly... |
| bandage_ng |
2022.09 |
|
|
GPL-3.0 |
X | | | | Bandage - a Bioinformatics Application for Navigating De novo Assembly... |
| banner |
0.0.2 |
|
|
MIT |
| | | X | BANNER is a tool that lives inside HULK and aims to make sense of hulk... |
| barcode_splitter |
0.18.6 |
|
|
GNU |
| | | X | Split multiple fastq files by matching barcodes in one or more of the... |
| baredsc |
1.1.3 |
|
|
GPL-3.0-or-later |
| | | X | baredSC (Bayesian Approach to Retreive Expression Distribution of... |
| barriers |
1.8.1 |
|
|
GPL |
X | X | | | Compute local minima and energy barriers of a landscape. |
| barrnap |
0.9 |
|
|
GPLv3 |
X | X | | X | Barrnap predicts the location of ribosomal RNA genes in genomes.... |
| barrnap-python |
0.0.5 |
|
dev |
GNU |
X | X | | X | python package for Torsten Seemann's barrnap package for annotating rRNAs |
| barseqcount |
0.1.5 |
doc |
|
GPL-3.0 |
| | | X | Analysis of DNA barcode sequencing experiments |
| bart |
0.1.2 |
|
|
MIT |
| | | X | bart - a bacterial read type |
| basenji |
0.6 |
|
|
Apache-2.0 |
| | | X | Sequential regulatory activity predictions with deep convolutional... |
| basic |
1.5.1 |
|
|
MIT |
X | X | | X | BASIC is a semi-de novo assembly method for assembling BCR and TCR... |
| batch_brb |
1.1.1 |
|
dev |
GPL3 |
| | | X | A tool for the automation of best reciprocal BLAST and phylogenetic... |
| bats |
0.4.0 |
|
|
Open |
X | X | | | Bash automated testing system |
| batvi |
1.04 |
|
|
GPLv3+ |
X | X | | | Detect viral integrations |
| bax2bam |
0.0.11 |
|
|
BSD-3-Clause-Clear |
X | X | | | bax2bam converts the legacy PacBio basecall format (bax.h5) into the... |
| bayesase |
21.1.13.1 |
|
|
MIT |
| | | X | Bayesian analysis of allele specific expression |
| bayescan |
2.0.1 |
|
|
GPL |
X | | | | Phylogenetics - Randomized Axelerated Maximum Likelihood. |
| bayescode |
1.3.3 |
|
|
MIT |
X | X | | | Mutation-Selection phylogenetic codon models to detect site-specific... |
| bayestyper |
1.5 |
doc |
dev |
MIT |
X | X | | | A method for variant graph genotyping based on exact alignment of k-mers. |
| baypass |
2.31 |
|
|
CECILL-B |
X | | | | Genome-Wide Scan for Adaptive Differentiation and Association Analysis... |
| bazam |
1.0.1 |
|
|
LGPL |
| | | X | A tool to extract paired reads in FASTQ format from coordinate sorted BAM files |
| bbknn |
1.6.0 |
|
|
MIT |
X | X | | X | Batch balanced KNN |
| bbmap |
39.18 |
doc |
dev |
UC-LBL |
X | X | | X | BBMap is a short read aligner, as well as various other bioinformatic tools. |
| bbmix |
0.2.2 |
|
dev |
Apache-2.0 |
| | | X | BBMix: inference of beta-binomial mixture model |
| bcalm |
2.2.3 |
|
|
MIT |
X | X | | | BCALM 2 is a bioinformatics tool for constructing the compacted de... |
| bcbio-gff |
0.7.1 |
|
|
Biopython |
| | | X | A Python library to read and write Generic Feature Format (GFF). |
| bcbio-nextgen |
1.2.9 |
|
|
MIT |
X | X | | X | Validated, scalable, community developed variant calling, RNA-seq and... |
| bcbio-nextgen-vm |
0.1.6 |
|
|
MIT |
X | X | | X | Run bcbio-nextgen genomic sequencing analyses using isolated containers... |
| bcbio-prioritize |
0.0.8 |
|
|
MIT |
X | X | | X | Prioritize small variants, structural variants and coverage based on... |
| bcbio-rnaseq |
1.2.0 |
|
|
MIT |
X | X | | | Report generation for bcbio-nextgen RNA-seq runs |
| bcbio-variation |
0.2.6 |
|
|
MIT |
X | X | | X | Toolkit to analyze genomic variation data, built on the GATK with Clojure |
| bcbio-variation-recall |
0.2.6 |
|
|
MIT |
X | X | | X | Parallel merging, squaring off and ensemble calling for genomic variants |
| bcbio_monitor |
1.0.6 |
|
|
MIT |
X | X | | X | bcbio-monitor is an extension of bcbio-nextgen to visualize its progress |
| bcbiogff |
0.6.6 |
|
|
Biopython |
X | X | | X | Read and write Generic Feature Format (GFF) with Biopython integration. |
| bcbreport |
0.99.29 |
|
|
MIT |
X | X | | X | Rmd templates for bcbio-nextgen analysis |
| bcftools |
1.21 |
|
|
GPL |
X | X | | | BCFtools is a set of utilities that manipulate variant calls in the... |
| bcftools-gtc2vcf-plugin |
1.19 |
|
|
MIT |
X | | | | Tools to convert Illumina and Affymetrix array intensity data files... |
| bcftools-snvphyl-plugin |
1.9 |
|
|
Apache-2.0 |
X | | | | The SNVPhyl (Single Nucleotide Variant PHYLogenomics) pipeline is a... |
| bcgtree |
1.2.1 |
|
|
MIT |
| | | X | Automatized phylogenetic tree building from bacterial core genomes |
| bcl2fastq-nextseq |
1.3.0 |
|
|
MIT |
X | X | | X | NextSeq .bcl Conversion |
| bcool |
1.0.0 |
|
|
AGPL-3.0 |
X | | | X | BCOOL is a read corrector for NGS sequencing data that align reads on a... |
| bcov |
1.0 |
|
|
file |
X | X | | | BCov is a software package designed for predicting protein beta-sheet... |
| bctools |
0.2.2 |
|
|
Apache |
X | X | | X | Tools for handling barcodes in NGS data. |
| bd2k-python-lib |
1.14a1.dev48 |
|
|
Apache |
X | X | | X | The BD2K Python module kitchen sink |
| beacon2-import |
2.2.4 |
|
|
CC-BY-NC-4.0 |
| | | X | Seamlessly import and query genomic variant data from a beacon |
| beacon2-ri-tools |
2.0.0 |
|
|
GPL-3.0-only |
| | | X | Script to parse a VCF having SnepEff/SnpSift annotations |
| beagle |
5.4_29Oct24.c8e |
doc |
|
GPL-3.0-or-later |
X | X | | X | Beagle is a software package for phasing genotypes and for imputing... |
| beagle-lib |
4.0.1 |
|
dev |
GPL-3.0-or-later |
X | X | | | A general purpose library for evaluating the likelihood of sequence... |
| beamspy |
1.2.0 |
|
|
GNU |
| | | X | BEAMSpy - Birmingham mEtabolite Annotation for Mass Spectrometry... |
| beast |
1.10.4 |
|
dev |
LGPL-2.1 |
X | X | | X | BEAST is a cross-platform program for Bayesian analysis of molecular... |
| beast2 |
2.6.3 |
|
|
LGPL-2.1-or-later |
X | X | | X | BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis... |
| beav |
1.4.0 |
|
|
GPL-3.0 |
| | | X | beav: Bacterial genome and mobile element annotation pipeline |
| bed2gff |
0.1.5 |
|
|
MIT |
X | X | | | BED-to-GFF3 converter that runs in parallel |
| bed2gtf |
1.9.3 |
|
|
MIT |
X | X | | | A high-performance BED-to-GTF converter written in Rust |
| bedgovcf |
0.1.1 |
|
|
MIT |
X | X | | | A simple tool to convert BED files to VCF files |
| bedops |
2.4.41 |
|
|
GPLv2 |
X | X | | | High-performance genomic feature operations. |
| bedparse |
0.2.3 |
|
|
MIT |
| | | X | A simple library and CLI tool to manipulate BED files |
| bedtk |
0.0.r25.dirty |
doc |
dev |
MIT |
X | X | | | Bedtk is a set of simple tools to process BED files. |
| bedtools |
2.31.1 |
|
|
MIT |
X | X | | | A powerful toolset for genome arithmetic |
| behst |
3.8 |
|
|
GPLv2 |
X | X | | X | BEHST reads an input dataset of chromosome regions, and intersects them... |
| bel-resources |
0.0.3 |
|
|
MIT |
| | | X | Utilities for BEL resource files. |
| bellerophon |
1.0 |
|
|
MIT |
| | | X | Filter reads that span a mapping junction, retaining the 5'-side. |
| bellmans-gapc |
2024.01.12 |
|
|
GPL-3.0-or-later |
X | X | | | A language and compiler for algebraic dynamic programming. |
| berokka |
0.2.3 |
|
|
GPL-3.0 |
X | X | | X | Trim, circularise and orient long read bacterial genome assemblies. |
| besst |
2.2.8 |
|
|
GPL-3.0 |
X | X | | X | Scaffolder for genomic assemblies. |
| bfc |
r181 |
|
|
MIT |
X | X | | | BFC is a standalone high-performance tool for correcting sequencing... |
| bftools |
8.0.0 |
|
|
GNU |
| | | X | Bio-Formats Command line tools |
| bg |
1.10 |
|
|
MIT |
| | | X | Implementation of Breakpoint Graph data structure |
| bgreat |
2.0.0 |
|
|
AGPL-3.0 |
X | | | | BGREAT2 is a read mapping tool for NGS sequencing data that align reads... |
| bgt |
r283 |
|
|
MIT |
X | X | | | Flexible genotype query among 30,000+ samples whole-genome. |
| bialign |
0.3 |
doc |
dev |
GNU |
X | X | | | Bialignment of RNAs and proteins |
| biasaway |
3.3.0 |
doc |
|
GPLv3 |
| | | X | BiasAway: a tool to generate composition-matched background sequences |
| bibliospec |
1.0 |
|
|
Apache |
X | | | | The BiblioSpec Spetral Library tool suite |
| bicseq2-norm |
0.2.4 |
|
|
Custom |
X | X | | | BICseq2-norm is for normalizing potential biases in the sequencing data. |
| bicseq2-seg |
0.7.2 |
|
|
Custom |
X | X | | | BICseq2-seg is for detecting CNVs based on the normalized data given by... |
| bifrost |
1.3.5 |
doc |
dev |
BSD-2-Clause |
X | X | | | Highly parallel construction and indexing of colored and compacted de... |
| bigscape |
1.1.9 |
doc |
|
AGPL-3.0-or-later |
| | | X | Biosynthetic Genes Similarity Clustering and Prospecting Engine. |
| bigsi |
0.3.1 |
|
|
LICENSE |
| | | X | BItsliced Genomic Signature Index [BIGSI] |
| bigslice |
2.0 |
doc |
dev |
AGPL-3.0-or-later |
| | | X | A highly scalable, user-interactive tool for the large scale analysis... |
| bigtools |
0.5.5 |
doc |
dev |
MIT |
X | X | | | Bigtools provides a high-level, performant API for reading and writing... |
| binchicken |
0.12.6 |
doc |
dev |
GPL-3.0-or-later |
| | | X | Targeted recovery of low abundance metagenome assembled genomes through... |
| bindash |
2.3 |
doc |
dev |
Apache-2.0 |
X | X | | | Fast and precise comparison of genomes and metagenomes (in the order of... |
| bindashtree |
0.1.1 |
|
|
MIT |
X | | | | bindashtree is a ultra-fast tool to build genome phylogenetic tree via... |
| binette |
1.1.0 |
doc |
|
GPL-3.0-only |
| | | X | A fast and accurate binning refinement tool to constructs high quality... |
| binlorry |
1.3.1 |
|
|
GPL-3.0 |
| | | X | BinLorry, a flexible tool for binning and filtering sequencing reads |
| binning_refiner |
1.4.3 |
|
|
GPL3 |
| | | X | Improving genome bins through the combination of different binning programs |
| binny |
2.2.18 |
|
|
GPL-3.0-or-later |
| | | X | An automated binning algorithm to recover high-quality genomes from... |
| binsanity |
0.5.4 |
|
|
GPL3 |
X | X | | X | Method to cluster contigs based a biphasic method with coverage and composition |
| binspreader |
3.16.0.dev |
|
|
GPL-2.0-only |
X | X | | | BinSPreader is a tool for improving existing binning using assembly... |
| bio |
1.7.1 |
|
dev |
MIT |
| | | X | Command-line utilities to make bioinformatics explorations more enjoyable. |
| bio-ting |
1.1.0 |
|
|
MIT |
| | | X | ting is a tool clustering large scale T cell receptor repertoires by... |
| bio-vcf |
0.9.5 |
|
|
MIT |
X | | | X | Smart VCF parser |
| bio_assembly_refinement |
0.5.1 |
|
|
GPLv3 |
X | X | | X | Assembly refinement tools, mostly useful for (but not limited to)... |
| bio_hansel |
2.6.1 |
|
|
GNU |
X | X | | X | Subtype Salmonella enterica genomes using 33bp k-mer typing schemes. |
| bioawk |
1.0 |
|
|
Free |
X | X | | | BWK awk modified for biological data |
| biobambam |
2.0.185 |
|
dev |
GPL-3.0-or-later |
X | | | | Tools for early stage alignment file processing. |
| biobasehttptools |
1.1.0 |
|
|
GPL-3 |
| | | X | Tools for querying bioinformatics web resources |
| biobb_adapters |
4.0.0 |
|
|
Apache |
| | | X | Biobb_adapters is the Biobb module collection to use the building... |
| biobb_amber |
5.0.4 |
|
|
Apache |
| | | X | Biobb_amber is a BioBB category for AMBER MD package. |
| biobb_analysis |
5.0.1 |
|
|
Apache |
| | | X | Biobb_analysis is the Biobb module collection to perform analysis of... |
| biobb_chemistry |
5.0.3 |
|
|
Apache |
| | | X | Biobb_chemistry is the Biobb module collection to perform chemical conversions. |
| biobb_cmip |
5.0.0 |
doc |
dev |
Apache |
| | | X | Biobb_cmip is the Biobb module collection to compute classical... |
| biobb_common |
5.0.0 |
doc |
dev |
Apache |
| | | X | Biobb_common is the base package required to use the biobb packages. |
| biobb_cp2k |
5.0.0 |
|
|
Apache |
| | | X | Biobb_cp2k is a BioBB category for CP2K QM package. |
| biobb_dna |
5.0.1 |
|
|
Apache |
| | | X | Biobb_dna is a package composed of different analyses for nucleic acid... |
| biobb_flexdyn |
5.0.0 |
|
dev |
Apache-2.0 |
| | | X | Biobb_flexdyn is a BioBB category for studies on the conformational... |
| biobb_flexserv |
5.0.0 |
|
|
Apache |
| | | X | Biobb_flexserv is the Biobb module collection for biomolecular... |
| biobb_godmd |
5.0.0 |
|
|
Apache |
| | | X | Biobb_godmd is a BioBB category for GOdMD tool (protein conformational... |
| biobb_gromacs |
5.0.0 |
doc |
dev |
Apache |
| | | X | biobb_gromacs is the Biobb module collection to perform molecular... |
| biobb_haddock |
5.0.0 |
doc |
dev |
Apache |
| | | X | biobb_haddock is the Biobb module collection to compute... |
| biobb_io |
5.0.1 |
|
|
Apache |
| | | X | Biobb_io is the Biobb module collection to fetch data to be consumed by... |
| biobb_md |
3.7.2 |
doc |
dev |
Apache |
| | | X | Deprecated Package: biobb_md is no longer maintained and has been... |
| biobb_mem |
5.0.6 |
doc |
dev |
Apache |
X | X | | X | Biobb_mem is the Biobb module for membrane structure analysis. |
| biobb_ml |
4.2.0 |
|
|
Apache |
| | | X | Biobb_ml is the Biobb module collection to perform machine learning predictions. |
| biobb_model |
5.0.0 |
|
|
Apache |
| | | X | Biobb_model is the Biobb module collection to check and model 3d... |
| biobb_morph |
5.0.1 |
doc |
dev |
Apache |
| | | X | biobb_morph is the Biobb module collection to perform molecular... |
| biobb_pdb_tools |
5.0.0 |
|
|
Apache |
| | | X | Biobb_pdb_tools is a swiss army knife for manipulating and editing PDB files. |
| biobb_pmx |
5.0.0 |
|
|
Apache |
| | | X | Biobb_pmx is the Biobb module collection to perform PMX... |
| biobb_pytorch |
5.0.0 |
doc |
dev |
Apache |
| | | X | biobb_pytorch is the Biobb module collection to create and train ML... |
| biobb_remote |
1.2.2 |
|
|
Apache |
| | | X | Biobb_remote is the Biobb module for remote execution via ssl. |
| biobb_structure_checking |
3.13.5 |
|
|
Apache |
| | | X | BioBB_structure_checking performs MDWeb structure checking set as a... |
| biobb_structure_manager |
3.0.2 |
|
|
Apache |
| | | X | BioBB_structure_manager is a library to efficiently load and process... |
| biobb_structure_utils |
5.0.0 |
|
|
Apache |
| | | X | Biobb_structure_utils is the Biobb module collection to modify or... |
| biobb_vs |
5.0.0 |
doc |
dev |
Apache-2.0 |
| | | X | Biobb_vs is the Biobb module collection to perform virtual screening studies. |
| biobb_wf_mutations |
0.0.6 |
|
|
Apache |
| | | X | Lysozyme plus Mutations workflow built using BioBB Based on the... |
| bioblend |
1.5.0 |
doc |
dev |
MIT |
X | X | | X | A Python library for interacting with the Galaxy API. |
| biobloomtools |
2.3.5 |
|
|
GPL-3.0 |
X | | | | Building Bloom filters and using them for categorizing sequences |
| biobox_add_taxid |
1.2 |
|
|
MIT |
| | | X | CAMI amber utility script for adding the taxid output from GTDB and BAT |
| biocamlib |
1.0.0 |
|
dev |
GPL-3.0-only |
X | X | | | An OCaml foundation upon which a number of the bioinformatics tools are built. |
| biocantor |
1.1.0 |
|
|
MIT |
| | | X | Coordinate Maniuplation and Genome Annotation Data Model |
| biocode |
0.12.0 |
|
|
MIT |
| | | X | Bioinformatics code libraries and scripts |
| biocommons.seqrepo |
0.6.9 |
|
|
Apache-2.0 |
| | | X | Python package for writing and reading a local collection of biological... |
| bioconda-repodata-patches |
20241219 |
|
|
CC-PDDC |
| | | X | generate tweaks to index metadata, hosted separately from anaconda.org index |
| bioconda-utils |
3.7.1 |
doc |
dev |
MIT |
X | X | | X | Utilities for building and managing bioconda recipes. |
| bioconda2biocontainer |
0.0.7 |
|
dev |
Public |
| | | X | BioContainers API client: find biocontainer images for Bioconda packages |
| bioconductor-a4 |
1.54.0 |
|
|
GPL-3 |
| | | X | Automated Affymetrix Array Analysis Umbrella Package |
| bioconductor-a4base |
1.54.0 |
|
|
GPL-3 |
X | X | | X | Automated Affymetrix Array Analysis Base Package |
| bioconductor-a4classif |
1.54.0 |
|
|
GPL-3 |
| | | X | Automated Affymetrix Array Analysis Classification Package |
| bioconductor-a4core |
1.54.0 |
|
|
GPL-3 |
X | X | | X | Automated Affymetrix Array Analysis Core Package |
| bioconductor-a4preproc |
1.54.0 |
|
|
GPL-3 |
X | X | | X | Automated Affymetrix Array Analysis Preprocessing Package |
| bioconductor-a4reporting |
1.54.0 |
|
|
GPL-3 |
X | X | | X | Automated Affymetrix Array Analysis Reporting Package |
| bioconductor-abadata |
1.24.0 |
|
|
GPL |
X | X | | X | Averaged gene expression in human brain regions from Allen Brain Atlas |
| bioconductor-abaenrichment |
1.24.0 |
|
|
GPL |
X | X | | | Gene expression enrichment in human brain regions |
| bioconductor-abarray |
1.74.0 |
|
|
GPL |
| | | X | Microarray QA and statistical data analysis for Applied Biosystems... |
| bioconductor-abseqr |
1.24.0 |
|
|
GPL-3 |
| | | X | Reporting and data analysis functionalities for Rep-Seq datasets of... |
| bioconductor-absseq |
1.60.0 |
|
|
GPL |
X | X | | X | ABSSeq: a new RNA-Seq analysis method based on modelling absolute... |
| bioconductor-acde |
1.36.0 |
|
|
GPL-3 |
X | X | | X | Artificial Components Detection of Differentially Expressed Genes |
| bioconductor-ace |
1.24.0 |
|
|
GPL-2 |
| | | X | Absolute Copy Number Estimation from Low-coverage Whole Genome Sequencing |
| bioconductor-acgh |
1.84.0 |
|
|
GPL-2 |
X | X | | | Classes and functions for Array Comparative Genomic Hybridization data |
| bioconductor-acme |
2.62.0 |
|
|
GPL |
X | X | | | Algorithms for Calculating Microarray Enrichment (ACME) |
| bioconductor-adacgh2 |
2.42.0 |
|
|
GPL |
X | X | | | Analysis of big data from aCGH experiments using parallel computing and... |
| bioconductor-adam |
1.22.0 |
|
|
GPL |
X | X | | | ADAM: Activity and Diversity Analysis Module |
| bioconductor-adamgui |
1.22.0 |
|
|
GPL |
| | | X | Activity and Diversity Analysis Module Graphical User Interface |
| bioconductor-adapt |
1.0.0 |
|
|
MIT |
X | | | | Analysis of Microbiome Differential Abundance by Pooling Tobit Models |
| bioconductor-adaptest |
1.7.1 |
|
|
GPL-2 |
| | | X | Data-Adaptive Statistics for High-Dimensional Multiple Testing |
| bioconductor-adductdata |
1.22.0 |
|
|
Artistic-2.0 |
| | | X | Data from untargeted MS of modifications to Cys34 of serum albumin |
| bioconductor-adductomicsr |
1.22.0 |
|
|
Artistic-2.0 |
| | | X | Processing of adductomic mass spectral datasets |
| bioconductor-adimpute |
1.16.0 |
|
|
GPL-3 |
| | | X | Adaptive Dropout Imputer (ADImpute) |
| bioconductor-adme16cod.db |
3.4.0 |
|
|
Artistic-2.0 |
| | | X | Codelink ADME Rat 16-Assay Bioarray annotation data (chip adme16cod) |
| bioconductor-adsplit |
1.76.0 |
|
|
GPL |
X | X | | | Annotation-Driven Clustering |
| bioconductor-adverscarial |
1.4.0 |
|
|
MIT |
| | | X | adverSCarial, generate and analyze the vulnerability of scRNA-seq... |
| bioconductor-affixcan |
1.24.0 |
|
|
GPL-3 |
| | | X | A Functional Approach To Impute Genetically Regulated Expression |
| bioconductor-affxparser |
1.78.0 |
|
|
LGPL |
X | X | | | Affymetrix File Parsing SDK |
| bioconductor-affy |
1.84.0 |
|
|
LGPL |
X | X | | | Methods for Affymetrix Oligonucleotide Arrays |
| bioconductor-affycomp |
1.82.0 |
|
|
GPL |
X | X | | X | Graphics Toolbox for Assessment of Affymetrix Expression Measures |
| bioconductor-affycompatible |
1.58.0 |
|
|
Artistic-2.0 |
X | X | | X | Affymetrix GeneChip software compatibility |
| bioconductor-affycompdata |
1.44.0 |
|
|
GPL |
| | | X | affycomp data |
| bioconductor-affycontam |
1.64.0 |
|
|
Artistic-2.0 |
X | X | | X | structured corruption of affymetrix cel file data |
| bioconductor-affycoretools |
1.78.0 |
|
|
Artistic-2.0 |
X | X | | X | Functions useful for those doing repetitive analyses with Affymetrix GeneChips |
| bioconductor-affydata |
1.54.0 |
|
|
GPL |
X | X | | X | Affymetrix Data for Demonstration Purpose |
| bioconductor-affyexpress |
1.56.0 |
|
|
LGPL |
X | X | | X | Affymetrix Quality Assessment and Analysis Tool |
| bioconductor-affyhgu133a2expr |
1.42.0 |
|
|
GPL |
| | | X | Affymetrix Human Genome U133A 2.0 Array (GPL571) Expression Data Package |
| bioconductor-affyhgu133aexpr |
1.44.0 |
|
|
GPL |
| | | X | Affymetrix Human hgu133a Array (GPL96) Expression Data Package |
| bioconductor-affyhgu133plus2expr |
1.40.0 |
|
|
GPL |
| | | X | Affyhgu133Plus2Expr (GPL570) Expression Data Package |
| bioconductor-affyilm |
1.58.0 |
|
|
GPL-3 |
X | X | | X | Linear Model of background subtraction and the Langmuir isotherm |
| bioconductor-affyio |
1.76.0 |
|
|
LGPL |
X | X | | | Tools for parsing Affymetrix data files |
| bioconductor-affylmgui |
1.80.0 |
|
|
GPL |
| | | X | GUI for limma Package with Affymetrix Microarrays |
| bioconductor-affymetrixdatatestfiles |
0.44.0 |
|
|
LGPL-2.1 |
| | | X | Affymetrix Data Files (CEL, CDF, CHP, EXP, PGF, PSI) for Testing |
| bioconductor-affymoe4302expr |
1.44.0 |
|
|
GPL |
| | | X | Affymetrix Mouse Genome 430 2.0 Array (GPL1261) Expression Data Package |
| bioconductor-affypara |
1.50.0 |
|
|
GPL-3 |
| | | X | Parallelized preprocessing methods for Affymetrix Oligonucleotide Arrays |
| bioconductor-affypdnn |
1.60.0 |
|
|
LGPL |
X | X | | X | Probe Dependent Nearest Neighbours (PDNN) for the affy package |
| bioconductor-affyplm |
1.82.0 |
|
|
GPL |
X | X | | | Methods for fitting probe-level models |
| bioconductor-affyqcreport |
1.68.0 |
|
|
LGPL |
| | | X | QC Report Generation for affyBatch objects |
| bioconductor-affyrnadegradation |
1.52.0 |
|
|
GPL-2 |
X | X | | X | Analyze and correct probe positional bias in microarray data due to RNA... |
| bioconductor-ag.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix AG Array annotation data (chip ag) |
| bioconductor-agcdf |
2.18.0 |
|
|
LGPL |
| | | X | agcdf |
| bioconductor-agdex |
1.54.0 |
|
|
GPL |
X | X | | X | Agreement of Differential Expression Analysis |
| bioconductor-aggregatebiovar |
1.16.0 |
|
|
GPL-3 |
| | | X | Differential Gene Expression Analysis for Multi-subject scRNA-seq |
| bioconductor-agilp |
3.38.0 |
|
|
GPL-3 |
X | X | | X | Agilent expression array processing package |
| bioconductor-agimicrorna |
2.56.0 |
|
|
GPL-3 |
| | | X | Processing and Differential Expression Analysis of Agilent microRNA chips |
| bioconductor-agprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type ag |
| bioconductor-ahcytobands |
0.99.1 |
|
|
Artistic-2.0 |
| | | X | CytoBands for AnnotationHub |
| bioconductor-ahensdbs |
1.1.10 |
|
|
Artistic-2.0 |
| | | X | EnsDbs for AnnotationHub |
| bioconductor-ahlrbasedbs |
1.8.0 |
|
|
Artistic-2.0 |
| | | X | LRBaseDbs for AnnotationHub |
| bioconductor-ahmassbank |
1.6.0 |
|
|
Artistic-2.0 |
| | | X | MassBank Annotation Resources for AnnotationHub |
| bioconductor-ahmeshdbs |
1.8.0 |
|
|
Artistic-2.0 |
| | | X | MeSHDbs for AnnotationHub |
| bioconductor-ahpathbankdbs |
0.99.5 |
|
|
Artistic-2.0 |
| | | X | Metabolites and proteins linked to PathBank pathways (for AnnotationHub) |
| bioconductor-ahpubmeddbs |
1.8.0 |
|
|
Artistic-2.0 |
| | | X | SQLites, tibbles, and data.tables for AnnotationHub |
| bioconductor-ahwikipathwaysdbs |
0.99.4 |
|
|
Artistic-2.0 |
| | | X | Metabolites linked to WikiPathways pathways (for AnnotationHub) |
| bioconductor-aims |
1.38.0 |
|
|
Artistic-2.0 |
X | X | | X | AIMS : Absolute Assignment of Breast Cancer Intrinsic Molecular Subtype |
| bioconductor-airpart |
1.14.0 |
|
|
GPL-2 |
| | | X | Differential cell-type-specific allelic imbalance |
| bioconductor-airway |
1.26.0 |
|
|
LGPL |
| | | X | RangedSummarizedExperiment for RNA-Seq in airway smooth muscle cells,... |
| bioconductor-alabaster |
1.6.0 |
|
|
MIT |
| | | X | Umbrella for the Alabaster Framework |
| bioconductor-alabaster.base |
1.6.0 |
|
|
MIT |
X | X | | | Save Bioconductor Objects To File |
| bioconductor-alabaster.bumpy |
1.6.0 |
|
|
MIT |
| | | X | Save and Load BumpyMatrices to/from file |
| bioconductor-alabaster.files |
1.4.0 |
|
|
MIT |
| | | X | Wrappers to Save Common File Formats |
| bioconductor-alabaster.mae |
1.6.0 |
|
|
MIT |
| | | X | Load and Save MultiAssayExperiments |
| bioconductor-alabaster.matrix |
1.6.0 |
|
|
MIT |
X | | | X | Load and Save Artifacts from File |
| bioconductor-alabaster.ranges |
1.6.0 |
|
|
MIT |
| | | X | Load and Save Ranges-related Artifacts from File |
| bioconductor-alabaster.sce |
1.6.0 |
|
|
MIT |
| | | X | Load and Save SingleCellExperiment from File |
| bioconductor-alabaster.schemas |
1.6.0 |
|
|
MIT |
| | | X | Schemas for the Alabaster Framework |
| bioconductor-alabaster.se |
1.6.0 |
|
|
MIT |
| | | X | Load and Save SummarizedExperiments from File |
| bioconductor-alabaster.spatial |
1.6.0 |
|
|
MIT |
| | | X | Save and Load Spatial 'Omics Data to/from File |
| bioconductor-alabaster.string |
1.6.0 |
|
|
MIT |
| | | X | Save and Load Biostrings to/from File |
| bioconductor-alabaster.vcf |
1.6.0 |
|
|
MIT |
| | | X | Save and Load Variant Data to/from File |
| bioconductor-aldex2 |
1.38.0 |
|
|
GPL |
X | X | | X | Analysis Of Differential Abundance Taking Sample and Scale Variation... |
| bioconductor-alevinqc |
1.22.0 |
|
|
MIT |
X | X | | X | Generate QC Reports For Alevin Output |
| bioconductor-all |
1.48.0 |
|
|
Artistic-2.0 |
X | X | | X | A data package |
| bioconductor-allelicimbalance |
1.44.0 |
|
|
GPL-3 |
| | | X | Investigates Allele Specific Expression |
| bioconductor-allenpvc |
1.4.0 |
|
|
CC0 |
| | | X | GEO accession data GSE71585 as a SingleCellExperiment |
| bioconductor-allmll |
1.46.0 |
|
|
GPL-2 |
| | | X | A subset of arrays from a large acute lymphoblastic leukemia (ALL) study |
| bioconductor-alphabeta |
1.20.0 |
|
|
GPL-3 |
| | | X | Computational inference of epimutation rates and spectra from... |
| bioconductor-alphamissense.v2023.hg19 |
3.18.2 |
|
|
Artistic-2.0 |
| | | X | AlphaMissense v2023 Pathogenicity Scores AnnotationHub Resource... |
| bioconductor-alphamissense.v2023.hg38 |
3.18.2 |
|
|
Artistic-2.0 |
| | | X | AlphaMissense v2023 Pathogenicity Scores AnnotationHub Resource... |
| bioconductor-alphamissenser |
1.2.0 |
|
|
Artistic-2.0 |
| | | X | Accessing AlphaMissense Data Resources in R |
| bioconductor-alpine |
1.26.0 |
|
|
GPL |
X | X | | X | alpine |
| bioconductor-alpinedata |
1.26.0 |
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|
GPL |
| | | X | Data for the alpine package vignette |
| bioconductor-alps |
1.5.0 |
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MIT |
| | | X | AnaLysis routines for ePigenomicS data |
| bioconductor-alpsnmr |
4.8.0 |
|
|
MIT |
| | | X | Automated spectraL Processing System for NMR |
| bioconductor-alsace |
1.30.0 |
|
|
GPL |
| | | X | ALS for the Automatic Chemical Exploration of mixtures |
| bioconductor-altcdfenvs |
2.68.0 |
|
|
GPL |
X | X | | X | alternative CDF environments (aka probeset mappings) |
| bioconductor-alternativesplicingevents.hg19 |
1.1.0 |
|
|
MIT |
| | | X | Alternative splicing event annotation for Human (hg19) |
| bioconductor-alternativesplicingevents.hg38 |
1.1.0 |
|
|
MIT |
| | | X | Alternative splicing event annotation for Human (hg38) |
| bioconductor-amaretto |
1.22.0 |
|
|
Apache |
X | X | | | Regulatory Network Inference and Driver Gene Evaluation using... |
| bioconductor-amountain |
1.32.0 |
|
|
GPL |
X | X | | | Active modules for multilayer weighted gene co-expression networks: a... |
| bioconductor-ampaffyexample |
1.46.0 |
|
|
LGPL |
| | | X | Example of Amplified Data |
| bioconductor-amplican |
1.28.0 |
|
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GPL-3 |
X | X | | X | Automated analysis of CRISPR experiments |
| bioconductor-ampliqueso |
1.20.0 |
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GPL-2 |
| | | X | The package provides tools and reports for the analysis of amplicon... |
| bioconductor-analysispageserver |
1.21.0 |
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|
Artistic-2.0 |
X | X | | | A framework for sharing interactive data and plots from R through the web |
| bioconductor-anamir |
1.13.0 |
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GPL-2 |
| | | X | An integrated analysis package of miRNA and mRNA expression data |
| bioconductor-anaquin |
2.30.0 |
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BSD_3_clause |
| | | X | Statistical analysis of sequins |
| bioconductor-ancombc |
2.8.0 |
|
|
Artistic-2.0 |
| | | X | Microbiome differential abudance and correlation analyses with bias correction |
| bioconductor-aneufinder |
1.34.0 |
|
|
Artistic-2.0 |
X | X | | | Analysis of Copy Number Variation in Single-Cell-Sequencing Data |
| bioconductor-aneufinderdata |
1.34.0 |
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|
file |
| | | X | WGSCS Data for Demonstration Purposes |
| bioconductor-anf |
1.28.0 |
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GPL-3 |
| | | X | Affinity Network Fusion for Complex Patient Clustering |
| bioconductor-animalcules |
1.22.0 |
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|
Artistic-2.0 |
| | | X | Interactive microbiome analysis toolkit |
| bioconductor-annaffy |
1.78.0 |
|
|
LGPL |
X | X | | X | Annotation tools for Affymetrix biological metadata |
| bioconductor-annmap |
1.48.0 |
|
|
GPL-2 |
X | X | | X | Genome annotation and visualisation package pertaining to Affymetrix... |
| bioconductor-annotate |
1.84.0 |
|
|
Artistic-2.0 |
X | X | | X | Annotation for microarrays |
| bioconductor-annotationdbi |
1.68.0 |
|
|
Artistic-2.0 |
X | X | | X | Manipulation of SQLite-based annotations in Bioconductor |
| bioconductor-annotationfilter |
1.30.0 |
|
|
Artistic-2.0 |
X | X | | X | Facilities for Filtering Bioconductor Annotation Resources |
| bioconductor-annotationforge |
1.48.0 |
|
|
Artistic-2.0 |
X | X | | X | Tools for building SQLite-based annotation data packages |
| bioconductor-annotationfuncs |
1.40.0 |
|
|
GPL-2 |
X | X | | X | Annotation translation functions |
| bioconductor-annotationhub |
3.14.0 |
|
|
Artistic-2.0 |
X | X | | X | Client to access AnnotationHub resources |
| bioconductor-annotationhubdata |
1.36.0 |
|
|
Artistic-2.0 |
X | X | | X | Transform public data resources into Bioconductor Data Structures |
| bioconductor-annotationtools |
1.80.0 |
|
|
GPL |
X | X | | X | Annotate microarrays and perform cross-species gene expression analyses... |
| bioconductor-annotatr |
1.32.0 |
|
|
GPL-3 |
| | | X | Annotation of Genomic Regions to Genomic Annotations |
| bioconductor-anopheles.db0 |
3.20.0 |
|
|
Artistic-2.0 |
| | | X | Base Level Annotation databases for anopheles |
| bioconductor-anota |
1.54.0 |
|
|
GPL-3 |
X | X | | X | ANalysis Of Translational Activity (ANOTA). |
| bioconductor-anota2seq |
1.28.0 |
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|
GPL-3 |
| | | X | Generally applicable transcriptome-wide analysis of translational... |
| bioconductor-antiprofiles |
1.46.0 |
|
|
Artistic-2.0 |
X | X | | X | Implementation of gene expression anti-profiles |
| bioconductor-antiprofilesdata |
1.38.0 |
|
|
Artistic-2.0 |
| | | X | Normal colon and cancer preprocessed affy data for antiProfile building. |
| bioconductor-anvil |
1.18.0 |
|
|
Artistic-2.0 |
| | | X | Bioconductor on the AnVIL compute environment |
| bioconductor-anvilaz |
1.0.0 |
|
|
Artistic-2.0 |
| | | X | R / Bioconductor Support for the AnVIL Azure Platform |
| bioconductor-anvilbase |
1.0.0 |
|
|
Artistic-2.0 |
| | | X | Generic functions for interacting with the AnVIL ecosystem |
| bioconductor-anvilbilling |
1.16.0 |
|
|
Artistic-2.0 |
| | | X | Provide functions to retrieve and report on usage expenses in NHGRI... |
| bioconductor-anvilgcp |
1.0.0 |
|
|
Artistic-2.0 |
| | | X | The GCP R Client for the AnVIL |
| bioconductor-anvilpublish |
1.16.0 |
|
|
Artistic-2.0 |
| | | X | Publish Packages and Other Resources to AnVIL Workspaces |
| bioconductor-anvilworkflow |
1.6.0 |
|
|
Artistic-2.0 |
| | | X | Run workflows implemented in Terra/AnVIL workspace |
| bioconductor-apalyzer |
1.20.0 |
|
|
LGPL-3 |
| | | X | A toolkit for APA analysis using RNA-seq data |
| bioconductor-apcomplex |
2.72.0 |
|
|
LGPL |
X | X | | X | Estimate protein complex membership using AP-MS protein data |
| bioconductor-apeglm |
1.28.0 |
|
|
GPL-2 |
X | X | | | Approximate posterior estimation for GLM coefficients |
| bioconductor-apl |
1.6.0 |
|
|
GPL |
| | | X | Association Plots |
| bioconductor-appreci8r |
1.16.0 |
|
|
LGPL-3 |
| | | X | appreci8R: an R/Bioconductor package for filtering SNVs and short... |
| bioconductor-arabidopsis.db0 |
3.20.0 |
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Artistic-2.0 |
| | | X | Base Level Annotation databases for arabidopsis |
| bioconductor-aracne.networks |
1.32.0 |
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|
file |
| | | X | ARACNe-inferred gene networks from TCGA tumor datasets |
| bioconductor-aroma.light |
3.36.0 |
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|
GPL |
X | X | | X | Light-Weight Methods for Normalization and Visualization of Microarray... |
| bioconductor-arrayexpress |
1.66.0 |
|
|
Artistic-2.0 |
X | X | | X | Access the ArrayExpress Collection at EMBL-EBI Biostudies and build... |
| bioconductor-arrayexpresshts |
1.44.0 |
|
|
Artistic |
X | X | | | ArrayExpress High Throughput Sequencing Processing Pipeline |
| bioconductor-arraymvout |
1.64.0 |
|
|
Artistic-2.0 |
| | | X | multivariate outlier detection for expression array QA |
| bioconductor-arrayquality |
1.84.0 |
|
|
LGPL |
X | X | | X | Assessing array quality on spotted arrays |
| bioconductor-arrayqualitymetrics |
3.62.0 |
|
|
LGPL |
X | X | | X | Quality metrics report for microarray data sets |
| bioconductor-arraytools |
1.50.0 |
|
|
LGPL |
X | X | | X | geneChip Analysis Package |
| bioconductor-arraytv |
1.25.0 |
|
|
GPL |
| | | X | Implementation of wave correction for arrays |
| bioconductor-arrmdata |
1.42.0 |
|
|
Artistic-2.0 |
X | X | | X | Example dataset for normalization of Illumina 450k Methylation data |
| bioconductor-arrmnormalization |
1.46.0 |
|
|
Artistic-2.0 |
X | X | | X | Adaptive Robust Regression normalization for Illumina methylation data |
| bioconductor-artms |
1.24.0 |
|
|
GPL |
| | | X | Analytical R tools for Mass Spectrometry |
| bioconductor-asafe |
1.32.0 |
|
|
Artistic-2.0 |
X | X | | X | Ancestry Specific Allele Frequency Estimation |
| bioconductor-aseb |
1.50.0 |
|
|
GPL |
X | X | | | Predict Acetylated Lysine Sites |
| bioconductor-asgsca |
1.40.0 |
|
|
GPL-3 |
X | X | | X | Association Studies for multiple SNPs and multiple traits using... |
| bioconductor-ashkenazimsonchr21 |
1.36.0 |
|
|
Artistic-2.0 |
| | | X | Annotated variants on the chromosome 21, human genome 19, Ashkenazim... |
| bioconductor-asics |
2.22.0 |
|
|
GPL |
| | | X | Automatic Statistical Identification in Complex Spectra |
| bioconductor-asicsdata |
1.26.0 |
|
|
GPL |
| | | X | Example of 1D NMR spectra data for ASICS package |
| bioconductor-aspediafi |
1.11.0 |
|
|
GPL-3 |
| | | X | ASpedia-FI: Functional Interaction Analysis of Alternative Splicing Events |
| bioconductor-aspli |
2.16.0 |
|
|
GPL |
X | X | | X | Analysis of Alternative Splicing Using RNA-Seq |
| bioconductor-assessorf |
1.24.0 |
|
|
GPL-3 |
| | | X | Assess Gene Predictions Using Proteomics and Evolutionary Conservation |
| bioconductor-assessorfdata |
1.20.0 |
|
|
GPL-3 |
| | | X | Data and Files for the AssessORF Package |
| bioconductor-asset |
2.24.0 |
|
|
GPL-2 |
| | | X | An R package for subset-based association analysis of heterogeneous... |
| bioconductor-assign |
1.42.0 |
|
|
MIT |
| | | X | Adaptive Signature Selection and InteGratioN (ASSIGN) |
| bioconductor-assorthead |
1.0.0 |
|
|
MIT |
| | | X | Assorted Header-Only C++ Libraries |
| bioconductor-asurat |
1.10.0 |
|
|
GPL-3 |
X | X | | | Functional annotation-driven unsupervised clustering for single-cell data |
| bioconductor-ataccogaps |
1.4.0 |
|
|
Artistic-2.0 |
| | | X | Analysis Tools for scATACseq Data with CoGAPS |
| bioconductor-atacseqqc |
1.30.0 |
|
|
GPL |
X | X | | X | ATAC-seq Quality Control |
| bioconductor-atacseqtfea |
1.8.0 |
|
|
GPL-3 |
| | | X | Transcription Factor Enrichment Analysis for ATAC-seq |
| bioconductor-atena |
1.12.0 |
|
|
Artistic-2.0 |
| | | X | Analysis of Transposable Elements |
| bioconductor-ath1121501.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix ATH1-121501 Array annotation data (chip ath1121501) |
| bioconductor-ath1121501cdf |
2.18.0 |
|
|
LGPL |
| | | X | ath1121501cdf |
| bioconductor-ath1121501frmavecs |
1.0.0 |
|
|
GPL |
| | | X | Vectors used by frma for microarrays of type ath1121501 |
| bioconductor-ath1121501probe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type ath1121501 |
| bioconductor-atlasrdf |
1.12.0 |
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|
Apache |
X | X | | | Query the Gene Expression Atlas RDF data at the European Bioinformatics... |
| bioconductor-atsnp |
1.22.0 |
|
|
GPL-2 |
X | X | | | Affinity test for identifying regulatory SNPs |
| bioconductor-attract |
1.58.0 |
|
|
LGPL |
| | | X | Methods to Find the Gene Expression Modules that Represent the Drivers... |
| bioconductor-aucell |
1.28.0 |
|
|
GPL-3 |
| | | X | AUCell: Analysis of 'gene set' activity in single-cell RNA-seq... |
| bioconductor-autonomics |
1.10.2 |
|
|
GPL-3 |
| | | X | Generifying and intuifying cross-platform omics analysis |
| bioconductor-autotuner |
1.7.0 |
|
|
MIT |
| | | X | Automated parameter selection for untargeted metabolomics data processing |
| bioconductor-awfisher |
1.20.0 |
|
|
GPL-3 |
X | X | | | An R package for fast computing for adaptively weighted fisher's method |
| bioconductor-awst |
1.14.0 |
|
|
MIT |
| | | X | Asymmetric Within-Sample Transformation |
| bioconductor-baalchip |
1.32.0 |
|
|
Artistic-2.0 |
X | X | | X | BaalChIP: Bayesian analysis of allele-specific transcription factor... |
| bioconductor-bac |
1.58.0 |
|
|
Artistic-2.0 |
X | X | | | Bayesian Analysis of Chip-chip experiment |
| bioconductor-bacon |
1.34.0 |
|
|
GPL |
X | X | | | Controlling bias and inflation in association studies using the... |
| bioconductor-bader |
1.44.0 |
|
|
GPL-2 |
X | X | | | Bayesian Analysis of Differential Expression in RNA Sequencing Data |
| bioconductor-badregionfinder |
1.34.0 |
|
|
LGPL-3 |
X | X | | X | BadRegionFinder: an R/Bioconductor package for identifying regions with... |
| bioconductor-bags |
2.46.0 |
|
|
Artistic-2.0 |
X | X | | | A Bayesian Approach for Geneset Selection |
| bioconductor-ballgown |
2.38.0 |
|
|
Artistic-2.0 |
X | X | | X | Flexible, isoform-level differential expression analysis |
| bioconductor-bambu |
3.8.3 |
|
|
GPL-3 |
X | X | | | Context-Aware Transcript Quantification from Long Read RNA-Seq data |
| bioconductor-bamsignals |
1.38.0 |
|
|
GPL-2 |
X | X | | | Extract read count signals from bam files |
| bioconductor-bandits |
1.22.0 |
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|
GPL |
X | X | | | BANDITS: Bayesian ANalysis of DIfferenTial Splicing |
| bioconductor-bandle |
1.6.0 |
|
|
Artistic-2.0 |
X | X | | | An R package for the Bayesian analysis of differential subcellular... |
| bioconductor-banocc |
1.30.0 |
|
|
MIT |
X | X | | X | Bayesian ANalysis Of Compositional Covariance |
| bioconductor-barcodetrackr |
1.14.0 |
|
|
file |
| | | X | Functions for Analyzing Cellular Barcoding Data |
| bioconductor-barley1cdf |
2.18.0 |
|
|
LGPL |
| | | X | barley1cdf |
| bioconductor-barley1probe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type barley1 |
| bioconductor-basecallqc |
1.30.0 |
|
|
GPL |
X | X | | X | Working with Illumina Basecalling and Demultiplexing input and output files |
| bioconductor-basespacer |
1.50.0 |
|
|
Apache |
X | X | | X | R SDK for BaseSpace RESTful API |
| bioconductor-basic4cseq |
1.42.0 |
|
|
LGPL-3 |
X | X | | X | Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data |
| bioconductor-basics |
2.18.0 |
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|
GPL-3 |
X | X | | | Bayesian Analysis of Single-Cell Sequencing data |
| bioconductor-basicstan |
1.8.0 |
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|
GPL-3 |
X | X | | | Stan implementation of BASiCS |
| bioconductor-basicstarrseq |
1.34.0 |
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|
LGPL-3 |
| | | X | Basic peak calling on STARR-seq data |
| bioconductor-basilisk |
1.18.0 |
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|
GPL-3 |
| | | X | Freezing Python Dependencies Inside Bioconductor Packages |
| bioconductor-basilisk.utils |
1.18.0 |
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|
GPL-3 |
| | | X | Basilisk Installation Utilities |
| bioconductor-batchelor |
1.22.0 |
|
|
GPL-3 |
X | X | | | Single-Cell Batch Correction Methods |
| bioconductor-batchqc |
2.2.0 |
|
|
MIT |
X | X | | X | Batch Effects Quality Control Software |
| bioconductor-bayesknockdown |
1.32.0 |
|
|
GPL-3 |
| | | X | BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data |
| bioconductor-bayespeak |
1.39.0 |
|
|
GPL |
X | X | | | Bayesian Analysis of ChIP-seq Data |
| bioconductor-bayesspace |
1.12.0 |
|
|
MIT |
X | X | | | Clustering and Resolution Enhancement of Spatial Transcriptomes |
| bioconductor-baynorm |
1.24.0 |
|
|
GPL |
X | X | | | Single-cell RNA sequencing data normalization |
| bioconductor-bayseq |
2.40.0 |
|
|
GPL-3 |
X | X | | X | Empirical Bayesian analysis of patterns of differential expression in count data |
| bioconductor-bbcanalyzer |
1.36.0 |
|
|
LGPL-3 |
X | X | | X | BBCAnalyzer: an R/Bioconductor package for visualizing base counts |
| bioconductor-bcellviper |
1.42.0 |
|
|
GPL |
| | | X | Human B-cell transcriptional interactome and normal human B-cell expression data |
| bioconductor-bcrank |
1.68.0 |
|
|
GPL-2 |
X | X | | | Predicting binding site consensus from ranked DNA sequences |
| bioconductor-bcseq |
1.28.0 |
|
|
GPL |
X | X | | | Fast Sequence Mapping in High-Throughput shRNA and CRISPR Screens |
| bioconductor-bdmmacorrect |
1.18.1 |
|
|
GPL |
X | X | | | Meta-analysis for the metagenomic read counts data from different cohorts |
| bioconductor-beachmat |
2.22.0 |
|
|
GPL-3 |
X | X | | | Compiling Bioconductor to Handle Each Matrix Type |
| bioconductor-beachmat.hdf5 |
1.4.0 |
|
|
GPL-3 |
X | X | | | beachmat bindings for HDF5-backed matrices |
| bioconductor-beadarray |
2.56.0 |
|
|
MIT |
X | X | | | Quality assessment and low-level analysis for Illumina BeadArray data |
| bioconductor-beadarrayexampledata |
1.44.0 |
|
|
GPL-2 |
| | | X | Example data for the beadarray package |
| bioconductor-beadarraysnp |
1.68.0 |
|
|
GPL-2 |
X | X | | X | Normalization and reporting of Illumina SNP bead arrays |
| bioconductor-beadarrayusecases |
1.40.0 |
|
|
GPL-2 |
| | | X | Analysing Illumina BeadArray expression data using Bioconductor |
| bioconductor-beaddatapackr |
1.58.0 |
|
|
GPL-2 |
X | X | | | Compression of Illumina BeadArray data |
| bioconductor-beadsorted.saliva.epic |
1.14.0 |
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GPL-3 |
| | | X | Illumina EPIC data on BeadSorted child saliva cells |
| bioconductor-bearscc |
1.22.0 |
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GPL-3 |
| | | X | BEARscc (Bayesian ERCC Assesstment of Robustness of Single Cell Clusters) |
| bioconductor-beat |
1.44.0 |
|
|
LGPL |
X | X | | X | BEAT - BS-Seq Epimutation Analysis Toolkit |
| bioconductor-beclear |
2.22.0 |
|
|
GPL-3 |
X | X | | X | Correction of batch effects in DNA methylation data |
| bioconductor-beer |
1.10.0 |
|
|
MIT |
| | | X | Bayesian Enrichment Estimation in R |
| bioconductor-benchdamic |
1.6.0 |
|
|
Artistic-2.0 |
| | | X | Benchmark of differential abundance methods on microbiome data |
| bioconductor-benchmarkfdrdata2019 |
1.20.0 |
|
|
MIT |
| | | X | Data and Benchmarking Results from Korthauer and Kimes et al. (2019) |
| bioconductor-beta7 |
1.44.0 |
|
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LGPL |
| | | X | Rodriguez et al. (2004) Differential Gene Expression by Memory/Effector... |
| bioconductor-betahmm |
1.2.0 |
|
|
GPL-3 |
| | | X | A Hidden Markov Model Approach for Identifying Differentially... |
| bioconductor-bettr |
1.2.0 |
|
|
MIT |
| | | X | A Better Way To Explore What Is Best |
| bioconductor-bg2 |
1.6.0 |
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|
GPL-3 |
| | | X | Performs Bayesian GWAS analysis for non-Gaussian data using BG2 |
| bioconductor-bgafun |
1.49.0 |
|
|
Artistic-2.0 |
X | X | | X | BGAfun A method to identify specifity determining residues in protein families |
| bioconductor-bgeecall |
1.22.0 |
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GPL-3 |
| | | X | Automatic RNA-Seq present/absent gene expression calls generation |
| bioconductor-bgeedb |
2.28.0 |
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GPL-3 |
X | X | | X | Annotation and gene expression data retrieval from Bgee database.... |
| bioconductor-bgmix |
1.59.0 |
|
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GPL-2 |
X | X | | | Bayesian models for differential gene expression |
| bioconductor-bgx |
1.68.0 |
|
|
GPL-2 |
X | X | | | Bayesian Gene eXpression |
| bioconductor-bhc |
1.54.0 |
|
|
GPL-3 |
X | X | | | Bayesian Hierarchical Clustering |
| bioconductor-bicare |
1.64.0 |
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|
GPL-2 |
X | X | | | Biclustering Analysis and Results Exploration |
| bioconductor-bifet |
1.26.0 |
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GPL-3 |
| | | X | Bias-free Footprint Enrichment Test |
| bioconductor-biggr |
1.34.0 |
|
|
file |
| | | X | Constraint based modeling in R using metabolic reconstruction databases |
| bioconductor-bigmelon |
1.32.0 |
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GPL-3 |
| | | X | Illumina methylation array analysis for large experiments |
| bioconductor-bigmemoryextras |
1.38.0 |
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|
Artistic-2.0 |
| | | X | An extension of the bigmemory package with added safety, convenience,... |
| bioconductor-bigpint |
1.15.0 |
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GPL-3 |
| | | X | Big multivariate data plotted interactively |
| bioconductor-bindingsitefinder |
2.4.0 |
|
|
Artistic-2.0 |
| | | X | Binding site defintion based on iCLIP data |
| bioconductor-bioassayr |
1.44.0 |
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|
Artistic-2.0 |
| | | X | Cross-target analysis of small molecule bioactivity |
| bioconductor-biobase |
2.66.0 |
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|
Artistic-2.0 |
X | X | | | Biobase: Base functions for Bioconductor |
| bioconductor-biobroom |
1.38.0 |
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LGPL |
| | | X | Turn Bioconductor objects into tidy data frames |
| bioconductor-biobtreer |
1.18.0 |
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MIT |
| | | X | Using biobtree tool from R |
| bioconductor-biocancer |
1.34.0 |
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AGPL-3 |
| | | X | Interactive Multi-Omics Cancers Data Visualization and Analysis |
| bioconductor-biocartaimage |
1.4.0 |
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MIT |
| | | X | BioCarta Pathway Images |
| bioconductor-biocbaseutils |
1.8.0 |
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Artistic-2.0 |
| | | X | General utility functions for developing Bioconductor packages |
| bioconductor-biocbook |
1.4.0 |
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MIT |
| | | X | Write, containerize, publish and version Quarto books with Bioconductor |
| bioconductor-bioccasestudies |
1.52.0 |
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Artistic-2.0 |
| | | X | BiocCaseStudies: Support for the Case Studies Monograph |
| bioconductor-bioccheck |
1.42.0 |
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Artistic-2.0 |
| | | X | Bioconductor-specific package checks |
| bioconductor-biocdockermanager |
1.11.0 |
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Artistic-2.0 |
| | | X | Access Bioconductor docker images |
| bioconductor-biocfhir |
1.8.0 |
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Artistic-2.0 |
| | | X | Illustration of FHIR ingestion and transformation using R |
| bioconductor-biocfilecache |
2.14.0 |
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Artistic-2.0 |
X | X | | X | Manage Files Across Sessions |
| bioconductor-biocgenerics |
0.52.0 |
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Artistic-2.0 |
X | X | | X | S4 generic functions used in Bioconductor |
| bioconductor-biocgraph |
1.68.0 |
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Artistic-2.0 |
X | X | | X | Graph examples and use cases in Bioinformatics |
| bioconductor-biochail |
1.2.0 |
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Artistic-2.0 |
| | | X | basilisk and hail |
| bioconductor-biochubsshiny |
1.6.0 |
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Artistic-2.0 |
| | | X | View AnnotationHub and ExperimentHub Resources Interactively |
| bioconductor-biocinstaller |
1.32.1 |
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|
Artistic-2.0 |
X | X | | X | This package is used to install and update Bioconductor, CRAN, and... |
| bioconductor-biocio |
1.16.0 |
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Artistic-2.0 |
| | | X | Standard Input and Output for Bioconductor Packages |
| bioconductor-biocneighbors |
2.0.0 |
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GPL-3 |
X | X | | | Nearest Neighbor Detection for Bioconductor Packages |
| bioconductor-bioconcotk |
1.22.0 |
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Artistic-2.0 |
| | | X | Bioconductor components for general cancer genomics |
| bioconductor-biocor |
1.30.0 |
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MIT |
| | | X | Functional similarities |
| bioconductor-biocparallel |
1.40.0 |
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|
GPL-2 |
X | X | | | Bioconductor facilities for parallel evaluation |
| bioconductor-biocpkgtools |
1.24.0 |
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MIT |
| | | X | Collection of simple tools for learning about Bioconductor Packages |
| bioconductor-biocroxytest |
1.2.0 |
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GPL |
| | | X | Handle Long Tests in Bioconductor Packages |
| bioconductor-biocset |
1.20.0 |
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Artistic-2.0 |
| | | X | Representing Different Biological Sets |
| bioconductor-biocsingular |
1.22.0 |
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GPL-3 |
X | X | | | Singular Value Decomposition for Bioconductor Packages |
| bioconductor-biocsklearn |
1.28.0 |
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|
Artistic-2.0 |
X | X | | X | interface to python sklearn via Rstudio reticulate |
| bioconductor-biocstyle |
2.34.0 |
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|
Artistic-2.0 |
X | X | | X | Standard styles for vignettes and other Bioconductor documents |
| bioconductor-biocthis |
1.16.0 |
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|
Artistic-2.0 |
| | | X | Automate package and project setup for Bioconductor packages |
| bioconductor-biocversion |
3.20.0 |
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|
Artistic-2.0 |
| | | X | Set the appropriate version of Bioconductor packages |
| bioconductor-biocviews |
1.74.0 |
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|
Artistic-2.0 |
X | X | | X | Categorized views of R package repositories |
| bioconductor-biocworkflowtools |
1.32.0 |
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MIT |
X | X | | X | Tools to aid the development of Bioconductor Workflow packages |
| bioconductor-biodb |
1.14.0 |
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AGPL-3 |
X | X | | | biodb, a library and a development framework for connecting to chemical... |
| bioconductor-biodbchebi |
1.12.0 |
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AGPL-3 |
| | | X | biodbChebi, a library for connecting to the ChEBI Database |
| bioconductor-biodbexpasy |
1.6.0 |
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AGPL-3 |
| | | X | biodbExpasy, a library for connecting to Expasy ENZYME database. |
| bioconductor-biodbhmdb |
1.12.0 |
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AGPL-3 |
X | X | | | biodbHmdb, a library for connecting to the HMDB Database |
| bioconductor-biodbkegg |
1.8.0 |
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AGPL-3 |
| | | X | biodbKegg, a library for connecting to the KEGG Database |
| bioconductor-biodblipidmaps |
1.8.0 |
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AGPL-3 |
| | | X | biodbLipidmaps, a library for connecting to the Lipidmaps Structure database |
| bioconductor-biodbmirbase |
1.5.0 |
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AGPL-3 |
| | | X | biodbMirbase, a library for connecting to miRBase mature database |
| bioconductor-biodbncbi |
1.10.0 |
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AGPL-3 |
| | | X | biodbNcbi, a library for connecting to NCBI Databases. |
| bioconductor-biodbnci |
1.10.0 |
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|
AGPL-3 |
X | X | | | biodbNci, a library for connecting to biodbNci, a library for... |
| bioconductor-biodbuniprot |
1.12.0 |
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AGPL-3 |
| | | X | biodbUniprot, a library for connecting to the Uniprot Database |
| bioconductor-biodist |
1.78.0 |
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|
Artistic-2.0 |
X | X | | X | Different distance measures |
| bioconductor-bioga |
1.0.0 |
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|
MIT |
X | | | | Bioinformatics Genetic Algorithm (BioGA) |
| bioconductor-bioimagedbs |
1.14.0 |
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|
Artistic-2.0 |
| | | X | Bio- and biomedical imaging dataset for machine learning and deep... |
| bioconductor-biomart |
2.62.0 |
|
|
Artistic-2.0 |
X | X | | X | Interface to BioMart databases (i.e. Ensembl) |
| bioconductor-biomartgogenesets |
0.99.11 |
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|
MIT |
| | | X | Gene Ontology Gene Sets from BioMart |
| bioconductor-biomformat |
1.34.0 |
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|
GPL-2 |
X | X | | X | An interface package for the BIOM file format |
| bioconductor-biomm |
1.15.0 |
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GPL-3 |
| | | X | BioMM: Biological-informed Multi-stage Machine learning framework for... |
| bioconductor-biomvcclass |
1.74.0 |
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LGPL |
X | X | | X | Model-View-Controller (MVC) Classes That Use Biobase |
| bioconductor-biomvrcns |
1.46.0 |
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|
GPL |
X | X | | | Copy Number study and Segmentation for multivariate biological data |
| bioconductor-bionar |
1.8.0 |
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Artistic-2.0 |
| | | X | Biological Network Analysis in R |
| bioconductor-bionero |
1.14.0 |
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GPL-3 |
| | | X | Biological Network Reconstruction Omnibus |
| bioconductor-bionet |
1.66.0 |
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|
GPL |
X | X | | X | Routines for the functional analysis of biological networks |
| bioconductor-bionetstat |
1.22.0 |
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|
GPL |
| | | X | Biological Network Analysis |
| bioconductor-bioplex |
1.12.0 |
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Artistic-2.0 |
| | | X | R-side access to BioPlex protein-protein interaction data |
| bioconductor-bioqc |
1.34.0 |
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|
GPL |
X | X | | | Detect tissue heterogeneity in expression profiles with gene sets |
| bioconductor-bioseqclass |
1.45.0 |
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LGPL |
| | | X | Classification for Biological Sequences |
| bioconductor-biosigner |
1.34.0 |
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CeCILL |
X | X | | X | Signature discovery from omics data |
| bioconductor-biostrings |
2.74.0 |
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|
Artistic-2.0 |
X | X | | | Efficient manipulation of biological strings |
| bioconductor-biosvd |
2.23.0 |
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|
Artistic-2.0 |
X | X | | X | Package for high-throughput data processing, outlier detection, noise... |
| bioconductor-biotip |
1.20.0 |
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|
GPL-2 |
| | | X | BioTIP: An R package for characterization of Biological Tipping-Point |
| bioconductor-biotmle |
1.30.0 |
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|
MIT |
| | | X | Targeted Learning with Moderated Statistics for Biomarker Discovery |
| bioconductor-biotmledata |
1.30.0 |
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|
file |
| | | X | Example experimental microarray data set for the "biotmle" R package |
| bioconductor-biovizbase |
1.54.0 |
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|
Artistic-2.0 |
X | X | | | Basic graphic utilities for visualization of genomic data. |
| bioconductor-birewire |
3.38.0 |
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GPL-3 |
X | X | | | High-performing routines for the randomization of a bipartite graph (or... |
| bioconductor-birta |
1.31.0 |
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|
GPL |
X | X | | | Bayesian Inference of Regulation of Transcriptional Activity |
| bioconductor-birte |
1.18.0 |
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|
GPL |
X | X | | | Expression levels of mRNA molecules are regulated by different... |
| bioconductor-biscuiteer |
1.20.0 |
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GPL-3 |
| | | X | Convenience Functions for Biscuit |
| bioconductor-biscuiteerdata |
1.20.0 |
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GPL-3 |
| | | X | Data Package for Biscuiteer |
| bioconductor-biseq |
1.46.0 |
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|
LGPL-3 |
X | X | | X | Processing and analyzing bisulfite sequencing data |
| bioconductor-bitseq |
1.38.0 |
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|
Artistic-2.0 |
X | X | | | Transcript expression inference and differential expression analysis... |
| bioconductor-blacksheepr |
1.20.0 |
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|
MIT |
| | | X | Outlier Analysis for pairwise differential comparison |
| bioconductor-bladderbatch |
1.44.0 |
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|
Artistic-2.0 |
X | X | | X | Bladder gene expression data illustrating batch effects |
| bioconductor-blima |
1.40.0 |
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GPL-3 |
X | X | | | Tools for the preprocessing and analysis of the Illumina microarrays on... |
| bioconductor-blimatestingdata |
1.26.0 |
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GPL-3 |
| | | X | Data for testing of the package blima. |
| bioconductor-blma |
1.30.0 |
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GPL |
| | | X | BLMA: A package for bi-level meta-analysis |
| bioconductor-bloodcancermultiomics2017 |
1.26.0 |
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LGPL |
| | | X | "Drug-perturbation-based stratification of blood cancer" by... |
| bioconductor-bloodgen3module |
1.14.0 |
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|
GPL-2 |
| | | X | This R package for performing module repertoire analyses and generating... |
| bioconductor-bluster |
1.16.0 |
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GPL-3 |
X | X | | | Clustering Algorithms for Bioconductor |
| bioconductor-bnbc |
1.28.0 |
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Artistic-2.0 |
X | X | | | Bandwise normalization and batch correction of Hi-C data |
| bioconductor-bnem |
1.10.0 |
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GPL-3 |
| | | X | Training of logical models from indirect measurements of perturbation... |
| bioconductor-bobafit |
1.10.0 |
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GPL |
| | | X | Refitting diploid region profiles using a clustering procedure |
| bioconductor-bodymaprat |
1.22.0 |
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|
CC |
| | | X | Experimental dataset from the rat BodyMap project |
| bioconductor-borealis |
1.10.0 |
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GPL-3 |
| | | X | Bisulfite-seq OutlieR mEthylation At singLe-sIte reSolution |
| bioconductor-bovine.db |
3.13.0 |
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Artistic-2.0 |
| | | X | Affymetrix Affymetrix Bovine Array annotation data (chip bovine) |
| bioconductor-bovine.db0 |
3.20.0 |
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Artistic-2.0 |
| | | X | Base Level Annotation databases for bovine |
| bioconductor-bovinecdf |
2.18.0 |
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LGPL |
| | | X | bovinecdf |
| bioconductor-bovineprobe |
2.18.0 |
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LGPL |
| | | X | Probe sequence data for microarrays of type bovine |
| bioconductor-bprmeth |
1.32.0 |
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|
GPL-3 |
X | X | | | Model higher-order methylation profiles |
| bioconductor-brain |
1.52.0 |
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GPL-2 |
X | X | | X | Baffling Recursive Algorithm for Isotope distributioN calculations |
| bioconductor-brainflowprobes |
1.16.0 |
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Artistic-2.0 |
| | | X | Plots and annotation for choosing BrainFlow target probe sequence |
| bioconductor-brainimager |
1.1.0 |
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|
CC |
| | | X | BrainImageR is a package that provides the user with information of... |
| bioconductor-brainimagerdata |
1.12.0 |
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|
CC |
| | | X | Image masks and expression data for use with BrainImageR |
| bioconductor-brainsaber |
1.8.0 |
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Artistic-2.0 |
| | | X | Brain Span Atlas in Biobase Expressionset R toolset |
| bioconductor-brainstars |
1.34.0 |
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|
Artistic-2.0 |
X | X | | X | query gene expression data and plots from BrainStars (B*) |
| bioconductor-branchpointer |
1.32.0 |
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|
BSD_3_clause |
| | | X | Prediction of intronic splicing branchpoints |
| bioconductor-breakpointr |
1.24.0 |
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|
file |
| | | X | Find breakpoints in Strand-seq data |
| bioconductor-breakpointrdata |
1.24.0 |
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|
file |
| | | X | Strand-seq data for demonstration purposes |
| bioconductor-breastcancermainz |
1.44.0 |
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Artistic-2.0 |
| | | X | Gene expression dataset published by Schmidt et al. [2008] (MAINZ). |
| bioconductor-breastcancernki |
1.44.0 |
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Artistic-2.0 |
| | | X | Genexpression dataset published by van't Veer et al. [2002] and van... |
| bioconductor-breastcancertransbig |
1.44.0 |
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Artistic-2.0 |
| | | X | Gene expression dataset published by Desmedt et al. [2007] (TRANSBIG). |
| bioconductor-breastcancerunt |
1.44.0 |
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Artistic-2.0 |
| | | X | Gene expression dataset published by Sotiriou et al. [2007] (UNT). |
| bioconductor-breastcancerupp |
1.44.0 |
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Artistic-2.0 |
| | | X | Gene expression dataset published by Miller et al. [2005] (UPP). |
| bioconductor-breastcancervdx |
1.44.0 |
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|
Artistic-2.0 |
| | | X | Gene expression datasets published by Wang et al. [2005] and Minn et... |
| bioconductor-brendadb |
1.20.0 |
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|
MIT |
X | X | | | The BRENDA Enzyme Database |
| bioconductor-brew3r.r |
1.2.0 |
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GPL-3 |
| | | X | R package associated to BREW3R |
| bioconductor-brgedata |
1.28.0 |
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MIT |
| | | X | Exposures, Gene Expression and Methylation data for ilustration purpouses |
| bioconductor-brgenomics |
1.13.0 |
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Artistic-2.0 |
| | | X | Tools for the Efficient Analysis of High-Resolution Genomics Data |
| bioconductor-bridge |
1.62.0 |
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|
GPL |
X | X | | | Bayesian Robust Inference for Differential Gene Expression |
| bioconductor-bridgedbr |
2.16.0 |
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AGPL-3 |
| | | X | Code for using BridgeDb identifier mapping framework from within R |
| bioconductor-broadseq |
1.0.0 |
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|
MIT |
| | | X | broadSeq : for streamlined exploration of RNA-seq data |
| bioconductor-bronchialil13 |
1.44.0 |
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|
GPL-2 |
| | | X | time course experiment involving il13 |
| bioconductor-browserviz |
2.28.0 |
|
|
GPL-2 |
X | X | | X | BrowserViz: interactive R/browser graphics using websockets and JSON |
| bioconductor-browservizdemo |
1.11.0 |
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|
GPL-2 |
X | X | | | A BrowserViz subclassing example, xy plotting in the browser using d3. |
| bioconductor-bsgenome |
1.74.0 |
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|
Artistic-2.0 |
X | X | | X | Software infrastructure for efficient representation of full genomes... |
| bioconductor-bsgenome.alyrata.jgi.v1 |
1.0.1 |
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|
Artistic-2.0 |
| | | X | Arabidopsis lyrata full genome (JGI version V1.0) |
| bioconductor-bsgenome.amellifera.beebase.assembly4 |
1.4.0 |
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|
Artistic-2.0 |
| | | X | Full genome sequences for Apis mellifera (BeeBase assembly4) |
| bioconductor-bsgenome.amellifera.ncbi.amelhav3.1 |
1.5.0 |
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|
Artistic-2.0 |
| | | X | Full genome sequences for Apis mellifera (Amel_HAv3.1) |
| bioconductor-bsgenome.amellifera.ucsc.apimel2 |
1.4.0 |
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|
Artistic-2.0 |
| | | X | Full genome sequences for Apis mellifera (UCSC version apiMel2) |
| bioconductor-bsgenome.amellifera.ucsc.apimel2.masked |
1.3.99 |
|
|
Artistic-2.0 |
| | | X | Full masked genome sequences for Apis mellifera (UCSC version apiMel2) |
| bioconductor-bsgenome.aofficinalis.ncbi.v1 |
1.0.0 |
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|
GPL-3 |
| | | X | Asparagus officinalis (Garden asparagus) full genome (NCBI version Aspof.V1) |
| bioconductor-bsgenome.athaliana.tair.04232008 |
1.3.1000 |
|
|
Artistic-2.0 |
| | | X | Full genome sequences for Arabidopsis thaliana (TAIR version from April... |
| bioconductor-bsgenome.athaliana.tair.tair9 |
1.3.1000 |
|
|
Artistic-2.0 |
| | | X | Full genome sequences for Arabidopsis thaliana (TAIR9) |
| bioconductor-bsgenome.btaurus.ucsc.bostau3 |
1.4.0 |
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Artistic-2.0 |
| | | X | Full genome sequences for Bos taurus (UCSC version bosTau3) |
| bioconductor-bsgenome.btaurus.ucsc.bostau3.masked |
1.3.99 |
|
|
Artistic-2.0 |
| | | X | Full masked genome sequences for Bos taurus (UCSC version bosTau3) |
| bioconductor-bsgenome.btaurus.ucsc.bostau4 |
1.4.0 |
|
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Artistic-2.0 |
| | | X | Full genome sequences for Bos taurus (UCSC version bosTau4) |
| bioconductor-bsgenome.btaurus.ucsc.bostau4.masked |
1.3.99 |
|
|
Artistic-2.0 |
| | | X | Full masked genome sequences for Bos taurus (UCSC version bosTau4) |
| bioconductor-bsgenome.btaurus.ucsc.bostau6 |
1.4.0 |
|
|
Artistic-2.0 |
| | | X | Full genome sequences for Bos taurus (UCSC version bosTau6) |
| bioconductor-bsgenome.btaurus.ucsc.bostau6.masked |
1.3.99 |
|
|
Artistic-2.0 |
| | | X | Full masked genome sequences for Bos taurus (UCSC version bosTau6) |
| bioconductor-bsgenome.btaurus.ucsc.bostau8 |
1.4.2 |
|
|
Artistic-2.0 |
| | | X | Full genome sequences for Bos taurus (UCSC version bosTau8) |
| bioconductor-bsgenome.btaurus.ucsc.bostau9 |
1.4.2 |
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Artistic-2.0 |
| | | X | Full genome sequences for Bos taurus (UCSC version bosTau9) |
| bioconductor-bsgenome.btaurus.ucsc.bostau9.masked |
1.4.4 |
|
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Artistic-2.0 |
| | | X | Full masked genome sequences for Bos taurus (UCSC version bosTau9) |
| bioconductor-bsgenome.carietinum.ncbi.v1 |
1.0.0 |
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|
GPL-3 |
| | | X | Cicer arietinum (Chickpea) full genome (NCBI version ASM33114v1) |
| bioconductor-bsgenome.celegans.ucsc.ce10 |
1.4.0 |
|
|
Artistic-2.0 |
X | X | | X | Full genome sequences for Caenorhabditis elegans (UCSC version ce10) |
| bioconductor-bsgenome.celegans.ucsc.ce11 |
1.4.2 |
|
|
Artistic-2.0 |
| | | X | Full genome sequences for Caenorhabditis elegans (UCSC version ce11) |
| bioconductor-bsgenome.celegans.ucsc.ce2 |
1.4.0 |
|
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Artistic-2.0 |
| | | X | Full genome sequences for Caenorhabditis elegans (UCSC version ce2) |
| bioconductor-bsgenome.celegans.ucsc.ce6 |
1.4.0 |
|
|
Artistic-2.0 |
X | X | | X | Full genome sequences for Caenorhabditis elegans (UCSC version ce6) |
| bioconductor-bsgenome.cfamiliaris.ucsc.canfam2 |
1.4.0 |
|
|
Artistic-2.0 |
| | | X | Full genome sequences for Canis lupus familiaris (UCSC version canFam2) |
| bioconductor-bsgenome.cfamiliaris.ucsc.canfam2.masked |
1.3.99 |
|
|
Artistic-2.0 |
| | | X | Full masked genome sequences for Canis lupus familiaris (UCSC version canFam2) |
| bioconductor-bsgenome.cfamiliaris.ucsc.canfam3 |
1.4.0 |
|
|
Artistic-2.0 |
| | | X | Full genome sequences for Canis lupus familiaris (UCSC version canFam3) |
| bioconductor-bsgenome.cfamiliaris.ucsc.canfam3.masked |
1.3.99 |
|
|
Artistic-2.0 |
| | | X | Full masked genome sequences for Canis lupus familiaris (UCSC version canFam3) |
| bioconductor-bsgenome.cjacchus.ucsc.caljac3 |
1.4.2 |
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Artistic-2.0 |
| | | X | Full genome sequences for Callithrix jacchus (UCSC version calJac3) |
| bioconductor-bsgenome.cjacchus.ucsc.caljac4 |
1.5.0 |
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Artistic-2.0 |
| | | X | Full genome sequences for Callithrix jacchus (UCSC version calJac4) |
| bioconductor-bsgenome.cneoformansvargrubiikn99.ncbi.asm221672v1 |
1.0.0 |
|
|
Artistic-2.0 |
| | | X | Full Genome Sequence for Cryptococcus neoformans var. grubii KN99 (ASM221672v1) |
| bioconductor-bsgenome.creinhardtii.jgi.v5.6 |
1.5.0 |
|
|
Artistic-2.0 |
| | | X | Full genome sequences for Chlamydomonas reinhardtii (v5.6) |
| bioconductor-bsgenome.dmelanogaster.ucsc.dm2 |
1.4.0 |
|
|
Artistic-2.0 |
| | | X | Full genome sequences for Drosophila melanogaster (UCSC version dm2) |
| bioconductor-bsgenome.dmelanogaster.ucsc.dm2.masked |
1.3.99 |
|
|
Artistic-2.0 |
| | | X | Full masked genome sequences for Drosophila melanogaster (UCSC version dm2) |
| bioconductor-bsgenome.dmelanogaster.ucsc.dm3 |
1.4.0 |
|
|
Artistic-2.0 |
X | X | | X | Full genome sequences for Drosophila melanogaster (UCSC version dm3) |
| bioconductor-bsgenome.dmelanogaster.ucsc.dm3.masked |
1.3.99 |
|
|
Artistic-2.0 |
| | | X | Full masked genome sequences for Drosophila melanogaster (UCSC version dm3) |
| bioconductor-bsgenome.dmelanogaster.ucsc.dm6 |
1.4.1 |
|
|
Artistic-2.0 |
| | | X | Full genome sequences for Drosophila melanogaster (UCSC version dm6) |
| bioconductor-bsgenome.drerio.ucsc.danrer10 |
1.4.2 |
|
|
Artistic-2.0 |
| | | X | Full genome sequences for Danio rerio (UCSC version danRer10) |
| bioconductor-bsgenome.drerio.ucsc.danrer11 |
1.4.2 |
|
|
Artistic-2.0 |
| | | X | Full genome sequences for Danio rerio (UCSC version danRer11) |
| bioconductor-bsgenome.drerio.ucsc.danrer5 |
1.4.0 |
|
|
Artistic-2.0 |
| | | X | Full genome sequences for Danio rerio (UCSC version danRer5) |
| bioconductor-bsgenome.drerio.ucsc.danrer5.masked |
1.3.99 |
|
|
Artistic-2.0 |
| | | X | Full masked genome sequences for Danio rerio (UCSC version danRer5) |
| bioconductor-bsgenome.drerio.ucsc.danrer6 |
1.4.0 |
|
|
Artistic-2.0 |
| | | X | Full genome sequences for Danio rerio (UCSC version danRer6) |
| bioconductor-bsgenome.drerio.ucsc.danrer6.masked |
1.3.99 |
|
|
Artistic-2.0 |
| | | X | Full masked genome sequences for Danio rerio (UCSC version danRer6) |
| bioconductor-bsgenome.drerio.ucsc.danrer7 |
1.4.0 |
|
|
Artistic-2.0 |
X | X | | X | Full genome sequences for Danio rerio (UCSC version danRer7) |
| bioconductor-bsgenome.drerio.ucsc.danrer7.masked |
1.3.99 |
|
|
Artistic-2.0 |
| | | X | Full masked genome sequences for Danio rerio (UCSC version danRer7) |
| bioconductor-bsgenome.dvirilis.ensembl.dvircaf1 |
1.4.3 |
|
|
Artistic-2.0 |
| | | X | Full genome sequences for Drosophila virilis (assembly dvir_caf1) |
| bioconductor-bsgenome.ecoli.ncbi.20080805 |
1.3.1000 |
|
|
Artistic-2.0 |
X | X | | X | Escherichia coli full genomes |
| bioconductor-bsgenome.gaculeatus.ucsc.gasacu1 |
1.4.0 |
|
|
Artistic-2.0 |
| | | X | Full genome sequences for Gasterosteus aculeatus (UCSC version gasAcu1) |
| bioconductor-bsgenome.gaculeatus.ucsc.gasacu1.masked |
1.3.99 |
|
|
Artistic-2.0 |
| | | X | Full masked genome sequences for Gasterosteus aculeatus (UCSC version gasAcu1) |
| bioconductor-bsgenome.ggallus.ucsc.galgal3 |
1.4.0 |
|
|
Artistic-2.0 |
| | | X | Full genome sequences for Gallus gallus (UCSC version galGal3) |
| bioconductor-bsgenome.ggallus.ucsc.galgal3.masked |
1.3.99 |
|
|
Artistic-2.0 |
| | | X | Full masked genome sequences for Gallus gallus (UCSC version galGal3) |
| bioconductor-bsgenome.ggallus.ucsc.galgal4 |
1.4.0 |
|
|
Artistic-2.0 |
| | | X | Full genome sequences for Gallus gallus (UCSC version galGal4) |
| bioconductor-bsgenome.ggallus.ucsc.galgal4.masked |
1.3.99 |
|
|
Artistic-2.0 |
| | | X | Full masked genome sequences for Gallus gallus (UCSC version galGal4) |
| bioconductor-bsgenome.ggallus.ucsc.galgal5 |
1.4.2 |
|
|
Artistic-2.0 |
| | | X | Full genome sequences for Gallus gallus (UCSC version galGal5) |
| bioconductor-bsgenome.ggallus.ucsc.galgal6 |
1.4.2 |
|
|
Artistic-2.0 |
| | | X | Full genome sequences for Gallus gallus (UCSC version galGal6) |
| bioconductor-bsgenome.gmax.ncbi.gmv40 |
4.0 |
|
|
Creative |
| | | X | Full genome sequences for Glycine max (Gmv40) |
| bioconductor-bsgenome.hsapiens.1000genomes.hs37d5 |
0.99.1 |
|
|
Artistic-2.0 |
| | | X | 1000genomes Reference Genome Sequence (hs37d5) |
| bioconductor-bsgenome.hsapiens.ncbi.grch38 |
1.3.1000 |
|
|
Artistic-2.0 |
| | | X | Full genome sequences for Homo sapiens (GRCh38) |
| bioconductor-bsgenome.hsapiens.ncbi.t2t.chm13v2.0 |
1.5.0 |
|
|
Artistic-2.0 |
| | | X | T2T-CHM13v2.0 assembly (Homo sapiens) wrapped in a BSgenome object |
| bioconductor-bsgenome.hsapiens.ucsc.hg17 |
1.3.1001 |
|
|
Artistic-2.0 |
| | | X | Full genome sequences for Homo sapiens (UCSC version hg17) |
| bioconductor-bsgenome.hsapiens.ucsc.hg17.masked |
1.3.999 |
|
|
Artistic-2.0 |
| | | X | Full masked genome sequences for Homo sapiens (UCSC version hg17) |
| bioconductor-bsgenome.hsapiens.ucsc.hg18 |
1.3.1000 |
|
|
Artistic-2.0 |
X | X | | X | Full genome sequences for Homo sapiens (UCSC version hg18) |
| bioconductor-bsgenome.hsapiens.ucsc.hg18.masked |
1.3.99 |
|
|
Artistic-2.0 |
| | | X | Full masked genome sequences for Homo sapiens (UCSC version hg18) |
| bioconductor-bsgenome.hsapiens.ucsc.hg19 |
1.4.3 |
|
|
Artistic-2.0 |
X | X | | X | Full genome sequences for Homo sapiens (UCSC version hg19, based on GRCh37.p13) |
| bioconductor-bsgenome.hsapiens.ucsc.hg19.masked |
1.3.993 |
|
|
Artistic-2.0 |
| | | X | Full masked genome sequences for Homo sapiens (UCSC version hg19, based... |
| bioconductor-bsgenome.hsapiens.ucsc.hg38 |
1.4.5 |
|
|
Artistic-2.0 |
X | X | | X | Full genomic sequences for Homo sapiens (UCSC genome hg38) |
| bioconductor-bsgenome.hsapiens.ucsc.hg38.dbsnp151.major |
0.0.9999 |
|
|
CC |
| | | X | Full genome sequences for Homo sapiens (UCSC version hg38, based on... |
| bioconductor-bsgenome.hsapiens.ucsc.hg38.dbsnp151.minor |
0.0.9999 |
|
|
CC |
| | | X | Full genome sequences for Homo sapiens (UCSC version hg38, based on... |
| bioconductor-bsgenome.hsapiens.ucsc.hg38.masked |
1.4.5 |
|
|
Artistic-2.0 |
| | | X | Full masked genomic sequences for Homo sapiens (UCSC version hg38) |
| bioconductor-bsgenome.hsapiens.ucsc.hs1 |
1.4.4 |
|
|
Artistic-2.0 |
| | | X | Full genomic sequences for UCSC genome hs1 (Homo sapiens) |
| bioconductor-bsgenome.mdomestica.ucsc.mondom5 |
1.4.2 |
|
|
Artistic-2.0 |
| | | X | Full genome sequences for Monodelphis domestica (UCSC version monDom5) |
| bioconductor-bsgenome.mfascicularis.ncbi.5.0 |
1.4.2 |
|
|
Artistic-2.0 |
| | | X | Full genome sequences for Macaca fascicularis (Macaca_fascicularis_5.0) |
| bioconductor-bsgenome.mfascicularis.ncbi.6.0 |
1.5.0 |
|
|
Artistic-2.0 |
| | | X | Full genome sequences for Macaca fascicularis (Macaca_fascicularis_6.0) |
| bioconductor-bsgenome.mfuro.ucsc.musfur1 |
1.4.1 |
|
|
Artistic-2.0 |
| | | X | Full genome sequences for Mustela putorius furo (UCSC version musFur1) |
| bioconductor-bsgenome.mmulatta.ucsc.rhemac10 |
1.4.2 |
|
|
Artistic-2.0 |
| | | X | Full genome sequences for Macaca mulatta (UCSC version rheMac10) |
| bioconductor-bsgenome.mmulatta.ucsc.rhemac2 |
1.4.0 |
|
|
Artistic-2.0 |
| | | X | Full genome sequences for Macaca mulatta (UCSC version rheMac2) |
| bioconductor-bsgenome.mmulatta.ucsc.rhemac2.masked |
1.3.99 |
|
|
Artistic-2.0 |
| | | X | Full masked genome sequences for Macaca mulatta (UCSC version rheMac2) |
| bioconductor-bsgenome.mmulatta.ucsc.rhemac3 |
1.4.0 |
|
|
Artistic-2.0 |
| | | X | Full genome sequences for Macaca mulatta (UCSC version rheMac3) |
| bioconductor-bsgenome.mmulatta.ucsc.rhemac3.masked |
1.3.99 |
|
|
Artistic-2.0 |
| | | X | Full masked genome sequences for Macaca mulatta (UCSC version rheMac3) |
| bioconductor-bsgenome.mmulatta.ucsc.rhemac8 |
1.4.2 |
|
|
Artistic-2.0 |
| | | X | Full genome sequences for Macaca mulatta (UCSC version rheMac8) |
| bioconductor-bsgenome.mmusculus.ucsc.mm10 |
1.4.3 |
|
|
Artistic-2.0 |
X | X | | X | Full genome sequences for Mus musculus (UCSC version mm10, based on GRCm38.p6) |
| bioconductor-bsgenome.mmusculus.ucsc.mm10.masked |
1.4.3 |
|
|
Artistic-2.0 |
| | | X | Full masked genome sequences for Mus musculus (UCSC genome mm10, based... |
| bioconductor-bsgenome.mmusculus.ucsc.mm39 |
1.4.3 |
|
|
Artistic-2.0 |
| | | X | Full genome sequences for Mus musculus (UCSC genome mm39, based on GRCm39) |
| bioconductor-bsgenome.mmusculus.ucsc.mm8 |
1.4.0 |
|
|
Artistic-2.0 |
| | | X | Full genome sequences for Mus musculus (UCSC version mm8) |
| bioconductor-bsgenome.mmusculus.ucsc.mm8.masked |
1.3.99 |
|
|
Artistic-2.0 |
| | | X | Full masked genome sequences for Mus musculus (UCSC version mm8) |
| bioconductor-bsgenome.mmusculus.ucsc.mm9 |
1.4.0 |
|
|
Artistic-2.0 |
X | X | | X | Full genome sequences for Mus musculus (UCSC version mm9) |
| bioconductor-bsgenome.mmusculus.ucsc.mm9.masked |
1.3.99 |
|
|
Artistic-2.0 |
| | | X | Full masked genome sequences for Mus musculus (UCSC version mm9) |
| bioconductor-bsgenome.osativa.msu.msu7 |
0.99.2 |
|
|
Artistic-2.0 |
| | | X | Oryza sativa full genome (MSU7) |
| bioconductor-bsgenome.ppaniscus.ucsc.panpan1 |
1.4.3 |
|
|
Artistic-2.0 |
| | | X | Full genome sequences for Pan paniscus (UCSC version panPan1) |
| bioconductor-bsgenome.ppaniscus.ucsc.panpan2 |
1.4.3 |
|
|
Artistic-2.0 |
| | | X | Full genome sequences for Pan paniscus (UCSC version panPan2) |
| bioconductor-bsgenome.ptroglodytes.ucsc.pantro2 |
1.4.0 |
|
|
Artistic-2.0 |
| | | X | Full genome sequences for Pan troglodytes (UCSC version panTro2) |
| bioconductor-bsgenome.ptroglodytes.ucsc.pantro2.masked |
1.3.99 |
|
|
Artistic-2.0 |
| | | X | Full masked genome sequences for Pan troglodytes (UCSC version panTro2) |
| bioconductor-bsgenome.ptroglodytes.ucsc.pantro3 |
1.4.0 |
|
|
Artistic-2.0 |
| | | X | Full genome sequences for Pan troglodytes (UCSC version panTro3) |
| bioconductor-bsgenome.ptroglodytes.ucsc.pantro3.masked |
1.3.99 |
|
|
Artistic-2.0 |
| | | X | Full masked genome sequences for Pan troglodytes (UCSC version panTro3) |
| bioconductor-bsgenome.ptroglodytes.ucsc.pantro5 |
1.4.2 |
|
|
Artistic-2.0 |
| | | X | Full genome sequences for Pan troglodytes (UCSC version panTro5) |
| bioconductor-bsgenome.ptroglodytes.ucsc.pantro6 |
1.4.2 |
|
|
Artistic-2.0 |
| | | X | Full genome sequences for Pan troglodytes (UCSC version panTro6) |
| bioconductor-bsgenome.rnorvegicus.ucsc.rn4 |
1.4.0 |
|
|
Artistic-2.0 |
| | | X | Full genome sequences for Rattus norvegicus (UCSC version rn4) |
| bioconductor-bsgenome.rnorvegicus.ucsc.rn4.masked |
1.3.99 |
|
|
Artistic-2.0 |
| | | X | Full masked genome sequences for Rattus norvegicus (UCSC version rn4) |
| bioconductor-bsgenome.rnorvegicus.ucsc.rn5 |
1.4.0 |
|
|
Artistic-2.0 |
| | | X | Full genome sequences for Rattus norvegicus (UCSC version rn5) |
| bioconductor-bsgenome.rnorvegicus.ucsc.rn5.masked |
1.3.99 |
|
|
Artistic-2.0 |
| | | X | Full masked genome sequences for Rattus norvegicus (UCSC version rn5) |
| bioconductor-bsgenome.rnorvegicus.ucsc.rn6 |
1.4.1 |
|
|
Artistic-2.0 |
| | | X | Full genome sequences for Rattus norvegicus (UCSC version rn6) |
| bioconductor-bsgenome.rnorvegicus.ucsc.rn7 |
1.4.3 |
|
|
Artistic-2.0 |
| | | X | Full genome sequences for Rattus norvegicus (UCSC genome rn7) |
| bioconductor-bsgenome.scerevisiae.ucsc.saccer1 |
1.4.0 |
|
|
Artistic-2.0 |
| | | X | Saccharomyces cerevisiae (Yeast) full genome (UCSC version sacCer1) |
| bioconductor-bsgenome.scerevisiae.ucsc.saccer2 |
1.4.0 |
|
|
Artistic-2.0 |
| | | X | Saccharomyces cerevisiae (Yeast) full genome (UCSC version sacCer2) |
| bioconductor-bsgenome.scerevisiae.ucsc.saccer3 |
1.4.0 |
|
|
Artistic-2.0 |
| | | X | Saccharomyces cerevisiae (Yeast) full genome (UCSC version sacCer3) |
| bioconductor-bsgenome.sscrofa.ucsc.susscr11 |
1.4.2 |
|
|
Artistic-2.0 |
| | | X | Full genome sequences for Sus scrofa (UCSC version susScr11) |
| bioconductor-bsgenome.sscrofa.ucsc.susscr3 |
1.4.0 |
|
|
Artistic-2.0 |
| | | X | Full genome sequences for Sus scrofa (UCSC version susScr3) |
| bioconductor-bsgenome.sscrofa.ucsc.susscr3.masked |
1.3.99 |
|
|
Artistic-2.0 |
| | | X | Full masked genome sequences for Sus scrofa (UCSC version susScr3) |
| bioconductor-bsgenome.tgondii.toxodb.7.0 |
0.99.1 |
|
|
GPL |
| | | X | Toxoplasma gondii ME49 (ToxoDB-7.0) |
| bioconductor-bsgenome.tguttata.ucsc.taegut1 |
1.4.0 |
|
|
Artistic-2.0 |
| | | X | Full genome sequences for Taeniopygia guttata (UCSC version taeGut1) |
| bioconductor-bsgenome.tguttata.ucsc.taegut1.masked |
1.3.99 |
|
|
Artistic-2.0 |
| | | X | Full masked genome sequences for Taeniopygia guttata (UCSC version taeGut1) |
| bioconductor-bsgenome.tguttata.ucsc.taegut2 |
1.4.2 |
|
|
Artistic-2.0 |
| | | X | Full genome sequences for Taeniopygia guttata (UCSC version taeGut2) |
| bioconductor-bsgenome.vvinifera.urgi.iggp12xv0 |
0.1 |
|
|
CC0 |
| | | X | Full reference nuclear genome sequences for Vitis vinifera subsp.... |
| bioconductor-bsgenome.vvinifera.urgi.iggp12xv2 |
0.1 |
|
|
CC0 |
| | | X | Full reference nuclear genome sequences for Vitis vinifera subsp.... |
| bioconductor-bsgenome.vvinifera.urgi.iggp8x |
0.1 |
|
|
CC0 |
| | | X | Full reference nuclear genome sequences for Vitis vinifera subsp.... |
| bioconductor-bsgenomeforge |
1.6.0 |
|
|
Artistic-2.0 |
| | | X | Forge your own BSgenome data package |
| bioconductor-bsseq |
1.42.0 |
|
|
Artistic-2.0 |
X | X | | | Analyze, manage and store whole-genome methylation data |
| bioconductor-bsseqdata |
0.44.0 |
|
|
Artistic-2.0 |
| | | X | Example whole genome bisulfite data for the bsseq package |
| bioconductor-bsubtiliscdf |
2.18.0 |
|
|
LGPL |
| | | X | bsubtiliscdf |
| bioconductor-bsubtilisprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type bsubtilis |
| bioconductor-bubbletree |
2.36.0 |
|
|
LGPL |
X | X | | X | BubbleTree: an intuitive visualization to elucidate tumoral aneuploidy... |
| bioconductor-bufferedmatrix |
1.70.0 |
|
|
LGPL |
X | X | | | A matrix data storage object held in temporary files |
| bioconductor-bufferedmatrixmethods |
1.70.0 |
|
|
GPL |
X | X | | | Microarray Data related methods that utlize BufferedMatrix objects |
| bioconductor-bugphyzz |
1.0.0 |
|
|
Artistic-2.0 |
| | | X | A harmonized data resource and software for enrichment analysis of... |
| bioconductor-bugsigdbr |
1.12.0 |
|
|
GPL-3 |
| | | X | R-side access to published microbial signatures from BugSigDB |
| bioconductor-bumhmm |
1.30.0 |
|
|
GPL-3 |
| | | X | Computational pipeline for computing probability of modification from... |
| bioconductor-bumphunter |
1.48.0 |
|
|
Artistic-2.0 |
X | X | | X | Bump Hunter |
| bioconductor-bumpymatrix |
1.14.0 |
|
|
MIT |
| | | X | Bumpy Matrix of Non-Scalar Objects |
| bioconductor-bus |
1.62.0 |
|
|
GPL-3 |
X | X | | | Gene network reconstruction |
| bioconductor-buscorrect |
1.24.0 |
|
|
GPL |
X | X | | | Batch Effects Correction with Unknown Subtypes |
| bioconductor-busparse |
1.20.0 |
|
|
BSD_2_clause |
X | X | | | kallisto | bustools R utilities |
| bioconductor-busseq |
1.12.0 |
|
|
Artistic-2.0 |
X | X | | | Batch Effect Correction with Unknow Subtypes for scRNA-seq data |
| bioconductor-cadd.v1.6.hg19 |
3.18.1 |
|
|
Artistic-2.0 |
| | | X | CADD v1.6 Pathogenicity Scores AnnotationHub Resource Metadata for hg19 |
| bioconductor-cadd.v1.6.hg38 |
3.18.1 |
|
|
Artistic-2.0 |
| | | X | CADD v1.6 Pathogenicity Scores AnnotationHub Resource Metadata for hg38 |
| bioconductor-cadra |
1.0.1 |
|
|
GPL-3 |
X | X | | | Candidate Driver Analysis |
| bioconductor-caen |
1.14.0 |
|
|
GPL-2 |
| | | X | Category encoding method for selecting feature genes for the... |
| bioconductor-cafe |
1.42.0 |
|
|
GPL-3 |
| | | X | Chromosmal Aberrations Finder in Expression data |
| bioconductor-cagefightr |
1.26.0 |
|
|
GPL-3 |
| | | X | Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor |
| bioconductor-cageminer |
1.12.0 |
|
|
GPL-3 |
| | | X | Candidate Gene Miner |
| bioconductor-cager |
2.12.0 |
|
|
GPL-3 |
X | X | | X | Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for... |
| bioconductor-calib |
1.52.0 |
|
|
LGPL |
X | X | | | Calibration model for estimating absolute expression levels from microarray data |
| bioconductor-calm |
1.20.0 |
|
|
GPL |
| | | X | Covariate Assisted Large-scale Multiple testing |
| bioconductor-camera |
1.62.0 |
|
|
GPL |
X | X | | | Collection of annotation related methods for mass spectrometry data |
| bioconductor-camthc |
1.4.0 |
|
|
GPL-2 |
| | | X | Convex Analysis of Mixtures for Tissue Heterogeneity Characterization |
| bioconductor-camutqc |
1.2.0 |
|
|
GPL-3 |
| | | X | An R Package for Comprehensive Filtration and Selection of Cancer... |
| bioconductor-cancer |
1.40.0 |
|
|
GPL-2 |
| | | X | A Graphical User Interface for accessing and modeling the Cancer... |
| bioconductor-cancerclass |
1.50.0 |
|
|
GPL |
X | X | | | Development and validation of diagnostic tests from high-dimensional... |
| bioconductor-cancerdata |
1.44.0 |
|
|
GPL |
| | | X | Development and validation of diagnostic tests from high-dimensional... |
| bioconductor-cancerinsilico |
2.18.0 |
|
|
GPL-2 |
X | X | | | An R interface for computational modeling of tumor progression |
| bioconductor-cancermutationanalysis |
1.32.0 |
|
|
GPL |
X | X | | | Cancer mutation analysis |
| bioconductor-cancersubtypes |
1.26.0 |
|
|
GPL |
X | X | | X | Cancer subtypes identification, validation and visualization based on... |
| bioconductor-cand |
1.26.0 |
|
|
Artistic-2.0 |
X | X | | X | Perform Chromosomal Ancestry Differences (CAnD) Analyses |
| bioconductor-canine.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix Canine Array annotation data (chip canine) |
| bioconductor-canine.db0 |
3.20.0 |
|
|
Artistic-2.0 |
| | | X | Base Level Annotation databases for canine |
| bioconductor-canine2.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix Canine_2 Array annotation data (chip canine2) |
| bioconductor-canine2cdf |
2.18.0 |
|
|
LGPL |
| | | X | canine2cdf |
| bioconductor-canine2probe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type canine2 |
| bioconductor-caninecdf |
2.18.0 |
|
|
LGPL |
| | | X | caninecdf |
| bioconductor-canineprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type canine |
| bioconductor-caomicsv |
1.24.0 |
|
|
GPL |
| | | X | Visualization of multi-dimentional cancer genomics data |
| bioconductor-cardelino |
1.8.0 |
|
|
GPL-3 |
| | | X | Clone Identification from Single Cell Data |
| bioconductor-cardinal |
3.8.0 |
|
|
Artistic-2.0 |
X | X | | X | A mass spectrometry imaging toolbox for statistical analysis |
| bioconductor-cardinalio |
1.4.0 |
|
|
Artistic-2.0 |
X | X | | | Read and write mass spectrometry imaging files |
| bioconductor-cardinalworkflows |
1.38.0 |
|
|
Artistic-2.0 |
| | | X | Datasets and workflows for the Cardinal MSI |
| bioconductor-carnival |
2.16.0 |
|
|
GPL-3 |
| | | X | A CAusal Reasoning tool for Network Identification (from gene... |
| bioconductor-casper |
2.40.0 |
|
|
GPL |
X | X | | | Characterization of Alternative Splicing based on Paired-End Reads |
| bioconductor-catalyst |
1.30.0 |
|
|
GPL |
| | | X | Cytometry dATa anALYSis Tools |
| bioconductor-category |
2.72.0 |
|
|
Artistic-2.0 |
X | X | | X | Category Analysis |
| bioconductor-categorycompare |
1.50.0 |
|
|
GPL-2 |
| | | X | Meta-analysis of high-throughput experiments using feature annotations |
| bioconductor-catscradle |
1.0.0 |
|
|
MIT |
| | | X | This package provides methods for analysing spatial transcriptomics... |
| bioconductor-causalr |
1.38.0 |
|
|
GPL |
X | X | | X | Causal network analysis methods |
| bioconductor-cbaf |
1.28.0 |
|
|
Artistic-2.0 |
| | | X | Automated functions for comparing various omic data from cbioportal.org |
| bioconductor-cbea |
1.6.0 |
|
|
MIT |
X | X | | | Competitive Balances for Taxonomic Enrichment Analysis in R |
| bioconductor-cbioportaldata |
2.18.0 |
|
|
AGPL-3 |
| | | X | Exposes and Makes Available Data from the cBioPortal Web Resources |
| bioconductor-cbnplot |
1.6.0 |
|
|
Artistic-2.0 |
| | | X | plot bayesian network inferred from gene expression data based on... |
| bioconductor-cbpmanager |
1.14.0 |
|
|
AGPL-3 |
| | | X | Generate, manage, and edit data and metadata files suitable for the... |
| bioconductor-ccdata |
1.32.0 |
|
|
MIT |
| | | X | Data for Combination Connectivity Mapping (ccmap) Package |
| bioconductor-ccfindr |
1.22.0 |
|
|
GPL |
X | X | | | Cancer Clone Finder |
| bioconductor-ccimpute |
1.8.0 |
|
|
GPL-3 |
X | X | | | ccImpute: an accurate and scalable consensus clustering based approach... |
| bioconductor-ccl4 |
1.44.0 |
|
|
Artistic-2.0 |
| | | X | Carbon Tetrachloride (CCl4) treated hepatocytes |
| bioconductor-ccmap |
1.28.0 |
|
|
MIT |
| | | X | Combination Connectivity Mapping |
| bioconductor-ccplotr |
1.4.0 |
|
|
MIT |
| | | X | Plots For Visualising Cell-Cell Interactions |
| bioconductor-ccpromise |
1.32.0 |
|
|
GPL |
| | | X | PROMISE analysis with Canonical Correlation for Two Forms of High... |
| bioconductor-ccrepe |
1.42.0 |
|
|
MIT |
| | | X | ccrepe_and_nc.score |
| bioconductor-cctutorial |
1.40.0 |
|
|
Artistic-2.0 |
| | | X | Data package for ChIP-chip tutorial |
| bioconductor-cdi |
1.4.0 |
|
|
GPL-3 |
| | | X | Clustering Deviation Index (CDI) |
| bioconductor-celaref |
1.24.0 |
|
|
GPL-3 |
| | | X | Single-cell RNAseq cell cluster labelling by reference |
| bioconductor-celarefdata |
1.24.0 |
|
|
GPL-3 |
| | | X | Processed scRNA data for celaref Vignette - cell labelling by reference |
| bioconductor-celda |
1.22.0 |
|
|
MIT |
X | X | | | CEllular Latent Dirichlet Allocation |
| bioconductor-celegans.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix Celegans Array annotation data (chip celegans) |
| bioconductor-celeganscdf |
2.18.0 |
|
|
LGPL |
| | | X | celeganscdf |
| bioconductor-celegansprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type celegans |
| bioconductor-cellarepertorium |
1.12.0 |
|
|
GPL-3 |
X | X | | | Data structures, clustering and testing for single cell immune receptor... |
| bioconductor-cellbarcode |
1.12.0 |
|
|
Artistic-2.0 |
X | X | | | Cellular DNA Barcode Analysis toolkit |
| bioconductor-cellbaser |
1.30.0 |
|
|
Apache |
| | | X | Querying annotation data from the high performance Cellbase web |
| bioconductor-cellbench |
1.22.0 |
|
|
GPL-3 |
| | | X | Construct Benchmarks for Single Cell Analysis Methods |
| bioconductor-celldex |
1.16.0 |
|
|
GPL-3 |
| | | X | Index of Reference Cell Type Datasets |
| bioconductor-cellgrowth |
1.30.0 |
|
|
Artistic-2.0 |
X | X | | X | Fitting cell population growth models |
| bioconductor-cellhashr |
1.04 |
|
dev |
MIT |
| | | X | An R package designed to demultiplex cell hashing data. More... |
| bioconductor-cellhts2 |
2.66.0 |
|
|
Artistic-2.0 |
X | X | | X | Analysis of cell-based screens - revised version of cellHTS |
| bioconductor-cellid |
1.14.0 |
|
|
GPL-3 |
X | X | | | Unbiased Extraction of Single Cell gene signatures using Multiple... |
| bioconductor-cellity |
1.34.0 |
|
|
GPL |
| | | X | Quality Control for Single-Cell RNA-seq Data |
| bioconductor-cellmapper |
1.32.0 |
|
|
Artistic-2.0 |
X | X | | X | Predict genes expressed selectively in specific cell types |
| bioconductor-cellmapperdata |
1.32.0 |
|
|
Artistic-2.0 |
| | | X | Pre-processed data for use with the CellMapper package |
| bioconductor-cellmigration |
1.14.0 |
|
|
GPL-2 |
| | | X | Track Cells, Analyze Cell Trajectories and Compute Migration Statistics |
| bioconductor-cellmixs |
1.22.0 |
|
|
GPL |
| | | X | Evaluate Cellspecific Mixing |
| bioconductor-cellnoptr |
1.52.0 |
|
|
GPL-3 |
X | X | | | Training of boolean logic models of signalling networks using prior... |
| bioconductor-cellscape |
1.30.0 |
|
|
GPL-3 |
| | | X | Explores single cell copy number profiles in the context of a single cell tree |
| bioconductor-cellscore |
1.26.0 |
|
|
GPL-3 |
| | | X | Tool for Evaluation of Cell Identity from Transcription Profiles |
| bioconductor-celltrails |
1.24.0 |
|
|
Artistic-2.0 |
| | | X | Reconstruction, visualization and analysis of branching trajectories |
| bioconductor-celltree |
1.27.0 |
|
|
Artistic-2.0 |
| | | X | Inference and visualisation of Single-Cell RNA-seq data as a... |
| bioconductor-cellxgenedp |
1.10.0 |
|
|
Artistic-2.0 |
| | | X | Discover and Access Single Cell Data Sets in the CELLxGENE Data Portal |
| bioconductor-cemitool |
1.30.0 |
|
|
GPL-3 |
| | | X | Co-expression Modules identification Tool |
| bioconductor-censcyt |
1.14.0 |
|
|
MIT |
| | | X | Differential abundance analysis with a right censored covariate in... |
| bioconductor-cepo |
1.12.0 |
|
|
MIT |
| | | X | Cepo for the identification of differentially stable genes |
| bioconductor-cernanetsim |
1.18.0 |
|
|
GPL |
| | | X | Regulation Simulator of Interaction between miRNA and Competing RNAs (ceRNA) |
| bioconductor-cetf |
1.18.0 |
|
|
GPL-3 |
X | X | | X | Coexpression for Transcription Factors using Regulatory Impact Factors... |
| bioconductor-ceu1kg |
0.26.0 |
|
|
Artistic-2.0 |
| | | X | CEU (N=60) genotypes from 1000 genomes pilot phase I |
| bioconductor-ceu1kgv |
0.32.0 |
|
|
Artistic-2.0 |
| | | X | expression + genotype on 79 unrelated CEU individuals |
| bioconductor-ceuhm3 |
0.26.0 |
|
|
Artistic-2.0 |
| | | X | ceuhm3: genotype (HapMap phase III) and expression data for CEPH CEU cohort |
| bioconductor-cexor |
1.44.0 |
|
|
Artistic-2.0 |
X | X | | X | An R package to uncover high-resolution protein-DNA interactions in... |
| bioconductor-cfassay |
1.40.0 |
|
|
LGPL |
X | X | | X | Statistical analysis for the Colony Formation Assay |
| bioconductor-cfdnakit |
1.4.0 |
|
|
GPL-3 |
| | | X | Fragmen-length analysis package from high-throughput sequencing of... |
| bioconductor-cfdnapro |
1.12.0 |
|
|
GPL-3 |
| | | X | cfDNAPro extracts and Visualises biological features from whole genome... |
| bioconductor-cftools |
1.6.0 |
|
|
file |
X | X | | | Informatics Tools for Cell-Free DNA Study |
| bioconductor-cftoolsdata |
1.4.0 |
|
|
file |
| | | X | ExperimentHub data for the cfTools package |
| bioconductor-cgdv17 |
0.28.0 |
|
|
Artistic-2.0 |
| | | X | Complete Genomics Diversity Panel, chr17 on 46 individuals |
| bioconductor-cgen |
3.42.0 |
|
|
GPL-2 |
X | X | | | An R package for analysis of case-control studies in genetic epidemiology |
| bioconductor-cghbase |
1.66.0 |
|
|
GPL |
X | X | | X | CGHbase: Base functions and classes for arrayCGH data analysis. |
| bioconductor-cghcall |
2.68.0 |
|
|
GPL |
X | X | | X | Calling aberrations for array CGH tumor profiles. |
| bioconductor-cghmcr |
1.64.0 |
|
|
LGPL |
X | X | | X | Find chromosome regions showing common gains/losses |
| bioconductor-cghnormaliter |
1.60.0 |
|
|
GPL |
X | X | | X | Normalization of array CGH data with imbalanced aberrations. |
| bioconductor-cghregions |
1.64.0 |
|
|
GPL |
X | X | | X | Dimension Reduction for Array CGH Data with Minimal Information Loss. |
| bioconductor-champ |
2.28.0 |
|
|
GPL-3 |
| | | X | Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC |
| bioconductor-champdata |
2.38.0 |
|
|
GPL-3 |
| | | X | Data Packages for ChAMP package |
| bioconductor-charge |
1.7.0 |
|
|
GPL-2 |
| | | X | CHARGE: CHromosome Assessment in R from Gene Expression data |
| bioconductor-charm |
2.28.0 |
|
|
LGPL |
| | | X | This package implements analysis tools for DNA methylation data... |
| bioconductor-charmdata |
1.18.0 |
|
|
LGPL |
| | | X | An example dataset for use with the charm package |
| bioconductor-chemminedrugs |
1.0.2 |
|
|
Artistic-2.0 |
| | | X | DrugBank data set |
| bioconductor-chemmineob |
1.40.0 |
|
|
file |
X | X | | | R interface to a subset of OpenBabel functionalities |
| bioconductor-chemminer |
3.58.0 |
|
|
Artistic-2.0 |
X | X | | | Cheminformatics Toolkit for R |
| bioconductor-chetah |
1.22.0 |
|
|
file |
| | | X | Fast and accurate scRNA-seq cell type identification |
| bioconductor-chic |
1.19.0 |
|
|
GPL-2 |
| | | X | Quality Control Pipeline for ChIP-Seq Data |
| bioconductor-chic.data |
1.22.0 |
|
|
GPL-2 |
| | | X | ChIC package data |
| bioconductor-chicago |
1.34.0 |
|
|
Artistic-2.0 |
X | X | | X | CHiCAGO: Capture Hi-C Analysis of Genomic Organization |
| bioconductor-chicken.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix Chicken Array annotation data (chip chicken) |
| bioconductor-chicken.db0 |
3.20.0 |
|
|
Artistic-2.0 |
| | | X | Base Level Annotation databases for chicken |
| bioconductor-chickencdf |
2.18.0 |
|
|
LGPL |
| | | X | chickencdf |
| bioconductor-chickenprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type chicken |
| bioconductor-chihaya |
1.6.0 |
|
|
GPL-3 |
X | X | | | Save Delayed Operations to a HDF5 File |
| bioconductor-chimera |
1.32.0 |
|
|
Artistic-2.0 |
X | X | | | A package for secondary analysis of fusion products |
| bioconductor-chimeraviz |
1.32.0 |
|
|
Artistic-2.0 |
X | X | | X | Visualization tools for gene fusions |
| bioconductor-chimp.db0 |
3.20.0 |
|
|
Artistic-2.0 |
| | | X | Base Level Annotation databases for chimp |
| bioconductor-chimphumanbraindata |
1.44.0 |
|
|
MIT |
| | | X | Chimp and human brain data package |
| bioconductor-chipanalyser |
1.28.0 |
|
|
GPL-3 |
| | | X | ChIPanalyser: Predicting Transcription Factor Binding Sites |
| bioconductor-chipcomp |
1.36.0 |
|
|
GPL |
X | X | | | Quantitative comparison of multiple ChIP-seq datasets |
| bioconductor-chipenrich |
2.30.0 |
|
|
GPL-3 |
| | | X | Gene Set Enrichment For ChIP-seq Peak Data |
| bioconductor-chipenrich.data |
2.30.0 |
|
|
GPL-3 |
| | | X | Companion package to chipenrich |
| bioconductor-chipexoqual |
1.30.0 |
|
|
GPL |
| | | X | ChIPexoQual |
| bioconductor-chipexoqualexample |
1.30.0 |
|
|
GPL |
| | | X | Example data for the ChIPexoQual package, which implements a quality... |
| bioconductor-chippeakanno |
3.40.0 |
|
|
GPL |
X | X | | X | Batch annotation of the peaks identified from either ChIP-seq,... |
| bioconductor-chipqc |
1.42.0 |
|
|
GPL |
X | X | | X | Quality metrics for ChIPseq data |
| bioconductor-chipseeker |
1.42.0 |
|
|
Artistic-2.0 |
X | X | | X | ChIPseeker for ChIP peak Annotation, Comparison, and Visualization |
| bioconductor-chipseq |
1.56.0 |
|
|
Artistic-2.0 |
X | X | | | chipseq: A package for analyzing chipseq data |
| bioconductor-chipseqdbdata |
1.22.0 |
|
|
CC |
| | | X | Data for the chipseqDB Workflow |
| bioconductor-chipseqr |
1.60.0 |
|
|
GPL |
X | X | | | Identifying Protein Binding Sites in High-Throughput Sequencing Data |
| bioconductor-chipseqspike |
1.9.0 |
|
|
Artistic-2.0 |
| | | X | ChIP-Seq data scaling according to spike-in control |
| bioconductor-chipsim |
1.60.0 |
|
|
GPL |
X | X | | X | Simulation of ChIP-seq experiments |
| bioconductor-chipxpress |
1.42.0 |
|
|
GPL(>=2) |
X | X | | X | ChIPXpress: enhanced transcription factor target gene identification... |
| bioconductor-chipxpressdata |
1.36.0 |
|
|
GPL |
X | X | | X | ChIPXpress Pre-built Databases |
| bioconductor-chopsticks |
1.72.0 |
|
|
GPL-3 |
X | X | | | The 'snp.matrix' and 'X.snp.matrix' Classes |
| bioconductor-chrogps |
2.4.0 |
|
|
GPL |
| | | X | chroGPS2: Generation, visualization and differential analysis of epigenome maps |
| bioconductor-chromdraw |
2.36.0 |
|
|
GPL-3 |
X | X | | | chromDraw is a R package for drawing the schemes of karyotypes in the... |
| bioconductor-chromheatmap |
1.60.0 |
|
|
Artistic-2.0 |
X | X | | X | Heat map plotting by genome coordinate |
| bioconductor-chromhmmdata |
0.99.2 |
|
|
GPL-3 |
| | | X | Chromosome Size, Coordinates and Anchor Files |
| bioconductor-chromplot |
1.34.0 |
|
|
GPL |
X | X | | X | Global visualization tool of genomic data |
| bioconductor-chromscape |
1.16.0 |
|
|
GPL-3 |
X | X | | X | Analysis of single-cell epigenomics datasets with a Shiny App |
| bioconductor-chromstar |
1.28.0 |
|
|
Artistic-2.0 |
X | X | | | Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data |
| bioconductor-chromstardata |
1.32.0 |
|
|
GPL-3 |
X | X | | X | ChIP-seq data for Demonstration Purposes |
| bioconductor-chromswitch |
1.22.0 |
|
|
MIT |
| | | X | An R package to detect chromatin state switches from epigenomic data |
| bioconductor-chromvar |
1.28.0 |
|
|
MIT |
X | X | | | Chromatin Variation Across Regions |
| bioconductor-chronos |
1.34.0 |
|
|
GPL-2 |
X | X | | X | CHRONOS: A time-varying method for microRNA-mediated sub-pathway... |
| bioconductor-cicero |
1.24.0 |
|
|
MIT |
| | | X | Predict cis-co-accessibility from single-cell chromatin accessibility data |
| bioconductor-cimice |
1.14.0 |
|
|
Artistic-2.0 |
| | | X | CIMICE-R: (Markov) Chain Method to Inferr Cancer Evolution |
| bioconductor-cindex |
1.34.0 |
|
|
GPL |
X | X | | X | Chromosome Instability Index |
| bioconductor-circrnaprofiler |
1.16.0 |
|
|
GPL-3 |
| | | X | circRNAprofiler: An R-Based Computational Framework for the Downstream... |
| bioconductor-circseqaligntk |
1.4.0 |
|
|
MIT |
| | | X | A toolkit for end-to-end analysis of RNA-seq data for circular genomes |
| bioconductor-cispath |
1.46.0 |
|
|
GPL |
X | X | | | Visualization and management of the protein-protein interaction networks. |
| bioconductor-citefuse |
1.18.0 |
|
|
GPL-3 |
X | X | | X | CiteFuse: multi-modal analysis of CITE-seq data |
| bioconductor-citruscdf |
2.18.0 |
|
|
LGPL |
| | | X | citruscdf |
| bioconductor-citrusprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type citrus |
| bioconductor-clariomdhumanprobeset.db |
8.8.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix clariomdhuman annotation data (chip clariomdhumanprobeset) |
| bioconductor-clariomdhumantranscriptcluster.db |
8.8.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix clariomdhuman annotation data (chip clariomdhumantranscriptcluster) |
| bioconductor-clariomshumanhttranscriptcluster.db |
8.8.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix clariomshumanht annotation data (chip... |
| bioconductor-clariomshumantranscriptcluster.db |
8.8.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix clariomshuman annotation data (chip clariomshumantranscriptcluster) |
| bioconductor-clariomsmousehttranscriptcluster.db |
8.8.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix clariomsmouseht annotation data (chip... |
| bioconductor-clariomsmousetranscriptcluster.db |
8.8.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix clariomsmouse annotation data (chip clariomsmousetranscriptcluster) |
| bioconductor-clariomsrathttranscriptcluster.db |
8.8.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix clariomsratht annotation data (chip clariomsrathttranscriptcluster) |
| bioconductor-clariomsrattranscriptcluster.db |
8.8.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix clariomsrat annotation data (chip clariomsrattranscriptcluster) |
| bioconductor-classifyr |
3.10.0 |
|
|
GPL-3 |
X | X | | X | A framework for cross-validated classification problems, with... |
| bioconductor-cleanupdtseq |
1.44.0 |
|
|
GPL-2 |
X | X | | X | cleanUpdTSeq cleans up artifacts from polyadenylation sites from... |
| bioconductor-cleanuprnaseq |
1.0.0 |
|
|
GPL-3 |
| | | X | Detect and Correct Genomic DNA Contamination in RNA-seq Data |
| bioconductor-cleaver |
1.44.0 |
|
|
GPL |
X | X | | X | Cleavage of Polypeptide Sequences |
| bioconductor-clevrvis |
1.6.0 |
|
|
LGPL-3 |
| | | X | Visualization Techniques for Clonal Evolution |
| bioconductor-clippda |
1.56.0 |
|
|
GPL |
| | | X | A package for the clinical proteomic profiling data analysis |
| bioconductor-clipper |
1.46.0 |
|
|
AGPL-3 |
X | X | | | Gene Set Analysis Exploiting Pathway Topology |
| bioconductor-cliprofiler |
1.12.0 |
|
|
Artistic-2.0 |
| | | X | A package for the CLIP data visualization |
| bioconductor-cliquems |
1.20.0 |
|
|
GPL |
X | X | | | Annotation of Isotopes, Adducts and Fragmentation Adducts for in-Source... |
| bioconductor-cll |
1.46.0 |
|
|
LGPL |
| | | X | A Package for CLL Gene Expression Data |
| bioconductor-cllmethylation |
1.26.0 |
|
|
LGPL |
| | | X | Methylation data of primary CLL samples in PACE project |
| bioconductor-clomial |
1.42.0 |
|
|
GPL |
X | X | | X | Infers clonal composition of a tumor |
| bioconductor-clonality |
1.47.0 |
|
|
GPL-3 |
X | X | | X | Clonality testing |
| bioconductor-clonotyper |
1.32.1 |
|
|
file |
X | X | | X | High throughput analysis of T cell antigen receptor sequences |
| bioconductor-clst |
1.54.0 |
|
|
GPL-3 |
X | X | | X | Classification by local similarity threshold |
| bioconductor-clstutils |
1.54.0 |
|
|
GPL-3 |
X | X | | X | Tools for performing taxonomic assignment |
| bioconductor-clumsid |
1.22.0 |
|
|
MIT |
| | | X | Clustering of MS2 Spectra for Metabolite Identification |
| bioconductor-clumsiddata |
1.22.0 |
|
|
MIT |
| | | X | Data for the CluMSID package |
| bioconductor-clustall |
1.2.0 |
|
|
GPL-2 |
| | | X | ClustAll: Data driven strategy to robustly identify stratification of... |
| bioconductor-clustcomp |
1.34.0 |
|
|
GPL |
X | X | | X | Clustering Comparison Package |
| bioconductor-clusterexperiment |
2.26.0 |
|
|
Artistic-2.0 |
X | X | | | Compare Clusterings for Single-Cell Sequencing |
| bioconductor-clusterfoldsimilarity |
1.2.0 |
|
|
Artistic-2.0 |
| | | X | Calculate similarity of clusters from different single cell samples... |
| bioconductor-clusterjudge |
1.28.0 |
|
|
Artistic-2.0 |
| | | X | Judging Quality of Clustering Methods using Mutual Information |
| bioconductor-clusterprofiler |
4.14.0 |
|
|
Artistic-2.0 |
X | X | | X | A universal enrichment tool for interpreting omics data |
| bioconductor-clusterseq |
1.30.0 |
|
|
GPL-3 |
| | | X | Clustering of high-throughput sequencing data by identifying... |
| bioconductor-clustersignificance |
1.34.0 |
|
|
GPL-3 |
X | X | | X | The ClusterSignificance package provides tools to assess if class... |
| bioconductor-clusterstab |
1.78.0 |
|
|
Artistic-2.0 |
X | X | | X | Compute cluster stability scores for microarray data |
| bioconductor-clustifyr |
1.18.0 |
|
|
MIT |
| | | X | Classifier for Single-cell RNA-seq Using Cell Clusters |
| bioconductor-clustifyrdatahub |
1.16.0 |
|
|
MIT |
| | | X | External data sets for clustifyr in ExperimentHub |
| bioconductor-clustirr |
1.4.0 |
|
|
GPL-3 |
X | X | | X | Clustering of immune receptor repertoires |
| bioconductor-cma |
1.64.0 |
|
|
GPL |
X | X | | X | Synthesis of microarray-based classification |
| bioconductor-cmap |
1.15.1 |
|
|
LGPL |
X | X | | X | A data package containing annotation data for cMAP |
| bioconductor-cmap2data |
1.42.0 |
|
|
GPL-3 |
X | X | | X | Connectivity Map (version 2) Data |
| bioconductor-cmapr |
1.18.0 |
|
|
file |
| | | X | CMap Tools in R |
| bioconductor-cn.farms |
1.54.0 |
|
|
LGPL |
X | X | | | cn.FARMS - factor analysis for copy number estimation |
| bioconductor-cn.mops |
1.52.0 |
|
|
LGPL |
X | X | | | cn.mops - Mixture of Poissons for CNV detection in NGS data |
| bioconductor-cnanorm |
1.52.0 |
|
|
GPL-2 |
X | X | | | A normalization method for Copy Number Aberration in cancer samples |
| bioconductor-cner |
1.42.0 |
|
|
GPL-2 |
X | X | | | CNE Detection and Visualization |
| bioconductor-cnordt |
1.48.0 |
|
|
GPL-2 |
X | X | | | Add-on to CellNOptR: Discretized time treatments |
| bioconductor-cnorfeeder |
1.46.0 |
|
|
GPL-3 |
| | | X | Integration of CellNOptR to add missing links |
| bioconductor-cnorfuzzy |
1.48.0 |
|
|
GPL-2 |
X | X | | | Addon to CellNOptR: Fuzzy Logic |
| bioconductor-cnorode |
1.48.0 |
|
|
GPL-2 |
X | X | | | ODE add-on to CellNOptR |
| bioconductor-cnpbayes |
1.13.5 |
|
|
Artistic-2.0 |
X | X | | | Bayesian hierarchical mixture models for batch effects and copy number. |
| bioconductor-cntools |
1.62.0 |
|
|
LGPL |
X | X | | | Convert segment data into a region by sample matrix to allow for other... |
| bioconductor-cnvfilter |
1.20.0 |
|
|
Artistic-2.0 |
| | | X | Identifies false positives of CNV calling tools by using SNV calls |
| bioconductor-cnvgears |
1.8.0 |
|
|
GPL-3 |
| | | X | A Framework of Functions to Combine, Analize and Interpret CNVs Calling Results |
| bioconductor-cnvgsa |
1.50.0 |
|
|
LGPL |
X | X | | X | Gene Set Analysis of (Rare) Copy Number Variants |
| bioconductor-cnvgsadata |
1.42.0 |
|
|
LGPL |
| | | X | Data used in the vignette of the cnvGSA package |
| bioconductor-cnviz |
1.14.0 |
|
|
Artistic-2.0 |
| | | X | Copy Number Visualization |
| bioconductor-cnvmetrics |
1.10.0 |
|
|
Artistic-2.0 |
| | | X | Copy Number Variant Metrics |
| bioconductor-cnvpanelizer |
1.38.0 |
|
|
GPL-3 |
X | X | | X | Reliable CNV detection in targeted sequencing applications |
| bioconductor-cnvranger |
1.22.0 |
|
|
Artistic-2.0 |
| | | X | Summarization and expression/phenotype association of CNV ranges |
| bioconductor-cnvrd2 |
1.44.0 |
|
|
GPL-2 |
| | | X | CNVrd2: a read depth-based method to detect and genotype complex common... |
| bioconductor-cnvtools |
1.81.0 |
|
|
GPL-3 |
X | X | | | A package to test genetic association with CNV data |
| bioconductor-cobindr |
1.25.0 |
|
|
Artistic-2.0 |
| | | X | Finding Co-occuring motifs of transcription factor binding sites |
| bioconductor-cocitestats |
1.78.0 |
|
|
CPL |
| | | X | Different test statistics based on co-citation. |
| bioconductor-cocoa |
2.20.0 |
|
|
GPL-3 |
| | | X | Coordinate Covariation Analysis |
| bioconductor-codelink |
1.74.0 |
|
|
GPL-2 |
X | X | | X | Manipulation of Codelink microarray data |
| bioconductor-codex |
1.38.0 |
|
|
GPL-2 |
X | X | | X | A Normalization and Copy Number Variation Detection Method for Whole... |
| bioconductor-coexnet |
1.19.1 |
|
|
LGPL |
| | | X | coexnet: An R package to build CO-EXpression NETworks from Microarray Data |
| bioconductor-cogaps |
3.26.0 |
|
|
BSD_3_clause |
X | X | | | Coordinated Gene Activity in Pattern Sets |
| bioconductor-cogena |
1.40.0 |
|
|
LGPL-3 |
X | X | | X | co-expressed gene-set enrichment analysis |
| bioconductor-cogeqc |
1.10.0 |
|
|
GPL-3 |
| | | X | Systematic quality checks on comparative genomics analyses |
| bioconductor-cogito |
1.12.0 |
|
|
LGPL-3 |
| | | X | Compare genomic intervals tool - Automated, complete, reproducible and... |
| bioconductor-cogps |
1.50.0 |
|
|
GPL-2 |
X | X | | X | cancer outlier Gene Profile Sets |
| bioconductor-cohcap |
1.48.0 |
|
|
GPL-3.0-only |
X | X | | | CpG Island Analysis Pipeline for Illumina Methylation Array and... |
| bioconductor-cohcapanno |
1.42.0 |
|
|
GPL-3 |
X | X | | X | Annotations for City of Hope CpG Island Analysis Pipeline |
| bioconductor-cola |
2.12.0 |
|
|
MIT |
X | X | | | A Framework for Consensus Partitioning |
| bioconductor-colonca |
1.48.0 |
|
|
LGPL |
| | | X | exprSet for Alon et al. (1999) colon cancer data |
| bioconductor-comapr |
1.10.0 |
|
|
MIT |
| | | X | Crossover analysis and genetic map construction |
| bioconductor-combi |
1.18.0 |
|
|
GPL-2 |
| | | X | Compositional omics model based visual integration |
| bioconductor-comet |
1.34.0 |
|
|
GPL |
| | | X | coMET: visualisation of regional epigenome-wide association scan (EWAS)... |
| bioconductor-comethdmr |
1.10.0 |
|
|
GPL-3 |
| | | X | Accurate identification of co-methylated and differentially methylated... |
| bioconductor-compartmap |
1.18.0 |
|
|
GPL-3 |
| | | X | Higher-order chromatin domain inference in single cells from scRNA-seq... |
| bioconductor-compass |
1.44.0 |
|
|
Artistic-2.0 |
X | X | | | Combinatorial Polyfunctionality Analysis of Single Cells |
| bioconductor-compcoder |
1.42.0 |
|
|
GPL |
| | | X | RNAseq data simulation, differential expression analysis and... |
| bioconductor-compepitools |
1.40.0 |
|
|
GPL |
X | X | | X | Tools for computational epigenomics |
| bioconductor-compgo |
1.26.0 |
|
|
GPL-2 |
| | | X | An R pipeline for .bed file annotation, comparing GO term enrichment... |
| bioconductor-complexheatmap |
2.22.0 |
|
|
MIT |
X | X | | X | Make Complex Heatmaps |
| bioconductor-compounddb |
1.10.0 |
|
|
Artistic-2.0 |
| | | X | Creating and Using (Chemical) Compound Annotation Databases |
| bioconductor-compran |
1.14.0 |
|
|
MIT |
| | | X | Complexome Profiling Analysis package |
| bioconductor-compspot |
1.4.0 |
|
|
Artistic-2.0 |
| | | X | compSPOT: Tool for identifying and comparing significantly mutated... |
| bioconductor-conclus |
1.5.0 |
|
|
GPL-3 |
| | | X | ScRNA-seq Workflow CONCLUS - From CONsensus CLUSters To A Meaningful CONCLUSion |
| bioconductor-concordexr |
1.6.0 |
|
|
Artistic-2.0 |
| | | X | Identify Spatial Homogeneous Regions with concordex |
| bioconductor-condcomp |
1.1.1 |
|
|
GPL |
| | | X | For a given clustered data, which can also be split into two... |
| bioconductor-condiments |
1.14.0 |
|
|
MIT |
| | | X | Differential Topology, Progression and Differentiation |
| bioconductor-confess |
1.34.0 |
|
|
GPL-2 |
| | | X | Cell OrderiNg by FluorEScence Signal |
| bioconductor-confessdata |
1.34.0 |
|
|
GPL-2 |
| | | X | Example dataset for CONFESS package |
| bioconductor-connectivitymap |
1.42.0 |
|
|
GPL-3 |
| | | X | Functional connections between drugs, genes and diseases as revealed by... |
| bioconductor-consensus |
1.24.0 |
|
|
BSD_3_clause |
| | | X | Cross-platform consensus analysis of genomic measurements via... |
| bioconductor-consensusclusterplus |
1.70.0 |
|
|
GPL |
X | X | | X | ConsensusClusterPlus |
| bioconductor-consensusde |
1.24.0 |
|
|
GPL-3 |
| | | X | RNA-seq analysis using multiple algorithms |
| bioconductor-consensusov |
1.24.0 |
|
|
Artistic-2.0 |
X | X | | X | Gene expression-based subtype classification for high-grade serous... |
| bioconductor-consensusseeker |
1.34.0 |
|
|
Artistic-2.0 |
X | X | | X | Detection of consensus regions inside a group of experiences using... |
| bioconductor-consica |
2.4.0 |
|
|
MIT |
| | | X | consensus Independent Component Analysis |
| bioconductor-constand |
1.14.0 |
|
|
file |
| | | X | Data normalization by matrix raking |
| bioconductor-contibait |
1.30.0 |
|
|
BSD_2_clause |
X | X | | | Improves Early Build Genome Assemblies using Strand-Seq Data |
| bioconductor-conumee |
1.32.0 |
|
|
GPL |
| | | X | Enhanced copy-number variation analysis using Illumina DNA methylation arrays |
| bioconductor-convert |
1.82.0 |
|
|
LGPL |
X | X | | X | Convert Microarray Data Objects |
| bioconductor-copa |
1.74.0 |
|
|
Artistic-2.0 |
X | X | | | Functions to perform cancer outlier profile analysis. |
| bioconductor-copdsexualdimorphism.data |
1.42.0 |
|
|
LGPL-2.1 |
| | | X | Data to support sexually dimorphic and COPD differential analysis for... |
| bioconductor-copyhelper |
1.38.0 |
|
|
GPL-2 |
X | X | | X | Helper files for CopywriteR |
| bioconductor-copyneutralima |
1.24.0 |
|
|
Artistic-2.0 |
| | | X | Copy Neutral Illumina Methylation Arrays |
| bioconductor-copynumber |
1.38.0 |
|
|
Artistic-2.0 |
X | X | | X | Segmentation of single- and multi-track copy number data by penalized... |
| bioconductor-copynumberplots |
1.22.0 |
|
|
Artistic-2.0 |
| | | X | Create Copy-Number Plots using karyoploteR functionality |
| bioconductor-copywriter |
2.29.0 |
|
|
GPL-2 |
X | X | | X | Copy number information from targeted sequencing using off-target reads |
| bioconductor-cordon |
1.24.0 |
|
|
Artistic-2.0 |
| | | X | Codon Usage Analysis and Prediction of Gene Expressivity |
| bioconductor-coregflux |
1.6.0 |
|
|
GPL-3 |
| | | X | CoRegFlux |
| bioconductor-coregnet |
1.38.0 |
|
|
GPL-3 |
X | X | | | CoRegNet : reconstruction and integrated analysis of co-regulatory networks |
| bioconductor-coregx |
2.10.0 |
|
|
GPL |
| | | X | Classes and Functions to Serve as the Basis for Other 'Gx' Packages |
| bioconductor-cormotif |
1.52.0 |
|
|
GPL-2 |
X | X | | X | Correlation Motif Fit |
| bioconductor-cormut |
1.29.0 |
|
|
GPL-2 |
| | | X | Detect the correlated mutations based on selection pressure |
| bioconductor-corral |
1.16.0 |
|
|
GPL-2 |
| | | X | Correspondence Analysis for Single Cell Data |
| bioconductor-correp |
1.68.0 |
|
|
GPL |
X | X | | X | Multivariate Correlation Estimator and Statistical Inference Procedures. |
| bioconductor-coseq |
1.30.0 |
|
|
GPL-3 |
| | | X | Co-Expression Analysis of Sequencing Data |
| bioconductor-cosia |
1.6.0 |
|
|
MIT |
| | | X | An Investigation Across Different Species and Tissues |
| bioconductor-cosiadata |
1.6.0 |
|
|
MIT |
| | | X | VST normalized RNA-Sequencing data with annotations for multiple... |
| bioconductor-cosmic.67 |
1.42.0 |
|
|
GPL-3 |
| | | X | COSMIC.67 |
| bioconductor-cosmiq |
1.40.0 |
|
|
GPL-3 |
X | X | | | cosmiq - COmbining Single Masses Into Quantities |
| bioconductor-cosmosr |
1.14.0 |
|
|
GPL-3 |
| | | X | COSMOS (Causal Oriented Search of Multi-Omic Space) |
| bioconductor-cosnet |
1.40.0 |
|
|
GPL |
X | X | | | Cost Sensitive Network for node label prediction on graphs with highly... |
| bioconductor-cotan |
2.6.0 |
|
|
GPL-3 |
| | | X | COexpression Tables ANalysis |
| bioconductor-cottoncdf |
2.18.0 |
|
|
LGPL |
| | | X | cottoncdf |
| bioconductor-cottonprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type cotton |
| bioconductor-countclust |
1.21.0 |
|
|
GPL |
X | X | | X | Clustering and Visualizing RNA-Seq Expression Data using Grade of... |
| bioconductor-countsimqc |
1.24.0 |
|
|
GPL |
| | | X | Compare Characteristic Features of Count Data Sets |
| bioconductor-coveb |
1.32.0 |
|
|
GPL-3 |
| | | X | Empirical Bayes estimate of block diagonal covariance matrices |
| bioconductor-coverageview |
1.44.0 |
|
|
Artistic-2.0 |
| | | X | Coverage visualization package for R |
| bioconductor-covrna |
1.32.0 |
|
|
GPL |
X | X | | X | Multivariate Analysis of Transcriptomic Data |
| bioconductor-cpvsnp |
1.38.0 |
|
|
Artistic-2.0 |
X | X | | X | Gene set analysis methods for SNP association p-values that lie in... |
| bioconductor-cqn |
1.52.0 |
|
|
Artistic-2.0 |
X | X | | X | Conditional quantile normalization |
| bioconductor-crcl18 |
1.26.0 |
|
|
GPL-2 |
| | | X | CRC cell line dataset |
| bioconductor-crimage |
1.54.0 |
|
|
Artistic-2.0 |
X | X | | X | CRImage a package to classify cells and calculate tumour cellularity |
| bioconductor-crisprbase |
1.10.0 |
|
|
MIT |
| | | X | Base functions and classes for CRISPR gRNA design |
| bioconductor-crisprbowtie |
1.10.0 |
|
|
MIT |
| | | X | Bowtie-based alignment of CRISPR gRNA spacer sequences |
| bioconductor-crisprbwa |
1.6.0 |
|
|
MIT |
| | | X | BWA-based alignment of CRISPR gRNA spacer sequences |
| bioconductor-crisprdesign |
1.8.0 |
|
|
MIT |
| | | X | Comprehensive design of CRISPR gRNAs for nucleases and base editors |
| bioconductor-crisprscore |
1.10.0 |
|
|
MIT |
| | | X | On-Target and Off-Target Scoring Algorithms for CRISPR gRNAs |
| bioconductor-crisprscoredata |
1.10.0 |
|
|
MIT |
| | | X | Pre-trained models for the crisprScore package |
| bioconductor-crisprseek |
1.46.0 |
|
|
GPL |
X | X | | X | Design of target-specific guide RNAs in CRISPR-Cas9, genome-editing systems |
| bioconductor-crisprseekplus |
1.26.0 |
|
|
GPL-3 |
X | X | | X | crisprseekplus |
| bioconductor-crisprshiny |
1.2.0 |
|
|
MIT |
| | | X | Exploring curated CRISPR gRNAs via Shiny |
| bioconductor-crisprvariants |
1.34.0 |
|
|
GPL-2 |
X | X | | X | Tools for counting and visualising mutations in a target location |
| bioconductor-crisprverse |
1.8.0 |
|
|
MIT |
| | | X | Easily install and load the crisprVerse ecosystem for CRISPR gRNA design |
| bioconductor-crisprviz |
1.8.0 |
|
|
MIT |
| | | X | Visualization Functions for CRISPR gRNAs |
| bioconductor-crlmm |
1.64.0 |
|
|
Artistic-2.0 |
X | X | | | Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix... |
| bioconductor-crossicc |
1.2.0 |
|
|
GPL-3 |
| | | X | An Interactive Consensus Clustering Framework for Multi-platform Data Analysis |
| bioconductor-crossmeta |
1.28.0 |
|
|
MIT |
| | | X | Cross Platform Meta-Analysis of Microarray Data |
| bioconductor-csar |
1.58.0 |
|
|
Artistic-2.0 |
X | X | | | Statistical tools for the analysis of ChIP-seq data |
| bioconductor-csaw |
1.40.0 |
|
|
GPL-3 |
X | X | | | ChIP-Seq Analysis with Windows |
| bioconductor-csdr |
1.12.0 |
|
|
GPL-3 |
X | X | | | Differential gene co-expression |
| bioconductor-cssp |
1.37.0 |
|
|
GPL-2 |
X | X | | | ChIP-Seq Statistical Power |
| bioconductor-cssq |
1.18.0 |
|
|
Artistic-2.0 |
| | | X | Chip-seq Signal Quantifier Pipeline |
| bioconductor-ctc |
1.80.0 |
|
|
GPL-2 |
X | X | | X | Cluster and Tree Conversion. |
| bioconductor-ctcf |
0.99.11 |
|
|
MIT |
| | | X | Genomic coordinates of CTCF binding sites, with orientation |
| bioconductor-ctdata |
1.6.0 |
|
|
Artistic-2.0 |
| | | X | Data companion to CTexploreR |
| bioconductor-ctdquerier |
2.14.0 |
|
|
MIT |
| | | X | Package for CTDbase data query, visualization and downstream analysis |
| bioconductor-ctexplorer |
1.2.0 |
|
|
Artistic-2.0 |
| | | X | Explores Cancer Testis Genes |
| bioconductor-ctggem |
1.6.0 |
|
|
GPL(>=2) |
| | | X | Generating Tree Hierarchy Visualizations from Gene Expression Data |
| bioconductor-ctrap |
1.24.0 |
|
|
MIT |
| | | X | Identification of candidate causal perturbations from differential gene... |
| bioconductor-ctsge |
1.32.0 |
|
|
GPL-2 |
X | X | | X | Clustering of Time Series Gene Expression data |
| bioconductor-ctsv |
1.8.0 |
|
|
GPL-3 |
| | | X | Identification of cell-type-specific spatially variable genes... |
| bioconductor-cummerbund |
2.48.0 |
|
|
Artistic-2.0 |
X | X | | X | Analysis, exploration, manipulation, and visualization of Cufflinks... |
| bioconductor-curatedadipoarray |
1.18.0 |
|
|
GPL-3 |
| | | X | A Curated Microarrays Dataset of MDI-induced Differentiated Adipocytes... |
| bioconductor-curatedadipochip |
1.22.0 |
|
|
GPL-3 |
| | | X | A Curated ChIP-Seq Dataset of MDI-induced Differentiated Adipocytes (3T3-L1) |
| bioconductor-curatedadiporna |
1.22.0 |
|
|
GPL-3 |
| | | X | A Curated RNA-Seq Dataset of MDI-induced Differentiated Adipocytes (3T3-L1) |
| bioconductor-curatedatlasqueryr |
1.4.0 |
|
|
GPL-3 |
| | | X | Queries the Human Cell Atlas |
| bioconductor-curatedbladderdata |
1.42.0 |
|
|
Artistic-2.0 |
| | | X | Bladder Cancer Gene Expression Analysis |
| bioconductor-curatedbreastdata |
2.34.0 |
|
|
GPL |
| | | X | Curated breast cancer gene expression data with survival and treatment... |
| bioconductor-curatedcrcdata |
2.34.0 |
|
|
Artistic-2.0 |
| | | X | Colorectal Cancer Gene Expression Analysis |
| bioconductor-curatedmetagenomicdata |
3.14.0 |
|
|
Artistic-2.0 |
X | X | | X | Curated Metagenomic Data of the Human Microbiome |
| bioconductor-curatedovariandata |
1.44.0 |
|
|
Artistic-2.0 |
X | X | | X | Clinically Annotated Data for the Ovarian Cancer Transcriptome |
| bioconductor-curatedtbdata |
2.2.0 |
|
|
MIT |
| | | X | Curation of existing tuberculosis transcriptomic studies |
| bioconductor-curatedtcgadata |
1.28.1 |
|
|
Artistic-2.0 |
| | | X | Curated Data from The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects |
| bioconductor-customcmpdb |
1.16.0 |
|
|
Artistic-2.0 |
| | | X | Customize and Query Compound Annotation Database |
| bioconductor-customprodb |
1.46.0 |
|
|
Artistic-2.0 |
X | X | | X | Generate customized protein database from NGS data, with a focus on... |
| bioconductor-cve |
1.11.2 |
|
|
GPL-3 |
X | X | | X | Cancer Variant Explorer |
| bioconductor-cyanofilter |
1.14.0 |
|
|
MIT |
| | | X | Phytoplankton Population Identification using Cell Pigmentation and/or... |
| bioconductor-cycle |
1.60.0 |
|
|
GPL-2 |
| | | X | Significance of periodic expression pattern in time-series data |
| bioconductor-cydar |
1.30.0 |
|
|
GPL-3 |
X | X | | | Using Mass Cytometry for Differential Abundance Analyses |
| bioconductor-cyp450cdf |
2.18.0 |
|
|
LGPL |
| | | X | cyp450cdf |
| bioconductor-cytodx |
1.26.0 |
|
|
GPL-2 |
| | | X | Robust prediction of clinical outcomes using cytometry data without cell gating |
| bioconductor-cytofast |
1.6.0 |
|
|
GPL-3 |
| | | X | cytofast - A quick visualization and analysis tool for CyTOF data |
| bioconductor-cytofpower |
1.8.0 |
|
|
LGPL-3 |
| | | X | Power analysis for CyTOF experiments |
| bioconductor-cytofqc |
1.6.0 |
|
|
Artistic-2.0 |
| | | X | Labels normalized cells for CyTOF data and assigns probabilities for each label |
| bioconductor-cytoglmm |
1.14.0 |
|
|
LGPL-3 |
| | | X | Conditional Differential Analysis for Flow and Mass Cytometry Experiments |
| bioconductor-cytokernel |
1.12.0 |
|
|
GPL-3 |
X | X | | | Differential expression using kernel-based score test |
| bioconductor-cytolib |
2.18.0 |
|
|
AGPL-3.0-only |
X | X | | X | C++ infrastructure for representing and interacting with the gated... |
| bioconductor-cytomapper |
1.18.0 |
|
|
GPL |
| | | X | Visualization of highly multiplexed imaging data in R |
| bioconductor-cytomds |
1.2.0 |
|
|
GPL-3 |
| | | X | Low Dimensions projection of cytometry samples |
| bioconductor-cytomem |
1.10.0 |
|
|
GPL-3 |
| | | X | Marker Enrichment Modeling (MEM) |
| bioconductor-cytomethic |
1.2.0 |
|
|
Artistic-2.0 |
| | | X | DNA methylation-based classification and regression |
| bioconductor-cytoml |
2.14.0 |
|
|
AGPL-3.0-only |
X | X | | X | A GatingML Interface for Cross Platform Cytometry Data Sharing |
| bioconductor-cytopipeline |
1.6.0 |
|
|
GPL-3 |
| | | X | Automation and visualization of flow cytometry data analysis pipelines |
| bioconductor-cytopipelinegui |
1.4.0 |
|
|
GPL-3 |
| | | X | GUI's for visualization of flow cytometry data analysis pipelines |
| bioconductor-cytotree |
1.0.3 |
|
|
GPL-3 |
X | X | | | A Toolkit for Flow And Mass Cytometry Data |
| bioconductor-cytoviewer |
1.6.0 |
|
|
GPL-3 |
| | | X | An interactive multi-channel image viewer for R |
| bioconductor-dada2 |
1.34.0 |
|
|
LGPL-2 |
X | X | | | Accurate, high-resolution sample inference from amplicon sequencing data |
| bioconductor-daglogo |
1.44.0 |
|
|
GPL |
| | | X | dagLogo: a Bioconductor package for visualizing conserved amino acid... |
| bioconductor-dama |
1.78.0 |
|
|
GPL |
X | X | | X | Efficient design and analysis of factorial two-colour microarray data |
| bioconductor-damefinder |
1.18.0 |
|
|
MIT |
| | | X | Finds DAMEs - Differential Allelicly MEthylated regions |
| bioconductor-damirseq |
2.18.0 |
|
|
GPL |
| | | X | Data Mining for RNA-seq data: normalization, feature selection and... |
| bioconductor-damsel |
1.2.0 |
|
|
MIT |
| | | X | Damsel: an end to end analysis of DamID |
| bioconductor-dapar |
1.38.0 |
|
|
Artistic-2.0 |
| | | X | Tools for the Differential Analysis of Proteins Abundance with R |
| bioconductor-dapardata |
1.36.0 |
|
|
GPL-2 |
| | | X | Data accompanying the DAPAR and Prostar packages |
| bioconductor-dar |
1.2.0 |
|
|
MIT |
| | | X | Differential Abundance Analysis by Consensus |
| bioconductor-dart |
1.54.0 |
|
|
GPL-2 |
| | | X | Denoising Algorithm based on Relevance network Topology |
| bioconductor-dasper |
1.9.0 |
|
|
Artistic-2.0 |
| | | X | Detecting abberant splicing events from RNA-sequencing data |
| bioconductor-data-packages |
20250105.1 |
|
|
MIT |
| | | X | A package to enable downloading and installation of Bioconductor data packages |
| bioconductor-davidtiling |
1.46.0 |
|
|
LGPL |
| | | X | Data and analysis scripts for David, Huber et al. yeast tiling array paper |
| bioconductor-dbchip |
1.32.0 |
|
|
GPL |
X | X | | X | Differential Binding of Transcription Factor with ChIP-seq |
| bioconductor-dcanr |
1.22.0 |
|
|
GPL-3 |
| | | X | Differential co-expression/association network analysis |
| bioconductor-dcats |
1.4.0 |
|
|
MIT |
| | | X | Differential Composition Analysis Transformed by a Similarity matrix |
| bioconductor-dce |
1.10.0 |
|
|
GPL-3 |
| | | X | Pathway Enrichment Based on Differential Causal Effects |
| bioconductor-dcgsa |
1.34.0 |
|
|
GPL-2 |
X | X | | X | Distance-correlation based Gene Set Analysis for longitudinal gene... |
| bioconductor-dchiprep |
1.18.0 |
|
|
MIT |
X | X | | X | DChIPRep - Analysis of chromatin modification ChIP-Seq data with replication |
| bioconductor-ddct |
1.62.0 |
|
|
LGPL-3 |
X | X | | X | The ddCt Algorithm for the Analysis of Quantitative Real-Time PCR (qRT-PCR) |
| bioconductor-ddpcrclust |
1.26.0 |
|
|
Artistic-2.0 |
| | | X | Clustering algorithm for ddPCR data |
| bioconductor-dearseq |
1.18.0 |
|
|
GPL-2 |
| | | X | Differential Expression Analysis for RNA-seq data through a robust... |
| bioconductor-debcam |
1.24.0 |
|
|
GPL-2 |
| | | X | Deconvolution by Convex Analysis of Mixtures |
| bioconductor-debrowser |
1.34.0 |
|
|
GPL-3 |
| | | X | Interactive Differential Expresion Analysis Browser |
| bioconductor-decipher |
3.2.0 |
|
|
GPL-3 |
X | X | | | Tools for curating, analyzing, and manipulating biological sequences |
| bioconductor-deco |
1.13.0 |
|
|
GPL |
| | | X | Decomposing Heterogeneous Cohorts using Omic Data Profiling |
| bioconductor-decomplexdisease |
1.18.0 |
|
|
GPL-3 |
X | X | | | A tool for differential expression analysis and DEGs based... |
| bioconductor-decomptumor2sig |
2.22.0 |
|
|
GPL-2 |
| | | X | Decomposition of individual tumors into mutational signatures by... |
| bioconductor-deconrnaseq |
1.48.0 |
|
|
GPL-2 |
| | | X | Deconvolution of Heterogeneous Tissue Samples for mRNA-Seq data |
| bioconductor-decontam |
1.26.0 |
|
|
Artistic-2.0 |
| | | X | Identify Contaminants in Marker-gene and Metagenomics Sequencing Data |
| bioconductor-decontx |
1.4.0 |
|
|
MIT |
X | X | | | Decontamination of single cell genomics data |
| bioconductor-deconvr |
1.12.0 |
|
|
Artistic-2.0 |
| | | X | Simulation and Deconvolution of Omic Profiles |
| bioconductor-decoupler |
2.12.0 |
|
|
GPL-3 |
| | | X | decoupleR: Ensemble of computational methods to infer biological... |
| bioconductor-deds |
1.60.0 |
|
|
LGPL |
X | X | | | Differential Expression via Distance Summary for Microarray Data |
| bioconductor-deepbluer |
1.24.0 |
|
|
GPL |
X | X | | X | DeepBlueR |
| bioconductor-deeppincs |
1.14.0 |
|
|
Artistic-2.0 |
| | | X | Protein Interactions and Networks with Compounds based on Sequences... |
| bioconductor-deepsnv |
1.52.0 |
|
|
GPL-3 |
X | X | | | Detection of subclonal SNVs in deep sequencing data. |
| bioconductor-deeptarget |
1.0.0 |
|
|
GPL-2 |
| | | X | Deep characterization of cancer drugs |
| bioconductor-deformats |
1.34.0 |
|
|
GPL-3 |
X | X | | X | Differential gene expression data formats converter |
| bioconductor-degcre |
1.2.0 |
|
|
MIT |
| | | X | Probabilistic association of DEGs to CREs from differential data |
| bioconductor-degnorm |
1.16.0 |
|
|
LGPL |
X | X | | | DegNorm: degradation normalization for RNA-seq data |
| bioconductor-degraph |
1.58.0 |
|
|
GPL-3 |
X | X | | X | Two-sample tests on a graph |
| bioconductor-degreport |
1.42.0 |
|
|
MIT |
X | X | | X | Report of DEG analysis |
| bioconductor-degseq |
1.60.0 |
|
|
LGPL |
X | X | | | Identify Differentially Expressed Genes from RNA-seq data |
| bioconductor-delayedarray |
0.32.0 |
|
|
Artistic-2.0 |
X | X | | | A unified framework for working transparently with on-disk and... |
| bioconductor-delayeddataframe |
1.22.0 |
|
|
GPL-3 |
| | | X | Delayed operation on DataFrame using standard DataFrame metaphor |
| bioconductor-delayedmatrixstats |
1.28.0 |
|
|
MIT |
X | X | | X | Functions that Apply to Rows and Columns of 'DelayedMatrix' Objects |
| bioconductor-delayedrandomarray |
1.14.0 |
|
|
GPL-3 |
X | X | | | Delayed Arrays of Random Values |
| bioconductor-delayedtensor |
1.12.0 |
|
|
Artistic-2.0 |
| | | X | R package for sparse and out-of-core arithmetic and decomposition of Tensor |
| bioconductor-delocal |
1.6.0 |
|
|
MIT |
| | | X | Identifies differentially expressed genes with respect to other local genes |
| bioconductor-deltacapturec |
1.20.0 |
|
|
MIT |
| | | X | This Package Discovers Meso-scale Chromatin Remodeling from 3C Data |
| bioconductor-deltagseg |
1.46.0 |
|
|
GPL-2 |
| | | X | deltaGseg |
| bioconductor-demand |
1.36.0 |
|
|
file |
X | X | | X | DeMAND |
| bioconductor-demixt |
1.22.0 |
|
|
GPL-3 |
X | X | | | Cell type-specific deconvolution of heterogeneous tumor samples with... |
| bioconductor-demuxmix |
1.8.0 |
|
|
Artistic-2.0 |
| | | X | Demultiplexing oligo-barcoded scRNA-seq data using regression mixture models |
| bioconductor-demuxsnp |
1.4.0 |
|
|
GPL-3 |
| | | X | scRNAseq demultiplexing using cell hashing and SNPs |
| bioconductor-densvis |
1.16.0 |
|
|
MIT |
X | X | | | Density-Preserving Data Visualization via Non-Linear Dimensionality Reduction |
| bioconductor-dep |
1.28.0 |
|
|
Artistic-2.0 |
| | | X | Differential Enrichment analysis of Proteomics data |
| bioconductor-depecher |
1.22.0 |
|
|
MIT |
X | X | | | Determination of essential phenotypic elements of clusters in... |
| bioconductor-depinfer |
1.10.0 |
|
|
GPL-3 |
| | | X | Inferring tumor-specific cancer dependencies through integrating... |
| bioconductor-depmap |
1.20.0 |
|
|
Artistic-2.0 |
| | | X | Cancer Dependency Map Data Package |
| bioconductor-deqms |
1.24.0 |
|
|
LGPL |
X | X | | X | a tool to perform statistical analysis of differential protein... |
| bioconductor-derfinder |
1.40.0 |
|
|
Artistic-2.0 |
X | X | | X | Annotation-agnostic differential expression analysis of RNA-seq data at... |
| bioconductor-derfinderdata |
2.24.0 |
|
|
Artistic-2.0 |
| | | X | Processed BigWigs from BrainSpan for examples |
| bioconductor-derfinderhelper |
1.40.0 |
|
|
Artistic-2.0 |
X | X | | X | derfinder helper package |
| bioconductor-derfinderplot |
1.40.0 |
|
|
Artistic-2.0 |
X | X | | X | Plotting functions for derfinder |
| bioconductor-descan2 |
1.26.0 |
|
|
Artistic-2.0 |
X | X | | | Differential Enrichment Scan 2 |
| bioconductor-deseq |
1.39.0 |
|
|
GPL |
X | X | | | Differential gene expression analysis based on the negative binomial... |
| bioconductor-deseq2 |
1.46.0 |
|
|
LGPL |
X | X | | | Differential gene expression analysis based on the negative binomial... |
| bioconductor-desingle |
1.26.0 |
|
|
GPL-2 |
| | | X | DEsingle for detecting three types of differential expression in... |
| bioconductor-desousa2013 |
1.42.0 |
|
|
Artistic-2.0 |
| | | X | Poor prognosis colon cancer is defined by a molecularly distinct... |
| bioconductor-despace |
1.6.0 |
|
|
GPL-3 |
| | | X | DESpace: a framework to discover spatially variable genes |
| bioconductor-destiny |
3.16.0 |
|
|
GPL-3 |
X | X | | | Creates diffusion maps |
| bioconductor-desubs |
1.32.0 |
|
|
GPL-3 |
| | | X | DEsubs: an R package for flexible identification of differentially... |
| bioconductor-dewseq |
1.20.0 |
|
|
LGPL |
| | | X | Differential Expressed Windows Based on Negative Binomial Distribution |
| bioconductor-dexma |
1.14.0 |
|
|
GPL-2 |
| | | X | Differential Expression Meta-Analysis |
| bioconductor-dexmadata |
1.14.0 |
|
|
GPL-2 |
| | | X | Data package for DExMA package |
| bioconductor-dexseq |
1.52.0 |
|
|
GPL |
X | X | | X | Inference of differential exon usage in RNA-Seq |
| bioconductor-dexus |
1.30.0 |
|
|
LGPL |
X | X | | | DEXUS - Identifying Differential Expression in RNA-Seq Studies with... |
| bioconductor-dfp |
1.64.0 |
|
|
GPL-2 |
X | X | | X | Gene Selection |
| bioconductor-dfplyr |
1.0.0 |
|
|
GPL-3 |
| | | X | A `DataFrame` (`S4Vectors`) backend for `dplyr` |
| bioconductor-dialignr |
2.10.0 |
|
|
GPL-3 |
X | X | | | Dynamic Programming Based Alignment of MS2 Chromatograms |
| bioconductor-diffbind |
3.16.0 |
|
|
Artistic-2.0 |
X | X | | | Differential Binding Analysis of ChIP-Seq Peak Data |
| bioconductor-diffcoexp |
1.26.0 |
|
|
GPL |
| | | X | Differential Co-expression Analysis |
| bioconductor-diffcyt |
1.26.0 |
|
|
MIT |
| | | X | Differential discovery in high-dimensional cytometry via... |
| bioconductor-differentialregulation |
2.4.0 |
|
|
GPL-3 |
X | X | | | Differentially regulated genes from scRNA-seq data |
| bioconductor-diffgeneanalysis |
1.88.0 |
|
|
GPL |
X | X | | X | Performs differential gene expression Analysis |
| bioconductor-diffhic |
1.38.0 |
|
|
GPL-3 |
X | X | | | Differential Analysis of Hi-C Data |
| bioconductor-difflogo |
2.30.0 |
|
|
GPL |
| | | X | DiffLogo: A comparative visualisation of biooligomer motifs |
| bioconductor-diffloop |
1.22.0 |
|
|
MIT |
X | X | | X | Identifying differential DNA loops from chromatin topology data |
| bioconductor-diffloopdata |
1.34.0 |
|
|
MIT |
| | | X | Example ChIA-PET Datasets for the diffloop Package |
| bioconductor-diffustats |
1.26.0 |
|
|
GPL-3 |
X | X | | | Diffusion scores on biological networks |
| bioconductor-diffutr |
1.14.0 |
|
|
GPL-3 |
| | | X | diffUTR: Streamlining differential exon and 3' UTR usage |
| bioconductor-diggit |
1.38.0 |
|
|
file |
| | | X | Inference of Genetic Variants Driving Cellular Phenotypes |
| bioconductor-diggitdata |
1.38.0 |
|
|
GPL |
| | | X | Example data for the diggit package |
| bioconductor-dino |
1.12.0 |
|
|
GPL-3 |
| | | X | Normalization of Single-Cell mRNA Sequencing Data |
| bioconductor-dinor |
1.2.0 |
|
|
MIT |
| | | X | Differential NOMe-seq analysis |
| bioconductor-dir.expiry |
1.14.0 |
|
|
GPL-3 |
| | | X | Managing Expiration for Cache Directories |
| bioconductor-director |
1.32.0 |
|
|
GPL-3 |
X | X | | X | A dynamic visualization tool of multi-level data |
| bioconductor-dirichletmultinomial |
1.48.0 |
|
|
LGPL-3 |
X | X | | | Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data |
| bioconductor-discordant |
1.30.0 |
|
|
GPL-3 |
X | X | | | The Discordant Method: A Novel Approach for Differential Correlation |
| bioconductor-discorhythm |
1.22.0 |
|
|
GPL-3 |
| | | X | Interactive Workflow for Discovering Rhythmicity in Biological Data |
| bioconductor-distinct |
1.18.0 |
|
|
GPL |
X | X | | | distinct: a method for differential analyses via hierarchical permutation tests |
| bioconductor-dittoseq |
1.18.0 |
|
|
MIT |
| | | X | User Friendly Single-Cell and Bulk RNA Sequencing Visualization |
| bioconductor-divergence |
1.22.0 |
|
|
GPL-2 |
| | | X | Divergence: Functionality for assessing omics data by divergence with... |
| bioconductor-dks |
1.52.0 |
|
|
GPL |
| | | X | The double Kolmogorov-Smirnov package for evaluating multiple testing... |
| bioconductor-dlbcl |
1.46.0 |
|
|
GPL |
| | | X | Diffuse large B-cell lymphoma expression data |
| bioconductor-dmcfb |
1.20.0 |
|
|
GPL-3 |
| | | X | Differentially Methylated Cytosines via a Bayesian Functional Approach |
| bioconductor-dmchmm |
1.28.0 |
|
|
GPL-3 |
| | | X | Differentially Methylated CpG using Hidden Markov Model |
| bioconductor-dmelsgi |
1.37.0 |
|
|
Artistic-2.0 |
| | | X | Experimental data and documented source code for the paper "A Map... |
| bioconductor-dmrcaller |
1.38.0 |
|
|
GPL-3 |
X | X | | | Differentially Methylated Regions caller |
| bioconductor-dmrcate |
2.12.0 |
|
|
file |
X | X | | X | Methylation array and sequencing spatial analysis methods |
| bioconductor-dmrcatedata |
2.20.0 |
|
|
GPL-3 |
X | X | | X | Data Package for DMRcate |
| bioconductor-dmrforpairs |
1.35.0 |
|
|
GPL |
| | | X | DMRforPairs: identifying Differentially Methylated Regions between... |
| bioconductor-dmrscan |
1.28.0 |
|
|
GPL-3 |
| | | X | Detection of Differentially Methylated Regions |
| bioconductor-dmrseq |
1.26.0 |
|
|
MIT |
| | | X | Detection and inference of differentially methylated regions from Whole... |
| bioconductor-dnabarcodecompatibility |
1.22.0 |
|
|
file |
X | X | | X | A Tool for Optimizing Combinations of DNA Barcodes Used in Multiplexed... |
| bioconductor-dnabarcodes |
1.36.0 |
|
|
GPL-2 |
X | X | | | A tool for creating and analysing DNA barcodes used in Next Generation... |
| bioconductor-dnacopy |
1.80.0 |
|
|
GPL |
X | X | | | DNA Copy Number Data Analysis |
| bioconductor-dnafusion |
1.8.0 |
|
|
GPL-3 |
| | | X | Identification of gene fusions using paired-end sequencing |
| bioconductor-dnashaper |
1.34.0 |
|
|
GPL-2 |
X | X | | | High-throughput prediction of DNA shape features |
| bioconductor-dnazoodata |
1.6.0 |
|
|
MIT |
| | | X | DNA Zoo data package |
| bioconductor-do.db |
2.9 |
|
|
Artistic-2.0 |
X | X | | X | A set of annotation maps describing the entire Disease Ontology |
| bioconductor-dominoeffect |
1.26.0 |
|
|
GPL |
| | | X | Identification and Annotation of Protein Hotspot Residues |
| bioconductor-dominosignal |
1.0.0 |
|
|
GPL-3 |
| | | X | Cell Communication Analysis for Single Cell RNA Sequencing |
| bioconductor-donapllp2013 |
1.44.0 |
|
|
Artistic-2.0 |
| | | X | Supplementary data package for Dona et al. (2013) containing example... |
| bioconductor-doppelgangr |
1.34.0 |
|
|
GPL |
X | X | | X | Identify likely duplicate samples from genomic or meta-data |
| bioconductor-doqtl |
1.19.0 |
|
|
GPL-3 |
X | X | | | DOQTL is a quantitative trait locus (QTL) mapping pipeline designed for... |
| bioconductor-dorothea |
1.18.0 |
|
|
GPL-3 |
| | | X | Collection Of Human And Mouse TF Regulons |
| bioconductor-doscheda |
1.28.0 |
|
|
GPL-3 |
| | | X | A DownStream Chemo-Proteomics Analysis Pipeline |
| bioconductor-dose |
4.0.0 |
|
|
Artistic-2.0 |
X | X | | X | Disease Ontology Semantic and Enrichment analysis |
| bioconductor-doser |
1.22.0 |
|
|
GPL |
| | | X | doseR |
| bioconductor-doubletrouble |
1.6.0 |
|
|
GPL-3 |
| | | X | Identification and classification of duplicated genes |
| bioconductor-dpeak |
1.12.0 |
|
|
GPL |
X | X | | | dPeak (Deconvolution of Peaks in ChIP-seq Analysis) |
| bioconductor-drawproteins |
1.26.0 |
|
|
MIT |
| | | X | Package to Draw Protein Schematics from Uniprot API output |
| bioconductor-dream4 |
1.30.0 |
|
|
GPL |
| | | X | Synthetic Expression Data for Gene Regulatory Network Inference from... |
| bioconductor-dresscheck |
0.44.0 |
|
|
Artistic-2.0 |
| | | X | data and software for checking Dressman JCO 25(5) 2007 |
| bioconductor-drimseq |
1.34.0 |
|
|
GPL |
X | X | | X | Differential transcript usage and tuQTL analyses with... |
| bioconductor-drivernet |
1.46.0 |
|
|
GPL-3 |
X | X | | X | Drivernet: uncovering somatic driver mutations modulating... |
| bioconductor-droplettestfiles |
1.16.0 |
|
|
GPL-3 |
| | | X | Test Files for Single-Cell Droplet Utilities |
| bioconductor-dropletutils |
1.26.0 |
|
|
GPL-3 |
X | X | | | Utilities for Handling Single-Cell Droplet Data |
| bioconductor-drosgenome1.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix DrosGenome1 Array annotation data (chip drosgenome1) |
| bioconductor-drosgenome1cdf |
2.18.0 |
|
|
LGPL |
| | | X | drosgenome1cdf |
| bioconductor-drosgenome1probe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type drosgenome1 |
| bioconductor-drosophila2.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix Drosophila_2 Array annotation data (chip drosophila2) |
| bioconductor-drosophila2cdf |
2.18.0 |
|
|
LGPL |
| | | X | drosophila2cdf |
| bioconductor-drosophila2probe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type drosophila2 |
| bioconductor-drugtargetinteractions |
1.14.0 |
|
|
Artistic-2.0 |
| | | X | Drug-Target Interactions |
| bioconductor-drugvsdisease |
2.48.0 |
|
|
GPL-3 |
X | X | | X | Comparison of disease and drug profiles using Gene set Enrichment Analysis |
| bioconductor-drugvsdiseasedata |
1.42.0 |
|
|
GPL-3 |
X | X | | X | Drug versus Disease Data |
| bioconductor-dsimer |
1.8.0 |
|
|
GPL |
X | X | | | dSimer is an R package which provides computation of nine methods for... |
| bioconductor-dsqtl |
0.28.0 |
|
|
Artistic-2.0 |
| | | X | dsQTL, data excerpt from Degner et al. 2012 Nature letter |
| bioconductor-dss |
2.54.0 |
|
|
GPL |
X | X | | | Dispersion shrinkage for sequencing data |
| bioconductor-dstruct |
1.12.0 |
|
|
GPL |
| | | X | Identifying differentially reactive regions from RNA structurome profiling data |
| bioconductor-dta |
2.52.0 |
|
|
Artistic-2.0 |
X | X | | X | Dynamic Transcriptome Analysis |
| bioconductor-dualks |
1.53.0 |
|
|
LGPL |
| | | X | Dual KS Discriminant Analysis and Classification |
| bioconductor-dune |
1.18.0 |
|
|
MIT |
| | | X | Improving replicability in single-cell RNA-Seq cell type discovery |
| bioconductor-duoclustering2018 |
1.24.0 |
|
|
GPL |
| | | X | Data, Clustering Results and Visualization Functions From Duò et al (2018) |
| bioconductor-dupchecker |
1.25.0 |
|
|
GPL |
X | X | | X | a package for checking high-throughput genomic data redundancy in meta-analysis |
| bioconductor-duplexdiscoverer |
1.0.0 |
|
|
GPL-3 |
| | | X | Analysis of the data from RNA duplex probing experiments |
| bioconductor-dupradar |
1.36.0 |
|
|
GPL-3 |
X | X | | X | Assessment of duplication rates in RNA-Seq datasets |
| bioconductor-dvddata |
1.42.0 |
|
|
GPL-3 |
| | | X | Drug versus Disease Data |
| bioconductor-dyebias |
1.66.0 |
|
|
GPL-3 |
X | X | | X | The GASSCO method for correcting for slide-dependent gene-specific dye bias |
| bioconductor-dyebiasexamples |
1.46.0 |
|
|
GPL-3 |
| | | X | Example data for the dyebias package, which implements the GASSCO method. |
| bioconductor-dyndoc |
1.84.0 |
|
|
Artistic-2.0 |
X | X | | X | Dynamic document tools |
| bioconductor-easier |
1.12.0 |
|
|
MIT |
| | | X | Estimate Systems Immune Response from RNA-seq data |
| bioconductor-easierdata |
1.12.0 |
|
|
MIT |
| | | X | easier internal data and exemplary dataset from IMvigor210CoreBiologies package |
| bioconductor-easycelltype |
1.8.0 |
|
|
Artistic-2.0 |
| | | X | Annotate cell types for scRNA-seq data |
| bioconductor-easylift |
1.4.0 |
|
|
MIT |
| | | X | An R package to perform genomic liftover |
| bioconductor-easyqpcr |
1.31.0 |
|
|
GPL |
| | | X | EasyqpcR for low-throughput real-time quantitative PCR data analysis |
| bioconductor-easyreporting |
1.18.0 |
|
|
Artistic-2.0 |
| | | X | Helps creating report for improving Reproducible Computational Research |
| bioconductor-easyrnaseq |
2.42.0 |
|
|
Artistic-2.0 |
X | X | | X | Count summarization and normalization for RNA-Seq data |
| bioconductor-eatonetalchipseq |
0.44.0 |
|
|
Artistic |
| | | X | ChIP-seq data of ORC-binding sites in Yeast excerpted from Eaton et al. 2010 |
| bioconductor-ebarrays |
2.70.0 |
|
|
GPL |
X | X | | | Unified Approach for Simultaneous Gene Clustering and Differential... |
| bioconductor-ebcoexpress |
1.50.0 |
|
|
GPL |
X | X | | | EBcoexpress for Differential Co-Expression Analysis |
| bioconductor-ebimage |
4.48.0 |
|
|
LGPL |
X | X | | | Image processing and analysis toolbox for R |
| bioconductor-ebsea |
1.34.0 |
|
|
GPL-2 |
X | X | | X | Exon Based Strategy for Expression Analysis of genes |
| bioconductor-ebseq |
2.4.0 |
|
|
Artistic-2.0 |
X | X | | X | An R package for gene and isoform differential expression analysis of... |
| bioconductor-ebseqhmm |
1.35.0 |
|
|
Artistic-2.0 |
| | | X | Bayesian analysis for identifying gene or isoform expression changes in... |
| bioconductor-ecoli2.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix E_coli_2 Array annotation data (chip ecoli2) |
| bioconductor-ecoli2cdf |
2.18.0 |
|
|
LGPL |
| | | X | ecoli2cdf |
| bioconductor-ecoli2probe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type ecoli2 |
| bioconductor-ecoliasv2cdf |
2.18.0 |
|
|
LGPL |
| | | X | ecoliasv2cdf |
| bioconductor-ecoliasv2probe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type ecoliasv2 |
| bioconductor-ecolicdf |
2.18.0 |
|
|
LGPL |
| | | X | ecolicdf |
| bioconductor-ecolik12.db0 |
3.20.0 |
|
|
Artistic-2.0 |
| | | X | Base Level Annotation databases for E coli K12 Strain |
| bioconductor-ecolileucine |
1.46.0 |
|
|
GPL |
| | | X | Experimental data with Affymetrix E. coli chips |
| bioconductor-ecoliprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type ecoli |
| bioconductor-ecolisakai.db0 |
3.20.0 |
|
|
Artistic-2.0 |
| | | X | Base Level Annotation databases for E coli Sakai Strain |
| bioconductor-ecolitk |
1.78.0 |
|
|
GPL |
| | | X | Meta-data and tools for E. coli |
| bioconductor-edaseq |
2.40.0 |
|
|
Artistic-2.0 |
X | X | | X | Exploratory Data Analysis and Normalization for RNA-Seq |
| bioconductor-edda |
1.26.0 |
|
|
GPL |
X | X | | | Experimental Design in Differential Abundance analysis |
| bioconductor-edge |
2.38.0 |
|
|
MIT |
X | X | | | Extraction of Differential Gene Expression |
| bioconductor-edger |
4.4.0 |
|
|
GPL |
X | X | | | Empirical Analysis of Digital Gene Expression Data in R |
| bioconductor-edirquery |
1.6.0 |
|
|
GPL-3 |
| | | X | Query the EDIR Database For Specific Gene |
| bioconductor-eds |
1.8.0 |
|
|
GPL-2 |
X | X | | | eds: Low-level reader for Alevin EDS format |
| bioconductor-eegc |
1.26.0 |
|
|
GPL-2 |
| | | X | Engineering Evaluation by Gene Categorization (eegc) |
| bioconductor-egad |
1.34.0 |
|
|
GPL-2 |
| | | X | Extending guilt by association by degree |
| bioconductor-egsea |
1.34.0 |
|
|
GPL-3 |
X | X | | X | Ensemble of Gene Set Enrichment Analyses |
| bioconductor-egseadata |
1.34.0 |
|
|
file |
X | X | | X | Gene set collections for the EGSEA package |
| bioconductor-eir |
1.46.0 |
|
|
Artistic-2.0 |
X | X | | | Accelerated similarity searching of small molecules |
| bioconductor-eisa |
1.42.0 |
|
|
GPL |
| | | X | Expression data analysis via the Iterative Signature Algorithm |
| bioconductor-eisar |
1.18.0 |
|
|
GPL-3 |
| | | X | Exon-Intron Split Analysis (EISA) in R |
| bioconductor-elbow |
1.26.0 |
|
|
file |
| | | X | ELBOW - Evaluating foLd change By the lOgit Way |
| bioconductor-elmer |
2.26.0 |
|
|
GPL-3 |
X | X | | X | Inferring Regulatory Element Landscapes and Transcription Factor... |
| bioconductor-elmer.data |
2.30.0 |
|
|
GPL-3 |
X | X | | X | Data for the ELMER package |
| bioconductor-emdomics |
2.36.0 |
|
|
MIT |
| | | X | Earth Mover's Distance for Differential Analysis of Genomics Data |
| bioconductor-empiricalbrownsmethod |
1.34.0 |
|
|
MIT |
X | X | | X | Uses Brown's method to combine p-values from dependent tests |
| bioconductor-emtdata |
1.14.0 |
|
|
GPL-3 |
| | | X | An ExperimentHub Package for data sets with an Epithelial to... |
| bioconductor-encodexplorer |
2.16.0 |
|
|
Artistic-2.0 |
X | X | | X | A compilation of ENCODE metadata |
| bioconductor-encodexplorerdata |
0.99.5 |
|
|
Artistic-2.0 |
| | | X | A compilation of ENCODE metadata |
| bioconductor-enhancedvolcano |
1.24.0 |
|
|
GPL-3 |
| | | X | Publication-ready volcano plots with enhanced colouring and labeling |
| bioconductor-enhancerhomologsearch |
1.12.0 |
|
|
GPL |
X | X | | | Identification of putative mammalian orthologs to given enhancer |
| bioconductor-enmcb |
1.18.0 |
|
|
GPL-2 |
| | | X | Predicting Disease Progression Based on Methylation Correlated Blocks... |
| bioconductor-enmix |
1.42.0 |
|
|
Artistic-2.0 |
| | | X | Quality control and analysis tools for Illumina DNA methylation BeadChip |
| bioconductor-enrichdo |
1.0.0 |
|
|
MIT |
| | | X | a Global Weighted Model for Disease Ontology Enrichment Analysis |
| bioconductor-enrichedheatmap |
1.36.0 |
|
|
MIT |
X | X | | | Making Enriched Heatmaps |
| bioconductor-enrichmentbrowser |
2.36.0 |
|
|
Artistic-2.0 |
X | | | X | Seamless navigation through combined results of set-based and... |
| bioconductor-enrichplot |
1.26.1 |
|
|
Artistic-2.0 |
X | X | | X | Visualization of Functional Enrichment Result |
| bioconductor-enrichtf |
1.18.0 |
|
|
GPL-3 |
| | | X | Transcription Factors Enrichment Analysis |
| bioconductor-enrichviewnet |
1.4.0 |
|
|
Artistic-2.0 |
| | | X | From functional enrichment results to biological networks |
| bioconductor-ensdb.hsapiens.v75 |
2.99.0 |
|
|
Artistic-2.0 |
X | X | | X | Ensembl based annotation package |
| bioconductor-ensdb.hsapiens.v79 |
2.99.0 |
|
|
Artistic-2.0 |
| | | X | Ensembl based annotation package |
| bioconductor-ensdb.hsapiens.v86 |
2.99.0 |
|
|
Artistic-2.0 |
| | | X | Ensembl based annotation package |
| bioconductor-ensdb.mmusculus.v75 |
2.99.0 |
|
|
Artistic-2.0 |
| | | X | Ensembl based annotation package |
| bioconductor-ensdb.mmusculus.v79 |
2.99.0 |
|
|
Artistic-2.0 |
| | | X | Ensembl based annotation package |
| bioconductor-ensdb.rnorvegicus.v75 |
2.99.0 |
|
|
Artistic-2.0 |
| | | X | Ensembl based annotation package |
| bioconductor-ensdb.rnorvegicus.v79 |
2.99.0 |
|
|
Artistic-2.0 |
| | | X | Ensembl based annotation package |
| bioconductor-ensembldb |
2.30.0 |
|
|
LGPL |
X | X | | X | Utilities to create and use Ensembl-based annotation databases |
| bioconductor-ensemblvep |
1.44.0 |
|
|
Artistic-2.0 |
X | X | | X | R Interface to Ensembl Variant Effect Predictor |
| bioconductor-envisionquery |
1.38.0 |
|
|
GPL-2 |
| | | X | Retrieval from the ENVISION bioinformatics data portal into R |
| bioconductor-epialleler |
1.14.0 |
|
|
Artistic-2.0 |
X | X | | | Fast, Epiallele-Aware Methylation Caller and Reporter |
| bioconductor-epicompare |
1.10.0 |
|
|
GPL-3 |
| | | X | Comparison, Benchmarking & QC of Epigenomic Datasets |
| bioconductor-epidecoder |
1.14.0 |
|
|
GPL-3 |
| | | X | epidecodeR: a functional exploration tool for epigenetic and... |
| bioconductor-epidish |
2.22.0 |
|
|
GPL-2 |
| | | X | Epigenetic Dissection of Intra-Sample-Heterogeneity |
| bioconductor-epigenomix |
1.46.0 |
|
|
LGPL-3 |
X | X | | X | Epigenetic and gene transcription data normalization and integration... |
| bioconductor-epigrahmm |
1.14.0 |
|
|
MIT |
X | X | | | Epigenomic R-based analysis with hidden Markov models |
| bioconductor-epihet |
1.13.0 |
|
|
Artistic-2.0 |
| | | X | Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data |
| bioconductor-epimix |
1.8.0 |
|
|
GPL-3 |
| | | X | EpiMix: an integrative tool for the population-level analysis of DNA methylation |
| bioconductor-epimix.data |
1.8.0 |
|
|
GPL-3 |
| | | X | Data for the EpiMix package |
| bioconductor-epimutacions |
1.10.0 |
|
|
MIT |
X | X | | | Robust outlier identification for DNA methylation data |
| bioconductor-epimutacionsdata |
1.10.0 |
|
|
MIT |
| | | X | Data for epimutacions package |
| bioconductor-epinem |
1.26.0 |
|
|
GPL-3 |
| | | X | epiNEM |
| bioconductor-epiregulon |
1.2.0 |
|
|
MIT |
X | | | | Gene regulatory network inference from single cell epigenomic data |
| bioconductor-epiregulon.extra |
1.2.0 |
|
|
MIT |
| | | X | Companion package to epiregulon with additional plotting, differential... |
| bioconductor-epistack |
1.12.0 |
|
|
MIT |
| | | X | Heatmaps of Stack Profiles from Epigenetic Signals |
| bioconductor-epistasisga |
1.8.0 |
|
|
GPL-3 |
X | X | | | An R package to identify multi-snp effects in nuclear family studies... |
| bioconductor-epitxdb |
1.18.0 |
|
|
Artistic-2.0 |
| | | X | Storing and accessing epitranscriptomic information using the... |
| bioconductor-epitxdb.hs.hg38 |
0.99.7 |
|
|
Artistic-2.0 |
| | | X | Annotation package for EpiTxDb objects |
| bioconductor-epitxdb.mm.mm10 |
0.99.6 |
|
|
Artistic-2.0 |
| | | X | Annotation package for EpiTxDb objects |
| bioconductor-epitxdb.sc.saccer3 |
0.99.5 |
|
|
Artistic-2.0 |
| | | X | Annotation package for EpiTxDb objects |
| bioconductor-epivizr |
2.36.0 |
|
|
Artistic-2.0 |
X | X | | X | R Interface to epiviz web app |
| bioconductor-epivizrchart |
1.28.0 |
|
|
Artistic-2.0 |
| | | X | R interface to epiviz web components |
| bioconductor-epivizrdata |
1.34.0 |
|
|
MIT |
X | X | | X | Data Management API for epiviz interactive visualization app |
| bioconductor-epivizrserver |
1.34.0 |
|
|
MIT |
X | X | | X | WebSocket server infrastructure for epivizr apps and packages |
| bioconductor-epivizrstandalone |
1.34.0 |
|
|
MIT |
X | X | | X | Run Epiviz Interactive Genomic Data Visualization App within R |
| bioconductor-erccdashboard |
1.40.0 |
|
|
GPL |
| | | X | Assess Differential Gene Expression Experiments with ERCC Controls |
| bioconductor-erma |
1.22.0 |
|
|
Artistic-2.0 |
| | | X | epigenomic road map adventures |
| bioconductor-erssa |
1.24.0 |
|
|
GPL-3 |
| | | X | Empirical RNA-seq Sample Size Analysis |
| bioconductor-esatac |
1.24.0 |
|
|
GPL-3.0-only |
X | X | | | An Easy-to-use Systematic pipeline for ATACseq data analysis |
| bioconductor-escape |
2.2.0 |
|
|
MIT |
| | | X | Easy single cell analysis platform for enrichment |
| bioconductor-escher |
1.6.0 |
|
|
MIT |
| | | X | Unified multi-dimensional visualizations with Gestalt principles |
| bioconductor-esetvis |
1.32.0 |
|
|
GPL-3 |
X | X | | X | Visualizations of expressionSet Bioconductor object |
| bioconductor-estrogen |
1.52.0 |
|
|
LGPL |
| | | X | Microarray dataset that can be used as example for 2x2 factorial designs |
| bioconductor-etec16s |
1.30.0 |
|
|
Artistic-2.0 |
| | | X | Individual-specific changes in the human gut microbiota after challenge... |
| bioconductor-eudysbiome |
1.36.0 |
|
|
GPL-2 |
X | X | | X | Cartesian plot and contingency test on 16S Microbial data |
| bioconductor-eupathdb |
1.0.1 |
|
|
Artistic-2.0 |
| | | X | Provides access to pathogen annotation resources available on EuPathDB databases |
| bioconductor-evaluomer |
1.18.0 |
|
|
GPL-3 |
| | | X | Evaluation of Bioinformatics Metrics |
| bioconductor-eventpointer |
3.14.0 |
|
|
Artistic-2.0 |
X | X | | X | An effective identification of alternative splicing events using... |
| bioconductor-ewce |
1.14.0 |
|
|
GPL-3 |
| | | X | Expression Weighted Celltype Enrichment |
| bioconductor-ewcedata |
1.14.0 |
|
|
Artistic-2.0 |
| | | X | The ewceData package provides reference data required for ewce |
| bioconductor-excluderanges |
0.99.8 |
|
|
MIT |
| | | X | Genomic coordinates of problematic genomic regions |
| bioconductor-excluster |
1.24.0 |
|
|
GPL-3 |
| | | X | ExCluster robustly detects differentially expressed exons between two... |
| bioconductor-eximir |
2.48.0 |
|
|
GPL-2 |
X | X | | X | R functions for the normalization of Exiqon miRNA array data |
| bioconductor-exomecopy |
1.48.0 |
|
|
GPL-3.0-or-later |
X | X | | | Copy number variant detection from exome sequencing read depth |
| bioconductor-exomepeak |
2.17.0 |
|
|
GPL-2 |
X | X | | X | The package is developed for the analysis of affinity-based... |
| bioconductor-exomepeak2 |
1.14.3 |
|
|
Artistic-2.0 |
| | | X | Peak Calling and differential analysis for MeRIP-Seq |
| bioconductor-experimenthub |
2.14.0 |
|
|
Artistic-2.0 |
X | X | | X | Client to access ExperimentHub resources |
| bioconductor-experimenthubdata |
1.32.0 |
|
|
Artistic-2.0 |
| | | X | Add resources to ExperimentHub |
| bioconductor-experimentsubset |
1.16.0 |
|
|
MIT |
| | | X | Manages subsets of data with Bioconductor Experiment objects |
| bioconductor-explorase |
1.53.0 |
|
|
GPL-2 |
| | | X | GUI for exploratory data analysis of systems biology data |
| bioconductor-exploremodelmatrix |
1.18.0 |
|
|
MIT |
| | | X | Graphical Exploration of Design Matrices |
| bioconductor-expressionatlas |
1.34.0 |
|
|
GPL |
| | | X | Download datasets from EMBL-EBI Expression Atlas |
| bioconductor-expressionnormalizationworkflow |
1.16.0 |
|
|
GPL |
X | X | | | Gene Expression Normalization Workflow |
| bioconductor-expressionview |
1.42.0 |
|
|
GPL |
X | X | | | Visualize biclusters identified in gene expression data |
| bioconductor-extrachips |
1.10.0 |
|
|
GPL-3 |
X | X | | X | Additional functions for working with ChIP-Seq data |
| bioconductor-faahko |
1.46.0 |
|
|
LGPL |
X | X | | X | Saghatelian et al. (2004) FAAH knockout LC/MS data |
| bioconductor-fabia |
2.52.0 |
|
|
LGPL |
X | X | | | FABIA: Factor Analysis for Bicluster Acquisition |
| bioconductor-fabiadata |
1.44.0 |
|
|
LGPL |
| | | X | Data sets for FABIA (Factor Analysis for Bicluster Acquisition) |
| bioconductor-facopy.annot |
1.6.0 |
|
|
GPL-3 |
| | | X | Annotation for the copy number alteration association and enrichment... |
| bioconductor-facsdorit |
1.30.0 |
|
|
GPL-2 |
| | | X | DKFZ FACS example data |
| bioconductor-factdesign |
1.82.0 |
|
|
LGPL |
| | | X | Factorial designed microarray experiment analysis |
| bioconductor-factr |
1.8.0 |
|
|
file |
| | | X | Functional Annotation of Custom Transcriptomes |
| bioconductor-famagg |
1.34.0 |
|
|
MIT |
| | | X | Pedigree Analysis and Familial Aggregation |
| bioconductor-famat |
1.16.0 |
|
|
GPL-3 |
| | | X | Functional analysis of metabolic and transcriptomic data |
| bioconductor-fantom3and4cage |
1.42.0 |
|
|
GPL-3 |
| | | X | CAGE data from FANTOM3 and FANTOM4 projects |
| bioconductor-farms |
1.52.0 |
|
|
LGPL |
X | X | | X | FARMS - Factor Analysis for Robust Microarray Summarization |
| bioconductor-fastliquidassociation |
1.42.0 |
|
|
GPL-2 |
| | | X | functions for genome-wide application of Liquid Association |
| bioconductor-fastqcleaner |
1.24.0 |
|
|
MIT |
X | X | | | A Shiny Application for Quality Control, Filtering and Trimming of FASTQ Files |
| bioconductor-fastreer |
1.10.0 |
|
|
GPL-3 |
| | | X | Phylogenetic, Distance and Other Calculations on VCF and Fasta Files |
| bioconductor-fastseg |
1.52.0 |
|
|
LGPL |
X | X | | | fastseg - a fast segmentation algorithm |
| bioconductor-fcbf |
2.8.0 |
|
|
MIT |
| | | X | Fast Correlation Based Filter for Feature Selection |
| bioconductor-fccac |
1.32.0 |
|
|
Artistic-2.0 |
X | X | | X | functional Canonical Correlation Analysis to evaluate Covariance... |
| bioconductor-fci |
1.36.0 |
|
|
GPL |
| | | X | f-divergence Cutoff Index for Differential Expression Analysis in... |
| bioconductor-fcoex |
1.13.0 |
|
|
GPL-3 |
| | | X | FCBF-based Co-Expression Networks for Single Cells |
| bioconductor-fcscan |
1.20.0 |
|
|
Artistic-2.0 |
| | | X | fcScan for detecting clusters of coordinates with user defined options |
| bioconductor-fdb.fantom4.promoters.hg19 |
1.0.0 |
|
|
Artistic-2.0 |
| | | X | Annotation package for FANTOM4 promoters identified from THP-1 cells |
| bioconductor-fdb.infiniummethylation.hg18 |
2.2.0 |
|
|
Artistic-2.0 |
| | | X | Annotation package for Illumina Infinium DNA methylation probes |
| bioconductor-fdb.infiniummethylation.hg19 |
2.2.0 |
|
|
Artistic-2.0 |
X | X | | X | Annotation package for Illumina Infinium DNA methylation probes |
| bioconductor-fdb.ucsc.snp135common.hg19 |
1.0.0 |
|
|
Artistic-2.0 |
| | | X | UCSC common SNPs track for dbSNP build 135 |
| bioconductor-fdb.ucsc.snp137common.hg19 |
1.0.0 |
|
|
Artistic-2.0 |
| | | X | UCSC common SNPs track for dbSNP build 137 |
| bioconductor-fdb.ucsc.trnas |
1.0.1 |
|
|
Artistic-2.0 |
| | | X | Annotation package for FeatureDb object(s) |
| bioconductor-fdrame |
1.78.0 |
|
|
GPL |
X | X | | | FDR adjustments of Microarray Experiments (FDR-AME) |
| bioconductor-feast |
1.14.0 |
|
|
GPL-2 |
X | X | | | FEAture SelcTion (FEAST) for Single-cell clustering |
| bioconductor-featseekr |
1.6.0 |
|
|
GPL-3 |
| | | X | FeatSeekR an R package for unsupervised feature selection |
| bioconductor-fedup |
1.14.0 |
|
|
MIT |
| | | X | Fisher's Test for Enrichment and Depletion of User-Defined Pathways |
| bioconductor-fella |
1.26.0 |
|
|
GPL-3 |
| | | X | Interpretation and enrichment for metabolomics data |
| bioconductor-fem |
3.15.0 |
|
|
GPL |
| | | X | Identification of Functional Epigenetic Modules |
| bioconductor-fenr |
1.4.0 |
|
|
MIT |
| | | X | Fast functional enrichment for interactive applications |
| bioconductor-ffpe |
1.50.0 |
|
|
GPL |
X | X | | X | Quality assessment and control for FFPE microarray expression data |
| bioconductor-ffpeexampledata |
1.44.0 |
|
|
GPL |
| | | X | Illumina DASL example microarray data |
| bioconductor-fgga |
1.14.0 |
|
|
GPL-3 |
| | | X | Hierarchical ensemble method based on factor graph |
| bioconductor-fgnet |
3.40.0 |
|
|
GPL |
| | | X | Functional Gene Networks derived from biological enrichment analyses |
| bioconductor-fgsea |
1.32.2 |
|
|
MIT |
X | X | | | Fast Gene Set Enrichment Analysis |
| bioconductor-fibroeset |
1.48.0 |
|
|
LGPL |
| | | X | exprSet for Karaman et al. (2003) fibroblasts data |
| bioconductor-fieldeffectcrc |
1.16.0 |
|
|
Artistic-2.0 |
| | | X | Tumor, tumor-adjacent normal, and healthy colorectal transcriptomes as... |
| bioconductor-filterffpe |
1.16.0 |
|
|
LGPL-3 |
| | | X | FFPE Artificial Chimeric Read Filter for NGS data |
| bioconductor-findit2 |
1.12.0 |
|
|
Artistic-2.0 |
| | | X | find influential TF and Target based on multi-omics data |
| bioconductor-findmyfriends |
1.23.0 |
|
|
GPL |
X | X | | | Microbial Comparative Genomics in R |
| bioconductor-fis |
1.34.0 |
|
|
GPL-3 |
X | X | | X | Human Functional Interactions (FIs) for splineTimeR package |
| bioconductor-fishalyser |
1.40.0 |
|
|
Artistic-2.0 |
X | X | | X | FISHalyseR a package for automated FISH quantification |
| bioconductor-fishpond |
2.12.0 |
|
|
GPL-2 |
X | X | | X | Fishpond: downstream methods and tools for expression data |
| bioconductor-fission |
1.26.0 |
|
|
LGPL |
| | | X | RangedSummarizedExperiment for time course RNA-Seq of fission yeast in... |
| bioconductor-fitcons.ucsc.hg19 |
3.7.1 |
|
|
Artistic-2.0 |
| | | X | UCSC fitCons fitness consequences scores for hg19 |
| bioconductor-fithic |
1.32.0 |
|
|
GPL |
X | X | | | Confidence estimation for intra-chromosomal contact maps |
| bioconductor-flagme |
1.62.0 |
|
|
LGPL |
X | X | | | Analysis of Metabolomics GC/MS Data |
| bioconductor-flames |
1.8.0 |
|
|
GPL |
X | X | | | FLAMES: Full Length Analysis of Mutations and Splicing in long read RNA-seq data |
| bioconductor-fletcher2013a |
1.42.0 |
|
|
GPL |
| | | X | Gene expression data from breast cancer cells under FGFR2 signalling... |
| bioconductor-fletcher2013b |
1.42.0 |
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|
GPL |
| | | X | Master regulators of FGFR2 signalling and breast cancer risk |
| bioconductor-flipflop |
1.18.0 |
|
|
GPL-3 |
X | X | | | Flipflop discovers which isoforms of a gene are expressed in a given... |
| bioconductor-flowai |
1.36.0 |
|
|
GPL |
X | X | | X | Automatic and interactive quality control for flow cytometry data |
| bioconductor-flowbeads |
1.44.0 |
|
|
Artistic-2.0 |
X | X | | X | flowBeads: Analysis of flow bead data |
| bioconductor-flowbin |
1.42.0 |
|
|
Artistic-2.0 |
| | | X | Combining multitube flow cytometry data by binning |
| bioconductor-flowcatchr |
1.40.0 |
|
|
BSD_3_clause |
| | | X | Tools to analyze in vivo microscopy imaging data focused on tracking... |
| bioconductor-flowchic |
1.40.0 |
|
|
GPL-2 |
| | | X | Analyze flow cytometric data using histogram information |
| bioconductor-flowcl |
1.35.0 |
|
|
Artistic-2.0 |
X | X | | X | Semantic labelling of flow cytometric cell populations |
| bioconductor-flowclean |
1.44.0 |
|
|
Artistic-2.0 |
X | X | | X | flowClean |
| bioconductor-flowclust |
3.44.0 |
|
|
MIT |
X | X | | | Clustering for Flow Cytometry |
| bioconductor-flowcore |
2.18.0 |
|
|
Artistic-2.0 |
X | X | | | flowCore: Basic structures for flow cytometry data |
| bioconductor-flowcut |
1.16.0 |
|
|
Artistic-2.0 |
| | | X | Automated Removal of Outlier Events and Flagging of Files Based on Time... |
| bioconductor-flowcybar |
1.42.0 |
|
|
GPL-2 |
| | | X | Analyze flow cytometric data using gate information |
| bioconductor-flowdensity |
1.40.0 |
|
|
Artistic-2.0 |
X | X | | X | Sequential Flow Cytometry Data Gating |
| bioconductor-flowfit |
1.24.0 |
|
|
Artistic-2.0 |
| | | X | Estimate proliferation in cell-tracking dye studies |
| bioconductor-flowfitexampledata |
1.26.0 |
|
|
Artistic-2.0 |
| | | X | Example data for the flowFit package |
| bioconductor-flowfp |
1.64.0 |
|
|
Artistic-2.0 |
X | X | | | Fingerprinting for Flow Cytometry |
| bioconductor-flowgate |
1.6.0 |
|
|
MIT |
| | | X | Interactive Cytometry Gating in R |
| bioconductor-flowgraph |
1.14.0 |
|
|
Artistic-2.0 |
| | | X | Identifying differential cell populations in flow cytometry data... |
| bioconductor-flowmap |
1.38.0 |
|
|
GPL |
X | X | | X | Mapping cell populations in flow cytometry data for cross-sample... |
| bioconductor-flowmatch |
1.42.0 |
|
|
Artistic-2.0 |
X | X | | | Matching and meta-clustering in flow cytometry |
| bioconductor-flowmeans |
1.66.0 |
|
|
Artistic-2.0 |
| | | X | Non-parametric Flow Cytometry Data Gating |
| bioconductor-flowmerge |
2.54.0 |
|
|
Artistic-2.0 |
| | | X | Cluster Merging for Flow Cytometry Data |
| bioconductor-flowpeaks |
1.52.0 |
|
|
Artistic-1.0 |
X | X | | | An R package for flow data clustering |
| bioconductor-flowploidy |
1.32.0 |
|
|
GPL-3 |
X | X | | X | Analyze flow cytometer data to determine sample ploidy |
| bioconductor-flowploidydata |
1.32.0 |
|
|
GPL-3 |
| | | X | Example Flow Cytometry Data |
| bioconductor-flowplots |
1.54.0 |
|
|
Artistic-2.0 |
| | | X | flowPlots: analysis plots and data class for gated flow cytometry data |
| bioconductor-flowq |
1.40.0 |
|
|
Artistic-2.0 |
X | X | | | Provides quality control and quality assessment tools for flow cytometry data. |
| bioconductor-flowqb |
2.11.1 |
|
|
Artistic-2.0 |
| | | X | flowQB is a fully automated R Bioconductor package to calculate... |
| bioconductor-flowqbdata |
1.10.0 |
|
|
Artistic |
| | | X | The flowQBData package provides data files used as examples and for... |
| bioconductor-flowrepositoryr |
1.23.0 |
|
|
Artistic-2.0 |
X | X | | X | FlowRepository R Interface |
| bioconductor-flowsom |
2.14.0 |
|
|
GPL |
X | X | | | Using self-organizing maps for visualization and interpretation of... |
| bioconductor-flowsorted.blood.450k |
1.44.0 |
|
|
Artistic-2.0 |
X | X | | X | Illumina HumanMethylation data on sorted blood cell populations |
| bioconductor-flowsorted.blood.epic |
2.10.0 |
|
|
GPL-3 |
| | | X | Illumina EPIC data on immunomagnetic sorted peripheral adult blood cells |
| bioconductor-flowsorted.cordblood.450k |
1.34.0 |
|
|
Artistic-2.0 |
| | | X | Illumina 450k data on sorted cord blood cells |
| bioconductor-flowsorted.cordbloodcombined.450k |
1.22.0 |
|
|
GPL-3 |
| | | X | Illumina 450k/EPIC data on FACS and MACS umbilical blood cells |
| bioconductor-flowsorted.cordbloodnorway.450k |
1.32.0 |
|
|
Artistic-2.0 |
| | | X | Illumina HumanMethylation data on sorted cord blood cell populations |
| bioconductor-flowsorted.dlpfc.450k |
1.42.0 |
|
|
Artistic-2.0 |
| | | X | Illumina HumanMethylation data on sorted frontal cortex cell populations |
| bioconductor-flowspecs |
1.20.0 |
|
|
MIT |
| | | X | Tools for processing of high-dimensional cytometry data |
| bioconductor-flowspy |
1.4.0 |
|
|
GPL-3 |
X | X | | | A Toolkit for Flow And Mass Cytometry Data |
| bioconductor-flowstats |
4.18.0 |
|
|
Artistic-2.0 |
| | | X | Statistical methods for the analysis of flow cytometry data |
| bioconductor-flowtime |
1.30.0 |
|
|
Artistic-2.0 |
| | | X | Annotation and analysis of biological dynamical systems using flow cytometry |
| bioconductor-flowtrans |
1.58.0 |
|
|
Artistic-2.0 |
| | | X | Parameter Optimization for Flow Cytometry Data Transformation |
| bioconductor-flowtype |
2.25.0 |
|
|
Artistic-2.0 |
X | | | | Phenotyping Flow Cytometry Assays |
| bioconductor-flowutils |
1.58.0 |
|
|
Artistic-2.0 |
X | X | | X | Utilities for flow cytometry |
| bioconductor-flowviz |
1.70.0 |
|
|
Artistic-2.0 |
X | X | | X | Visualization for flow cytometry |
| bioconductor-flowvs |
1.38.0 |
|
|
Artistic-2.0 |
| | | X | Variance stabilization in flow cytometry (and microarrays) |
| bioconductor-flowworkspace |
4.18.0 |
|
|
AGPL-3.0-only |
X | X | | | Infrastructure for representing and interacting with gated and ungated... |
| bioconductor-flowworkspacedata |
3.18.0 |
|
|
GPL-2 |
| | | X | A data package containing two flowJo, one diva xml workspace and the... |
| bioconductor-fly.db0 |
3.20.0 |
|
|
Artistic-2.0 |
| | | X | Base Level Annotation databases for fly |
| bioconductor-fmcsr |
1.48.0 |
|
|
Artistic-2.0 |
X | X | | | Mismatch Tolerant Maximum Common Substructure Searching |
| bioconductor-fmrs |
1.16.0 |
|
|
GPL-3 |
X | X | | | Variable Selection in Finite Mixture of AFT Regression and FMR Models |
| bioconductor-fobitools |
1.14.0 |
|
|
GPL-3 |
| | | X | Tools for Manipulating the FOBI Ontology |
| bioconductor-focalcall |
1.21.0 |
|
|
GPL-2 |
X | X | | X | Detection of focal aberrations in DNA copy number data |
| bioconductor-foldgo |
1.18.0 |
|
|
GPL-3 |
| | | X | Package for Fold-specific GO Terms Recognition |
| bioconductor-fourcseq |
1.24.0 |
|
|
GPL |
X | X | | X | Package analyse 4C sequencing data |
| bioconductor-fourdndata |
1.6.0 |
|
|
MIT |
| | | X | 4DN data package |
| bioconductor-fraser |
2.2.0 |
|
dev |
MIT |
X | X | | | Find RAre Splicing Events in RNA-Seq Data |
| bioconductor-frenchfish |
1.18.0 |
|
|
Artistic-2.0 |
| | | X | Poisson Models for Quantifying DNA Copy-number from FISH Images of... |
| bioconductor-frgepistasis |
1.42.0 |
|
|
GPL-2 |
| | | X | Epistasis Analysis for Quantitative Traits by Functional Regression Model |
| bioconductor-frma |
1.58.0 |
|
|
GPL |
X | X | | X | Frozen RMA and Barcode |
| bioconductor-frmaexampledata |
1.42.0 |
|
|
GPL |
| | | X | Frma Example Data |
| bioconductor-frmatools |
1.58.0 |
|
|
GPL |
X | X | | X | Frozen RMA Tools |
| bioconductor-fscanr |
1.10.0 |
|
|
Artistic-2.0 |
| | | X | Detect Programmed Ribosomal Frameshifting Events from mRNA/cDNA BLASTX Output |
| bioconductor-funchip |
1.28.0 |
|
|
Artistic-2.0 |
X | X | | | Clustering and Alignment of ChIP-Seq peaks based on their shapes |
| bioconductor-funcisnp |
1.32.0 |
|
|
GPL-3 |
| | | X | Integrating Functional Non-coding Datasets with Genetic Association... |
| bioconductor-funcisnp.data |
1.22.0 |
|
|
GPL-3 |
| | | X | Various data sets for use with the FunciSNP package |
| bioconductor-funtoonorm |
1.30.0 |
|
|
GPL-3 |
| | | X | Normalization Procedure for Infinium HumanMethylation450 BeadChip Kit |
| bioconductor-furrowseg |
1.34.0 |
|
|
Artistic-2.0 |
| | | X | Furrow Segmentation |
| bioconductor-fusesom |
1.8.0 |
|
|
GPL-2 |
X | X | | | A Correlation Based Multiview Self Organizing Maps Clustering For IMC Datasets |
| bioconductor-ga4ghclient |
1.30.0 |
|
|
GPL |
| | | X | A Bioconductor package for accessing GA4GH API data servers |
| bioconductor-ga4ghshiny |
1.28.0 |
|
|
GPL-3 |
| | | X | Shiny application for interacting with GA4GH-based data servers |
| bioconductor-gaga |
2.52.0 |
|
|
GPL |
X | X | | | GaGa hierarchical model for high-throughput data analysis |
| bioconductor-gage |
2.56.0 |
|
|
GPL |
X | X | | X | Generally Applicable Gene-set Enrichment for Pathway Analysis |
| bioconductor-gagedata |
2.44.0 |
|
|
GPL |
X | X | | X | Auxillary data for gage package |
| bioconductor-gaggle |
1.70.0 |
|
|
GPL |
| | | X | Broadcast data between R and Gaggle |
| bioconductor-gaia |
2.38.0 |
|
|
GPL-2 |
| | | X | GAIA: An R package for genomic analysis of significant chromosomal aberrations. |
| bioconductor-gapgom |
1.10.0 |
|
|
MIT |
| | | X | GAPGOM (novel Gene Annotation Prediction and other GO Metrics) |
| bioconductor-gaprediction |
1.32.0 |
|
|
GPL |
X | X | | X | Prediction of gestational age with Illumina HumanMethylation450 data |
| bioconductor-garfield |
1.34.0 |
|
|
GPL-3 |
X | X | | | GWAS Analysis of Regulatory or Functional Information Enrichment with... |
| bioconductor-gars |
1.26.0 |
|
|
GPL |
| | | X | GARS: Genetic Algorithm for the identification of Robust Subsets of... |
| bioconductor-gaschyhs |
1.44.0 |
|
|
Artistic-2.0 |
| | | X | ExpressionSet for response of yeast to heat shock and other... |
| bioconductor-gatefinder |
1.26.0 |
|
|
Artistic-2.0 |
| | | X | Projection-based Gating Strategy Optimization for Flow and Mass Cytometry |
| bioconductor-gatingmldata |
2.37.1 |
|
|
GPL |
| | | X | Data and XML files for Gating-ML Test suite |
| bioconductor-gatom |
1.4.0 |
|
|
MIT |
| | | X | Finding an Active Metabolic Module in Atom Transition Network |
| bioconductor-gbscleanr |
2.0.2 |
|
|
GPL-3 |
X | X | | | Error correction tool for noisy genotyping by sequencing (GBS) data |
| bioconductor-gcapc |
1.30.0 |
|
|
GPL-3 |
| | | X | GC Aware Peak Caller |
| bioconductor-gcatest |
2.6.0 |
|
|
GPL |
X | X | | X | Genotype Conditional Association TEST |
| bioconductor-gcmap |
1.32.0 |
|
|
Artistic-2.0 |
| | | X | Tools for Connectivity Map-like analyses |
| bioconductor-gcmapweb |
1.27.0 |
|
|
Artistic-2.0 |
| | | X | A web interface for gene-set enrichment analyses |
| bioconductor-gcrisprtools |
2.12.0 |
|
|
Artistic-2.0 |
X | X | | X | Suite of Functions for Pooled Crispr Screen QC and Analysis |
| bioconductor-gcrma |
2.78.0 |
|
|
LGPL |
X | X | | | Background Adjustment Using Sequence Information |
| bioconductor-gcsconnection |
1.6.0 |
|
|
GPL |
X | X | | | Creating R Connection with Google Cloud Storage |
| bioconductor-gcsfilesystem |
1.4.0 |
|
|
GPL |
| | | X | Mounting a Google Cloud bucket to a local directory |
| bioconductor-gcspikelite |
1.44.0 |
|
|
LGPL |
X | X | | X | Spike-in data for GC/MS data and methods within flagme |
| bioconductor-gcsscore |
1.14.0 |
|
|
GPL |
| | | X | GCSscore: an R package for microarray analysis for Affymetrix/Thermo... |
| bioconductor-gdcrnatools |
1.26.0 |
|
|
Artistic-2.0 |
| | | X | GDCRNATools: an R/Bioconductor package for integrative analysis of... |
| bioconductor-gdnainrnaseqdata |
1.6.0 |
|
|
Artistic-2.0 |
| | | X | RNA-seq data with different levels of gDNA contamination |
| bioconductor-gdnax |
1.4.0 |
|
|
Artistic-2.0 |
| | | X | Diagnostics for assessing genomic DNA contamination in RNA-seq data |
| bioconductor-gdr |
1.4.0 |
|
|
Artistic-2.0 |
| | | X | Umbrella package for R packages in the gDR suite |
| bioconductor-gdrcore |
1.4.0 |
|
|
Artistic-2.0 |
X | X | | | Processing functions and interface to process and analyze drug... |
| bioconductor-gdrimport |
1.4.0 |
|
|
Artistic-2.0 |
| | | X | Package for handling the import of dose-response data |
| bioconductor-gdrstyle |
1.4.0 |
|
|
Artistic-2.0 |
| | | X | A package with style requirements for the gDR suite |
| bioconductor-gdrtestdata |
1.4.0 |
|
|
Artistic-2.0 |
| | | X | gDRtestData - R data package with testing dose response data |
| bioconductor-gdrutils |
1.4.0 |
|
|
Artistic-2.0 |
| | | X | A package with helper functions for processing drug response data |
| bioconductor-gdsarray |
1.26.0 |
|
|
GPL-3 |
| | | X | Representing GDS files as array-like objects |
| bioconductor-gdsfmt |
1.42.0 |
|
|
LGPL-3 |
X | X | | | R Interface to CoreArray Genomic Data Structure (GDS) Files |
| bioconductor-geecc |
1.21.0 |
|
|
GPL |
X | X | | | Gene Set Enrichment Analysis Extended to Contingency Cubes |
| bioconductor-gem |
1.32.0 |
|
|
Artistic-2.0 |
| | | X | GEM: fast association study for the interplay of Gene, Environment and... |
| bioconductor-gemini |
1.20.0 |
|
|
BSD_3_clause |
| | | X | GEMINI: Variational inference approach to infer genetic interactions... |
| bioconductor-gemma.r |
3.2.0 |
|
|
Apache |
| | | X | A wrapper for Gemma's Restful API to access curated gene expression... |
| bioconductor-genarise |
1.82.0 |
|
|
file |
| | | X | Microarray Analysis tool |
| bioconductor-genbankr |
1.27.0 |
|
|
Artistic-2.0 |
X | X | | X | Parsing GenBank files into semantically useful objects |
| bioconductor-geneaccord |
1.15.0 |
|
|
file |
| | | X | Detection of clonally exclusive gene or pathway pairs in a cohort of... |
| bioconductor-geneanswers |
2.36.0 |
|
|
LGPL |
| | | X | Integrated Interpretation of Genes |
| bioconductor-geneattribution |
1.32.0 |
|
|
Artistic-2.0 |
X | X | | X | Identification of candidate genes associated with genetic variation |
| bioconductor-genebreak |
1.36.0 |
|
|
GPL-2 |
X | X | | X | Gene Break Detection |
| bioconductor-geneclassifiers |
1.30.0 |
|
|
GPL-2 |
| | | X | Application of gene classifiers |
| bioconductor-geneexpressionsignature |
1.52.0 |
|
|
GPL-2 |
| | | X | Gene Expression Signature based Similarity Metric |
| bioconductor-genefilter |
1.88.0 |
|
|
Artistic-2.0 |
X | X | | | genefilter: methods for filtering genes from high-throughput experiments |
| bioconductor-genefu |
2.34.0 |
|
|
Artistic-2.0 |
X | X | | X | Computation of Gene Expression-Based Signatures in Breast Cancer |
| bioconductor-genega |
1.56.0 |
|
|
GPL |
X | X | | X | Design gene based on both mRNA secondary structure and codon usage bias... |
| bioconductor-genegeneinter |
1.32.0 |
|
|
GPL |
X | X | | X | Tools for Testing Gene-Gene Interaction at the Gene Level |
| bioconductor-genelendatabase |
1.42.0 |
|
|
LGPL |
X | X | | X | Lengths of mRNA transcripts for a number of genomes |
| bioconductor-genemeta |
1.78.0 |
|
|
Artistic-2.0 |
X | X | | X | MetaAnalysis for High Throughput Experiments |
| bioconductor-genenetworkbuilder |
1.48.0 |
|
|
GPL |
X | X | | | GeneNetworkBuilder: a bioconductor package for building regulatory... |
| bioconductor-geneoverlap |
1.42.0 |
|
|
GPL-3 |
X | X | | X | Test and visualize gene overlaps |
| bioconductor-geneplast |
1.32.0 |
|
|
GPL |
X | X | | X | Evolutionary and plasticity analysis of orthologous groups |
| bioconductor-geneplast.data |
0.99.9 |
|
|
Artistic-2.0 |
| | | X | Input data for the geneplast package via AnnotationHub |
| bioconductor-geneplast.data.string.v91 |
0.99.6 |
|
|
Artistic-2.0 |
| | | X | Input data for the geneplast package |
| bioconductor-geneplotter |
1.84.0 |
|
|
Artistic-2.0 |
X | X | | X | Graphics related functions for Bioconductor |
| bioconductor-generecommender |
1.78.0 |
|
|
GPL |
X | X | | X | A gene recommender algorithm to identify genes coexpressed with a query... |
| bioconductor-generegionscan |
1.62.0 |
|
|
GPL |
X | X | | X | GeneRegionScan |
| bioconductor-generxcluster |
1.42.0 |
|
|
GPL |
X | X | | | gRx Differential Clustering |
| bioconductor-geneselectmmd |
2.50.0 |
|
|
GPL |
X | X | | | Gene selection based on the marginal distributions of gene profiles... |
| bioconductor-geneselector |
2.32.0 |
|
|
GPL |
X | X | | | The term 'GeneSelector' refers to a filter selecting those... |
| bioconductor-genesis |
2.36.0 |
|
|
GPL-3 |
X | X | | X | GENetic EStimation and Inference in Structured samples (GENESIS):... |
| bioconductor-genestructuretools |
1.22.0 |
|
|
BSD_3_clause |
| | | X | Tools for spliced gene structure manipulation and analysis |
| bioconductor-genesummary |
0.99.6 |
|
|
MIT |
| | | X | RefSeq Gene Summaries |
| bioconductor-genetclassifier |
1.46.0 |
|
|
GPL |
X | X | | X | Classify diseases and build associated gene networks using gene... |
| bioconductor-geneticsdesign |
1.55.0 |
|
|
GPL-2 |
X | X | | X | Functions for designing genetics studies |
| bioconductor-geneticsped |
1.68.0 |
|
|
LGPL |
X | X | | | Pedigree and genetic relationship functions |
| bioconductor-genetonic |
3.0.0 |
|
|
MIT |
| | | X | Enjoy Analyzing And Integrating The Results From Differential... |
| bioconductor-genextender |
1.32.0 |
|
|
GPL |
X | X | | | Optimized Functional Annotation Of ChIP-seq Data |
| bioconductor-genie3 |
1.28.0 |
|
|
GPL |
X | X | | | GEne Network Inference with Ensemble of trees |
| bioconductor-genocn |
1.58.0 |
|
|
GPL |
X | X | | | genotyping and copy number study tools |
| bioconductor-genogam |
2.11.0 |
|
|
GPL-2 |
X | X | | | A GAM based framework for analysis of ChIP-Seq data |
| bioconductor-genomation |
1.38.0 |
|
|
Artistic-2.0 |
X | X | | | Summary, annotation and visualization of genomic data |
| bioconductor-genomationdata |
1.38.0 |
|
|
GPL-3 |
| | | X | Experimental data for showing functionalities of the genomation package |
| bioconductor-genomautomorphism |
1.8.0 |
|
|
Artistic-2.0 |
| | | X | Compute the automorphisms between DNA's Abelian group representations |
| bioconductor-genomegraphs |
1.46.0 |
|
|
Artistic-2.0 |
X | X | | X | Plotting genomic information from Ensembl |
| bioconductor-genomeinfodb |
1.42.0 |
|
|
Artistic-2.0 |
X | X | | X | Utilities for manipulating chromosome names, including modifying them... |
| bioconductor-genomeinfodbdata |
1.2.13 |
|
|
Artistic-2.0 |
X | X | | X | Species and taxonomy ID look up tables used by GenomeInfoDb |
| bioconductor-genomeintervals |
1.62.0 |
|
|
Artistic-2.0 |
X | X | | X | Operations on genomic intervals |
| bioconductor-genomes |
3.36.0 |
|
|
GPL-3 |
| | | X | Genome sequencing project metadata |
| bioconductor-genomewidesnp5crlmm |
1.0.6 |
|
|
Artistic-2.0 |
| | | X | Metadata for fast genotyping with the 'crlmm' package |
| bioconductor-genomewidesnp6crlmm |
1.0.7 |
|
|
Artistic-2.0 |
| | | X | Metadata for fast genotyping with the 'crlmm' package |
| bioconductor-genomicalignments |
1.42.0 |
|
|
Artistic-2.0 |
X | X | | | Representation and manipulation of short genomic alignments |
| bioconductor-genomicdatacommons |
1.30.0 |
|
|
Artistic-2.0 |
X | X | | X | NIH / NCI Genomic Data Commons Access |
| bioconductor-genomicdistributions |
1.14.0 |
|
|
BSD_2_clause |
| | | X | GenomicDistributions: fast analysis of genomic intervals with Bioconductor |
| bioconductor-genomicdistributionsdata |
1.14.0 |
|
|
BSD_2_clause |
| | | X | Reference data for GenomicDistributions package |
| bioconductor-genomicfeatures |
1.58.0 |
|
|
Artistic-2.0 |
X | X | | X | Query the gene models of a given organism/assembly |
| bioconductor-genomicfiles |
1.42.0 |
|
|
Artistic-2.0 |
X | X | | X | Distributed computing by file or by range |
| bioconductor-genomicinstability |
1.12.0 |
|
|
file |
| | | X | Genomic Instability estimation for scRNA-Seq |
| bioconductor-genomicinteractionnodes |
1.10.0 |
|
|
file |
| | | X | A R/Bioconductor package to detect the interaction nodes from... |
| bioconductor-genomicinteractions |
1.40.0 |
|
|
GPL-3 |
X | X | | X | Utilities for handling genomic interaction data |
| bioconductor-genomicozone |
1.20.0 |
|
|
LGPL |
| | | X | Delineate outstanding genomic zones of differential gene activity |
| bioconductor-genomicplot |
1.4.0 |
|
|
GPL-2 |
| | | X | Plot profiles of next generation sequencing data in genomic features |
| bioconductor-genomicranges |
1.58.0 |
|
|
Artistic-2.0 |
X | X | | | Representation and manipulation of genomic intervals |
| bioconductor-genomicscores |
2.18.0 |
|
|
Artistic-2.0 |
X | X | | X | Infrastructure to work with genomewide position-specific scores |
| bioconductor-genomicstate |
0.99.15 |
|
|
Artistic-2.0 |
| | | X | Build and access GenomicState objects for use with derfinder tools from... |
| bioconductor-genomicsupersignature |
1.14.0 |
|
|
Artistic-2.0 |
| | | X | Interpretation of RNA-seq experiments through robust, efficient... |
| bioconductor-genomictuples |
1.40.0 |
|
|
Artistic-2.0 |
X | X | | | Representation and Manipulation of Genomic Tuples |
| bioconductor-genominator |
1.40.0 |
|
|
Artistic-2.0 |
X | X | | X | Analyze, manage and store genomic data |
| bioconductor-genoset |
1.45.1 |
|
|
Artistic-2.0 |
X | X | | | A RangedSummarizedExperiment with methods for copy number analysis |
| bioconductor-genotypeeval |
1.30.0 |
|
|
file |
| | | X | QA/QC of a gVCF or VCF file |
| bioconductor-genphen |
1.22.0 |
|
|
GPL |
X | X | | | genphen: tool for quantification of genotype-phenotype associations in... |
| bioconductor-genproseq |
1.10.0 |
|
|
Artistic-2.0 |
| | | X | Generating Protein Sequences with Deep Generative Models |
| bioconductor-genrank |
1.15.0 |
|
|
Artistic-2.0 |
X | X | | X | Candidate gene prioritization based on convergent evidence |
| bioconductor-genvisr |
1.38.0 |
|
|
GPL-3 |
X | X | | X | Genomic Visualizations in R |
| bioconductor-geodiff |
1.12.0 |
|
|
MIT |
X | X | | | Count model based differential expression and normalization on GeoMx RNA data |
| bioconductor-geoexplorer |
1.12.0 |
|
|
GPL-3 |
| | | X | GEOexplorer: a webserver for gene expression analysis and visualisation |
| bioconductor-geofastq |
1.14.0 |
|
|
MIT |
| | | X | Downloads ENA Fastqs With GEO Accessions |
| bioconductor-geometadb |
1.64.0 |
|
|
Artistic-2.0 |
X | X | | X | A compilation of metadata from NCBI GEO |
| bioconductor-geomxtools |
3.10.0 |
|
|
MIT |
| | | X | NanoString GeoMx Tools |
| bioconductor-geoquery |
2.74.0 |
|
|
MIT |
X | X | | X | Get data from NCBI Gene Expression Omnibus (GEO) |
| bioconductor-geosubmission |
1.58.0 |
|
|
GPL |
X | X | | X | Prepares microarray data for submission to GEO |
| bioconductor-geotcgadata |
2.6.0 |
|
|
Artistic-2.0 |
| | | X | Processing Various Types of Data on GEO and TCGA |
| bioconductor-gep2pep |
1.26.0 |
|
|
GPL-3 |
| | | X | Creation and Analysis of Pathway Expression Profiles (PEPs) |
| bioconductor-gesper |
1.34.0 |
|
|
GPL-3 |
| | | X | Gene-Specific Phenotype EstimatoR |
| bioconductor-getdee2 |
1.16.0 |
|
|
GPL-3 |
| | | X | Programmatic access to the DEE2 RNA expression dataset |
| bioconductor-geuvadistranscriptexpr |
1.34.0 |
|
|
GPL |
| | | X | Data package with transcript expression and bi-allelic genotypes from... |
| bioconductor-geuvpack |
1.22.0 |
|
|
Artistic-2.0 |
| | | X | summarized experiment with expression data from GEUVADIS |
| bioconductor-geuvstore2 |
1.18.0 |
|
|
Artistic-2.0 |
| | | X | demonstrate storage discipline for eQTL enumerations, revised |
| bioconductor-geva |
1.14.0 |
|
|
LGPL-3 |
| | | X | Gene Expression Variation Analysis (GEVA) |
| bioconductor-gewist |
1.50.0 |
|
|
GPL-2 |
X | X | | X | Gene Environment Wide Interaction Search Threshold |
| bioconductor-gg4way |
1.4.0 |
|
|
MIT |
| | | X | 4way Plots of Differential Expression |
| bioconductor-ggbase |
3.52.0 |
|
|
Artistic-2.0 |
X | X | | X | GGBase infrastructure for genetics of gene expression package GGtools |
| bioconductor-ggbio |
1.54.0 |
|
|
Artistic-2.0 |
X | X | | X | Visualization tools for genomic data |
| bioconductor-ggcyto |
1.34.0 |
|
|
file |
X | X | | X | Visualize Cytometry data with ggplot |
| bioconductor-ggdata |
1.28.0 |
|
|
LGPL |
| | | X | all 90 hapmap CEU samples, 47K expression, 4mm SNP |
| bioconductor-gghumanmethcancerpanelv1.db |
1.4.1 |
|
|
Artistic-2.0 |
| | | X | Illumina Golden Gate Human Methylation Cancer Panel Version 1... |
| bioconductor-ggkegg |
1.4.0 |
|
|
MIT |
| | | X | Analyzing and visualizing KEGG information using the grammar of graphics |
| bioconductor-ggmanh |
1.10.0 |
|
|
MIT |
| | | X | Visualization Tool for GWAS Result |
| bioconductor-ggmsa |
1.12.0 |
|
|
Artistic-2.0 |
| | | X | Plot Multiple Sequence Alignment using 'ggplot2' |
| bioconductor-ggpa |
1.18.0 |
|
|
GPL |
X | X | | | graph-GPA: A graphical model for prioritizing GWAS results and... |
| bioconductor-ggsc |
1.4.0 |
|
|
Artistic-2.0 |
X | X | | | Visualizing Single Cell and Spatial Transcriptomics |
| bioconductor-ggseqalign |
1.0.0 |
|
|
Artistic-2.0 |
| | | X | Minimal Visualization of Sequence Alignments |
| bioconductor-ggspavis |
1.12.0 |
|
|
MIT |
| | | X | Visualization functions for spatial transcriptomics data |
| bioconductor-ggtools |
5.24.0 |
|
|
Artistic-2.0 |
X | X | | X | software and data for analyses in genetics of gene expression |
| bioconductor-ggtree |
3.14.0 |
|
|
Artistic-2.0 |
X | X | | X | an R package for visualization of tree and annotation data |
| bioconductor-ggtreedendro |
1.8.0 |
|
|
Artistic-2.0 |
| | | X | Drawing 'dendrogram' using 'ggtree' |
| bioconductor-ggtreeextra |
1.16.0 |
|
|
GPL |
| | | X | An R Package To Add Geometric Layers On Circular Or Other Layout Tree... |
| bioconductor-gigsea |
1.24.0 |
|
|
LGPL-3 |
| | | X | Genotype Imputed Gene Set Enrichment Analysis |
| bioconductor-gigseadata |
1.24.0 |
|
|
LGPL-3 |
| | | X | Gene set collections for the GIGSEA package |
| bioconductor-girafe |
1.58.0 |
|
|
Artistic-2.0 |
X | X | | | Genome Intervals and Read Alignments for Functional Exploration |
| bioconductor-gispa |
1.26.0 |
|
|
GPL-2 |
| | | X | GISPA: Method for Gene Integrated Set Profile Analysis |
| bioconductor-glad |
2.70.0 |
|
|
GPL-2 |
X | X | | | Gain and Loss Analysis of DNA |
| bioconductor-gladiatox |
1.22.0 |
|
|
GPL-2 |
| | | X | R Package for Processing High Content Screening data |
| bioconductor-glimma |
2.16.0 |
|
|
GPL-3 |
X | X | | X | Interactive visualizations for gene expression analysis |
| bioconductor-glmgampoi |
1.18.0 |
|
|
GPL-3 |
X | X | | | Fit a Gamma-Poisson Generalized Linear Model |
| bioconductor-glmsparsenet |
1.24.0 |
|
|
GPL-3 |
| | | X | Network Centrality Metrics for Elastic-Net Regularized Models |
| bioconductor-globalancova |
4.24.0 |
|
|
GPL |
X | X | | | Global test for groups of variables via model comparisons |
| bioconductor-globalseq |
1.34.0 |
|
|
GPL-3 |
X | X | | X | Global Test for Counts |
| bioconductor-globaltest |
5.60.0 |
|
|
GPL |
X | X | | X | Testing Groups of Covariates/Features for Association with a Response... |
| bioconductor-gloscope |
1.4.0 |
|
|
Artistic-2.0 |
| | | X | Population-level Representation on scRNA-Seq data |
| bioconductor-gmapr |
1.48.0 |
|
|
Artistic-2.0 |
X | X | | | An R interface to the GMAP/GSNAP/GSTRUCT suite |
| bioconductor-gmicr |
1.20.0 |
|
|
GPL-2 |
| | | X | Combines WGCNA and xCell readouts with bayesian network learrning to... |
| bioconductor-gmoviz |
1.18.0 |
|
|
GPL-3 |
| | | X | Seamless visualization of complex genomic variations in GMOs and edited... |
| bioconductor-gmrp |
1.34.0 |
|
|
GPL |
X | X | | X | GWAS-based Mendelian Randomization and Path Analyses |
| bioconductor-gnet2 |
1.18.0 |
|
|
Apache |
X | X | | | Constructing gene regulatory networks from expression data through... |
| bioconductor-gnosis |
1.4.0 |
|
|
MIT |
| | | X | Genomics explorer using statistical and survival analysis in R |
| bioconductor-go.db |
3.20.0 |
|
|
Artistic-2.0 |
X | X | | X | A set of annotation maps describing the entire Gene Ontology |
| bioconductor-goexpress |
1.40.0 |
|
|
GPL |
| | | X | Visualise microarray and RNAseq data using gene ontology annotations |
| bioconductor-gofuncr |
1.26.0 |
|
|
GPL |
X | X | | | Gene ontology enrichment using FUNC |
| bioconductor-gofunction |
1.35.0 |
|
|
GPL |
X | X | | X | GO-function: deriving biologcially relevant functions from... |
| bioconductor-golubesets |
1.48.0 |
|
|
LGPL |
X | X | | X | exprSets for golub leukemia data |
| bioconductor-googlegenomics |
2.4.0 |
|
|
Apache |
X | X | | | Provides an R package to interact with the Google Genomics API. |
| bioconductor-gopro |
1.32.0 |
|
|
GPL-3 |
X | X | | | Find the most characteristic gene ontology terms for groups of human genes |
| bioconductor-goprofiles |
1.68.0 |
|
|
GPL-2 |
| | | X | goProfiles: an R package for the statistical analysis of functional profiles |
| bioconductor-gosemsim |
2.32.0 |
|
|
Artistic-2.0 |
X | X | | | GO-terms Semantic Similarity Measures |
| bioconductor-goseq |
1.58.0 |
|
|
LGPL |
X | X | | X | Gene Ontology analyser for RNA-seq and other length biased data |
| bioconductor-gosim |
1.40.0 |
|
|
GPL |
X | X | | | Computation of functional similarities between GO terms and gene... |
| bioconductor-gosorensen |
1.8.0 |
|
|
GPL-3 |
| | | X | Statistical inference based on the Sorensen-Dice dissimilarity and the... |
| bioconductor-gostag |
1.30.0 |
|
|
GPL-3 |
| | | X | A tool to use GO Subtrees to Tag and Annotate Genes within a set |
| bioconductor-gostats |
2.72.0 |
|
|
Artistic-2.0 |
X | X | | X | Tools for manipulating GO and microarrays |
| bioconductor-gosummaries |
2.37.0 |
|
|
GPL |
X | X | | | Word cloud summaries of GO enrichment analysis |
| bioconductor-gothic |
1.42.0 |
|
|
GPL-3 |
X | X | | X | Binomial test for Hi-C data analysis |
| bioconductor-gotools |
1.80.0 |
|
|
GPL-2 |
X | X | | X | Functions for Gene Ontology database |
| bioconductor-gp53cdf |
2.18.0 |
|
|
LGPL |
| | | X | gp53cdf |
| bioconductor-gpa |
1.18.0 |
|
|
GPL |
X | X | | | GPA (Genetic analysis incorporating Pleiotropy and Annotation) |
| bioconductor-gpaexample |
1.18.0 |
|
|
GPL |
| | | X | Example data for the GPA package (Genetic analysis incorporating... |
| bioconductor-gpart |
1.12.0 |
|
|
MIT |
X | X | | | Human genome partitioning of dense sequencing data by identifying... |
| bioconductor-gpls |
1.78.0 |
|
|
Artistic-2.0 |
X | X | | X | Classification using generalized partial least squares |
| bioconductor-gprege |
1.38.0 |
|
|
AGPL-3 |
| | | X | Gaussian Process Ranking and Estimation of Gene Expression time-series |
| bioconductor-gpumagic |
1.22.0 |
|
|
GPL-3 |
X | X | | | An openCL compiler with the capacity to compile R functions and run the... |
| bioconductor-gqtlbase |
1.20.0 |
|
|
Artistic-2.0 |
| | | X | gQTLBase: infrastructure for eQTL, mQTL and similar studies |
| bioconductor-gqtlstats |
1.20.0 |
|
|
Artistic-2.0 |
| | | X | gQTLstats: computationally efficient analysis for eQTL and allied studies |
| bioconductor-gramm4r |
1.4.0 |
|
|
GPL-2 |
| | | X | Generalized correlation analysis and model construction strategy for... |
| bioconductor-granie |
1.10.0 |
|
|
Artistic-2.0 |
| | | X | GRaNIE: Reconstruction cell type specific gene regulatory networks... |
| bioconductor-granulator |
1.14.0 |
|
|
GPL-3 |
| | | X | Rapid benchmarking of methods for *in silico* deconvolution of bulk RNA-seq data |
| bioconductor-graper |
1.22.0 |
|
|
GPL |
X | X | | | Adaptive penalization in high-dimensional regression and classification... |
| bioconductor-graph |
1.84.0 |
|
|
Artistic-2.0 |
X | X | | | graph: A package to handle graph data structures |
| bioconductor-graphalignment |
1.70.0 |
|
|
file |
X | X | | | GraphAlignment |
| bioconductor-graphat |
1.78.0 |
|
|
LGPL |
X | X | | X | Graph Theoretic Association Tests |
| bioconductor-graphite |
1.52.0 |
|
|
AGPL-3 |
X | X | | X | GRAPH Interaction from pathway Topological Environment |
| bioconductor-graphpac |
1.44.0 |
|
|
GPL-2 |
X | X | | X | Identification of Mutational Clusters in Proteins via a Graph... |
| bioconductor-grasp2db |
1.1.0 |
|
|
Artistic-2.0 |
| | | X | grasp2db, sqlite wrap of GRASP 2.0 |
| bioconductor-greengenes13.5mgdb |
2.0.0 |
|
|
Artistic-2.0 |
| | | X | Greengenes 13.5 16S rRNA Database Annotation Data |
| bioconductor-grenits |
1.58.0 |
|
|
GPL |
X | X | | | Gene Regulatory Network Inference Using Time Series |
| bioconductor-greylistchip |
1.38.0 |
|
|
Artistic-2.0 |
| | | X | Grey Lists -- Mask Artefact Regions Based on ChIP Inputs |
| bioconductor-grmetrics |
1.32.0 |
|
|
GPL-3 |
X | X | | X | Calculate growth-rate inhibition (GR) metrics |
| bioconductor-grndata |
1.38.0 |
|
|
GPL-3 |
| | | X | Synthetic Expression Data for Gene Regulatory Network Inference |
| bioconductor-grohmm |
1.36.0 |
|
|
GPL-3.0-only |
X | X | | | GRO-seq Analysis Pipeline |
| bioconductor-grridge |
1.22.0 |
|
|
GPL-3 |
| | | X | Better prediction by use of co-data: Adaptive group-regularized ridge regression |
| bioconductor-gsalightning |
1.34.0 |
|
|
GPL |
X | X | | X | Fast Permutation-based Gene Set Analysis |
| bioconductor-gsar |
1.40.0 |
|
|
GPL |
| | | X | Gene Set Analysis in R |
| bioconductor-gsbenchmark |
1.26.0 |
|
|
GPL-2 |
| | | X | Gene Set Benchmark |
| bioconductor-gsca |
2.36.0 |
|
|
GPL(>=2) |
X | X | | X | GSCA: Gene Set Context Analysis |
| bioconductor-gscreend |
1.20.0 |
|
|
GPL-3 |
| | | X | Analysis of pooled genetic screens |
| bioconductor-gse103322 |
1.12.0 |
|
|
Artistic-2.0 |
| | | X | GEO accession data GSE103322 as a SingleCellExperiment |
| bioconductor-gse13015 |
1.14.0 |
|
|
MIT |
| | | X | GEO accession data GSE13015_GPL6106 as a SummarizedExperiment |
| bioconductor-gse159526 |
1.12.0 |
|
|
MIT |
| | | X | Placental cell DNA methylation data from GEO accession GSE159526 |
| bioconductor-gse62944 |
1.34.0 |
|
|
Artistic-2.0 |
| | | X | GEO accession data GSE62944 as a SummarizedExperiment |
| bioconductor-gseabase |
1.68.0 |
|
|
Artistic-2.0 |
X | X | | X | Gene set enrichment data structures and methods |
| bioconductor-gseabenchmarker |
1.26.0 |
|
|
Artistic-2.0 |
| | | X | Reproducible GSEA Benchmarking |
| bioconductor-gsealm |
1.66.0 |
|
|
Artistic-2.0 |
X | X | | X | Linear Model Toolset for Gene Set Enrichment Analysis |
| bioconductor-gseamining |
1.16.0 |
|
|
GPL-3 |
| | | X | Make Biological Sense of Gene Set Enrichment Analysis Outputs |
| bioconductor-gsean |
1.26.0 |
|
|
Artistic-2.0 |
X | X | | X | Gene Set Enrichment Analysis with Networks |
| bioconductor-gsgalgor |
1.16.0 |
|
|
MIT |
| | | X | An Evolutionary Framework for the Identification and Study of... |
| bioconductor-gskb |
1.22.0 |
|
|
Artistic-2.0 |
| | | X | Gene Set data for pathway analysis in mouse |
| bioconductor-gsreg |
1.40.0 |
|
|
GPL-2 |
X | X | | | Gene Set Regulation (GS-Reg) |
| bioconductor-gsri |
2.54.0 |
|
|
GPL-3 |
X | X | | X | Gene Set Regulation Index |
| bioconductor-gsva |
2.0.0 |
|
|
GPL |
X | X | | | Gene Set Variation Analysis for Microarray and RNA-Seq Data |
| bioconductor-gsvadata |
1.42.0 |
|
|
Artistic-2.0 |
| | | X | Data employed in the vignette of the GSVA package |
| bioconductor-gtrellis |
1.38.0 |
|
|
MIT |
X | X | | X | Genome Level Trellis Layout |
| bioconductor-guideseq |
1.36.0 |
|
|
GPL |
X | X | | X | GUIDE-seq and PEtag-seq analysis pipeline |
| bioconductor-guitar |
2.22.0 |
|
|
GPL-2 |
| | | X | Guitar |
| bioconductor-gviz |
1.50.0 |
|
|
Artistic-2.0 |
X | X | | X | Plotting data and annotation information along genomic coordinates |
| bioconductor-gwas.bayes |
1.16.0 |
|
|
GPL-3 |
X | X | | X | Bayesian analysis of Gaussian GWAS data |
| bioconductor-gwascat |
2.38.0 |
|
|
Artistic-2.0 |
| | | X | representing and modeling data in the EMBL-EBI GWAS catalog |
| bioconductor-gwascatdata |
0.99.6 |
|
|
Artistic-2.0 |
| | | X | A text file in cloud with March 30 2021 snapshot of EBI/EMBL GWAS catalog |
| bioconductor-gwasdata |
1.44.0 |
|
|
Artistic-2.0 |
| | | X | Data used in the examples and vignettes of the GWASTools package |
| bioconductor-gwastools |
1.52.0 |
|
|
Artistic-2.0 |
| | | X | Tools for Genome Wide Association Studies |
| bioconductor-gwasurvivr |
1.24.0 |
|
|
Artistic-2.0 |
| | | X | gwasurvivr: an R package for genome wide survival analysis |
| bioconductor-gwena |
1.16.0 |
|
|
GPL-3 |
| | | X | Pipeline for augmented co-expression analysis |
| bioconductor-gypsum |
1.2.0 |
|
|
MIT |
| | | X | Interface to the gypsum REST API |
| bioconductor-h10kcod.db |
3.4.0 |
|
|
Artistic-2.0 |
| | | X | Codelink UniSet Human I Bioarray (~10 000 human genes) annotation data... |
| bioconductor-h20kcod.db |
3.4.0 |
|
|
Artistic-2.0 |
| | | X | Codelink UniSet Human 20k I Bioarray annotation data (chip h20kcod) |
| bioconductor-h5vc |
2.40.0 |
|
|
GPL |
X | X | | | Managing alignment tallies using a hdf5 backend |
| bioconductor-h5vcdata |
2.26.0 |
|
|
GPL |
| | | X | Example data for the h5vc package |
| bioconductor-hapfabia |
1.48.0 |
|
|
LGPL |
X | X | | | hapFabia: Identification of very short segments of identity by descent... |
| bioconductor-hapmap100khind |
1.48.0 |
|
|
GPL |
| | | X | Sample data - Hapmap 100K HIND Affymetrix |
| bioconductor-hapmap100kxba |
1.48.0 |
|
|
GPL |
| | | X | Sample data - Hapmap 100K XBA Affymetrix |
| bioconductor-hapmap370k |
1.0.1 |
|
|
GPL |
| | | X | Example Illumina 370k HapMap Data |
| bioconductor-hapmap500knsp |
1.48.0 |
|
|
GPL |
| | | X | Sample data - Hapmap 500K NSP Affymetrix |
| bioconductor-hapmap500ksty |
1.48.0 |
|
|
GPL |
| | | X | Sample data - Hapmap 500K STY Affymetrix |
| bioconductor-hapmapsnp5 |
1.48.0 |
|
|
GPL |
| | | X | Sample data - Hapmap SNP 5.0 Affymetrix |
| bioconductor-hapmapsnp6 |
1.48.0 |
|
|
GPL |
| | | X | Sample data - Hapmap SNP 6.0 Affymetrix |
| bioconductor-harbchip |
1.44.0 |
|
|
Artistic-2.0 |
| | | X | Experimental Data Package: harbChIP |
| bioconductor-harman |
1.34.0 |
|
|
GPL-3 |
X | X | | | The removal of batch effects from datasets using a PCA and constrained... |
| bioconductor-harmandata |
1.34.0 |
|
|
GPL-3 |
| | | X | Data for the Harman package |
| bioconductor-harmonizedtcgadata |
1.28.0 |
|
|
GPL-3 |
| | | X | Processed Harmonized TCGA Data of Five Selected Cancer Types |
| bioconductor-harmonizr |
1.4.0 |
|
|
GPL-3 |
| | | X | Handles missing values and makes more data available |
| bioconductor-harshlight |
1.78.0 |
|
|
GPL |
X | X | | | A "corrective make-up" program for microarray chips |
| bioconductor-hca |
1.14.0 |
|
|
MIT |
| | | X | Exploring the Human Cell Atlas Data Coordinating Platform |
| bioconductor-hcabrowser |
1.6.0 |
|
|
Artistic-2.0 |
| | | X | Browse the Human Cell Atlas data portal |
| bioconductor-hcadata |
1.22.0 |
|
|
MIT |
| | | X | Accessing The Datasets Of The Human Cell Atlas in R/Bioconductor |
| bioconductor-hcaexplorer |
1.4.0 |
|
|
Artistic-2.0 |
| | | X | Browse the Human Cell Atlas data portal |
| bioconductor-hcamatrixbrowser |
1.0.1 |
|
|
Artistic-2.0 |
| | | X | Extract and manage matrix data from the Human Cell Atlas project |
| bioconductor-hcatonsildata |
1.4.0 |
|
|
MIT |
| | | X | Provide programmatic access to the tonsil cell atlas datasets |
| bioconductor-hcg110.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix HC_G110 Array annotation data (chip hcg110) |
| bioconductor-hcg110cdf |
2.18.0 |
|
|
LGPL |
| | | X | hcg110cdf |
| bioconductor-hcg110probe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type hcg110 |
| bioconductor-hd2013sgi |
1.46.0 |
|
|
Artistic-2.0 |
| | | X | Mapping genetic interactions in human cancer cells with RNAi and... |
| bioconductor-hdcytodata |
1.26.0 |
|
|
MIT |
| | | X | Collection of high-dimensional cytometry benchmark datasets in... |
| bioconductor-hdf5array |
1.34.0 |
|
|
Artistic-2.0 |
X | X | | X | HDF5 datasets as array-like objects in R |
| bioconductor-hdo.db |
1.0.0 |
|
|
Artistic-2.0 |
| | | X | A set of annotation maps describing the entire Human Disease Ontology |
| bioconductor-hdtd |
1.40.0 |
|
|
GPL-3 |
X | X | | | Statistical Inference about the Mean Matrix and the Covariance Matrices... |
| bioconductor-hdxmsqc |
1.2.0 |
|
|
file |
| | | X | An R package for quality Control for hydrogen deuterium exchange mass... |
| bioconductor-healthycontrolspresencechecker |
1.10.0 |
|
|
GPL-3 |
| | | X | Dowloads A Gene Expression Dataset From GEO And Checks If It Contains... |
| bioconductor-healthyflowdata |
1.44.0 |
|
|
Artistic-2.0 |
| | | X | Healthy dataset used by the flowMatch package |
| bioconductor-heatmaps |
1.30.0 |
|
|
Artistic-2.0 |
X | X | | X | Flexible Heatmaps for Functional Genomics and Sequence Features |
| bioconductor-heatplus |
3.14.0 |
|
|
GPL |
X | X | | X | Heatmaps with row and/or column covariates and colored clusters |
| bioconductor-heebodata |
1.44.0 |
|
|
LGPL |
| | | X | HEEBO set and HEEBO controls. |
| bioconductor-helloranges |
1.32.0 |
|
|
GPL |
X | X | | X | Introduce *Ranges to bedtools users |
| bioconductor-hellorangesdata |
1.32.0 |
|
|
GPL |
| | | X | Data for the HelloRanges tutorial vignette |
| bioconductor-help |
1.64.0 |
|
|
GPL |
X | X | | X | Tools for HELP data analysis |
| bioconductor-hem |
1.78.0 |
|
|
GPL |
X | X | | | Heterogeneous error model for identification of differentially... |
| bioconductor-hermes |
1.10.0 |
|
|
Apache |
| | | X | Preprocessing, analyzing, and reporting of RNA-seq data |
| bioconductor-heron |
1.4.0 |
|
|
GPL |
| | | X | Hierarchical Epitope pROtein biNding |
| bioconductor-herper |
1.16.0 |
|
|
GPL-3 |
| | | X | The Herper package is a simple toolset to install and manage conda... |
| bioconductor-hgc |
1.14.0 |
|
|
GPL-3 |
X | X | | | A fast hierarchical graph-based clustering method |
| bioconductor-hgfocus.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix HG-Focus Array annotation data (chip hgfocus) |
| bioconductor-hgfocuscdf |
2.18.0 |
|
|
LGPL |
| | | X | hgfocuscdf |
| bioconductor-hgfocusprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type hgfocus |
| bioconductor-hgu133a.db |
3.13.0 |
|
|
Artistic-2.0 |
X | X | | X | Affymetrix Affymetrix HG-U133A Array annotation data (chip hgu133a) |
| bioconductor-hgu133a2.db |
3.13.0 |
|
|
Artistic-2.0 |
X | X | | X | Affymetrix Affymetrix HG-U133A_2 Array annotation data (chip hgu133a2) |
| bioconductor-hgu133a2cdf |
2.18.0 |
|
|
LGPL |
| | | X | hgu133a2cdf |
| bioconductor-hgu133a2frmavecs |
1.2.0 |
|
|
GPL |
| | | X | Vectors used by frma for microarrays of type hgu133a2 |
| bioconductor-hgu133a2probe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type hgu133a2 |
| bioconductor-hgu133abarcodevecs |
1.44.0 |
|
|
GPL |
| | | X | hgu133a data for barcode |
| bioconductor-hgu133acdf |
2.18.0 |
|
|
LGPL |
| | | X | hgu133acdf |
| bioconductor-hgu133afrmavecs |
1.5.0 |
|
|
GPL |
| | | X | Vectors used by frma for microarrays of type hgu133a |
| bioconductor-hgu133aprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type hgu133a |
| bioconductor-hgu133atagcdf |
2.18.0 |
|
|
LGPL |
| | | X | hgu133atagcdf |
| bioconductor-hgu133atagprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type hgu133atag |
| bioconductor-hgu133b.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix HG-U133B Array annotation data (chip hgu133b) |
| bioconductor-hgu133bcdf |
2.18.0 |
|
|
LGPL |
| | | X | hgu133bcdf |
| bioconductor-hgu133bprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type hgu133b |
| bioconductor-hgu133plus2.db |
3.13.0 |
|
|
Artistic-2.0 |
X | X | | X | Affymetrix Affymetrix HG-U133_Plus_2 Array annotation data (chip hgu133plus2) |
| bioconductor-hgu133plus2barcodevecs |
1.44.0 |
|
|
GPL |
| | | X | hgu133plus2 data for barcode |
| bioconductor-hgu133plus2cdf |
2.18.0 |
|
|
LGPL |
| | | X | hgu133plus2cdf |
| bioconductor-hgu133plus2cellscore |
1.26.0 |
|
|
GPL-3 |
| | | X | CellScore Standard Cell Types Expression Dataset [hgu133plus2] |
| bioconductor-hgu133plus2frmavecs |
1.5.0 |
|
|
GPL |
| | | X | Vectors used by frma for microarrays of type hgu133plus2 |
| bioconductor-hgu133plus2probe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type hgu133plus2 |
| bioconductor-hgu219.db |
3.2.3 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Human Genome 219 Plate annotation data (chip hgu219) |
| bioconductor-hgu219cdf |
2.18.0 |
|
|
LGPL |
| | | X | hgu219cdf |
| bioconductor-hgu219probe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type hgu219 |
| bioconductor-hgu2beta7 |
1.46.0 |
|
|
Artistic-2.0 |
| | | X | A data package containing annotation data for hgu2beta7 |
| bioconductor-hgu95a.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix HG U95A Array annotation data (chip hgu95a) |
| bioconductor-hgu95acdf |
2.18.0 |
|
|
LGPL |
| | | X | hgu95acdf |
| bioconductor-hgu95aprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type hgu95a |
| bioconductor-hgu95av2 |
2.2.0 |
|
|
The |
| | | X | Affymetrix Human Genome U95 Set Annotation Data (hgu95av2) |
| bioconductor-hgu95av2.db |
3.13.0 |
|
|
Artistic-2.0 |
X | X | | X | Affymetrix Affymetrix HG U95Av2 Array annotation data (chip hgu95av2) |
| bioconductor-hgu95av2cdf |
2.18.0 |
|
|
LGPL |
| | | X | hgu95av2cdf |
| bioconductor-hgu95av2probe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type hgu95av2 |
| bioconductor-hgu95b.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix HG U95B Array annotation data (chip hgu95b) |
| bioconductor-hgu95bcdf |
2.18.0 |
|
|
LGPL |
| | | X | hgu95bcdf |
| bioconductor-hgu95bprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type hgu95b |
| bioconductor-hgu95c.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix HG U95C Array annotation data (chip hgu95c) |
| bioconductor-hgu95ccdf |
2.18.0 |
|
|
LGPL |
| | | X | hgu95ccdf |
| bioconductor-hgu95cprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type hgu95c |
| bioconductor-hgu95d.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix HG U95D Array annotation data (chip hgu95d) |
| bioconductor-hgu95dcdf |
2.18.0 |
|
|
LGPL |
| | | X | hgu95dcdf |
| bioconductor-hgu95dprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type hgu95d |
| bioconductor-hgu95e.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix HG U95E Array annotation data (chip hgu95e) |
| bioconductor-hgu95ecdf |
2.18.0 |
|
|
LGPL |
| | | X | hgu95ecdf |
| bioconductor-hgu95eprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type hgu95e |
| bioconductor-hguatlas13k.db |
3.2.3 |
|
|
Artistic-2.0 |
| | | X | Clontech BD Atlas Long Oligos Human 13K annotation data (chip hguatlas13k) |
| bioconductor-hgubeta7.db |
3.2.3 |
|
|
Artistic-2.0 |
| | | X | Unknown annotation data (chip hgubeta7) |
| bioconductor-hgudkfz31.db |
3.2.3 |
|
|
Artistic-2.0 |
| | | X | Unknown annotation data (chip hguDKFZ31) |
| bioconductor-hgug4100a.db |
3.2.3 |
|
|
Artistic-2.0 |
| | | X | Agilent Human 1 cDNA Microarray Kit annotation data (chip hgug4100a) |
| bioconductor-hgug4101a.db |
3.2.3 |
|
|
Artistic-2.0 |
| | | X | Agilent Human 2 cDNA Microarry Kit annotation data (chip hgug4101a) |
| bioconductor-hgug4110b.db |
3.2.3 |
|
|
Artistic-2.0 |
| | | X | Agilent Human 1A (V2) annotation data (chip hgug4110b) |
| bioconductor-hgug4111a.db |
3.2.3 |
|
|
Artistic-2.0 |
| | | X | Agilent Human 1B annotation data (chip hgug4111a) |
| bioconductor-hgug4112a.db |
3.2.3 |
|
|
Artistic-2.0 |
| | | X | Agilent "Human Genome, Whole" annotation data (chip hgug4112a) |
| bioconductor-hgug4845a.db |
0.0.3 |
|
|
Artistic-2.0 |
| | | X | agilent AMADID 026652 annotation data (chip hgug4845a) |
| bioconductor-hguqiagenv3.db |
3.2.3 |
|
|
Artistic-2.0 |
| | | X | Qiagen Qiagen V3.0 oligo set annotation data (chip hguqiagenv3) |
| bioconductor-hi16cod.db |
3.4.0 |
|
|
Artistic-2.0 |
| | | X | Codelink Human Inflammation 16 Bioarray annotation data (chip hi16cod) |
| bioconductor-hiannotator |
1.40.0 |
|
|
GPL |
X | X | | X | Functions for annotating GRanges objects |
| bioconductor-hibag |
1.42.0 |
|
|
GPL-3 |
X | X | | | HLA Genotype Imputation with Attribute Bagging |
| bioconductor-hibed |
1.4.0 |
|
|
GPL-3 |
| | | X | HiBED |
| bioconductor-hicaggr |
1.2.0 |
|
|
MIT |
| | | X | Set of 3D genomic interaction analysis tools |
| bioconductor-hicbricks |
1.24.0 |
|
|
MIT |
| | | X | Framework for Storing and Accessing Hi-C Data Through HDF Files |
| bioconductor-hiccompare |
1.28.0 |
|
|
MIT |
X | X | | X | HiCcompare: Joint normalization and comparative analysis of multiple... |
| bioconductor-hicdatahumanimr90 |
1.26.0 |
|
|
GPL-3 |
| | | X | Human IMR90 Fibroblast HiC data from Dixon et al. 2012 |
| bioconductor-hicdatalymphoblast |
1.42.0 |
|
|
GPL-3 |
| | | X | Human lymphoblastoid HiC data from Lieberman-Aiden et al. 2009 |
| bioconductor-hicdcplus |
1.14.0 |
|
|
GPL-3 |
X | X | | | Hi-C Direct Caller Plus |
| bioconductor-hicdoc |
1.8.0 |
|
|
LGPL-3 |
X | X | | | A/B compartment detection and differential analysis |
| bioconductor-hicexperiment |
1.6.0 |
|
|
MIT |
| | | X | Bioconductor class for interacting with Hi-C files in R |
| bioconductor-hicontacts |
1.8.0 |
|
|
MIT |
| | | X | Analysing cool files in R with HiContacts |
| bioconductor-hicontactsdata |
1.8.0 |
|
|
MIT |
| | | X | HiContacts companion data package |
| bioconductor-hicool |
1.6.0 |
|
|
MIT |
| | | X | HiCool |
| bioconductor-hicrep |
1.11.0 |
|
|
GPL |
X | X | | X | Measuring the reproducibility of Hi-C data |
| bioconductor-hicvenndiagram |
1.4.0 |
|
|
GPL-3 |
| | | X | Venn Diagram for genomic interaction data |
| bioconductor-hiergwas |
1.36.0 |
|
|
GPL-3 |
| | | X | Asessing statistical significance in predictive GWA studies |
| bioconductor-hierinf |
1.24.0 |
|
|
GPL-3 |
| | | X | Hierarchical Inference |
| bioconductor-highlyreplicatedrnaseq |
1.18.0 |
|
|
MIT |
| | | X | Collection of Bulk RNA-Seq Experiments With Many Replicates |
| bioconductor-hiiragi2013 |
1.41.0 |
|
|
Artistic-2.0 |
| | | X | Cell-to-cell expression variability followed by signal reinforcement... |
| bioconductor-hilbertcurve |
2.0.0 |
|
|
MIT |
X | X | | X | Making 2D Hilbert Curve |
| bioconductor-hilbertvis |
1.64.0 |
|
|
GPL |
X | X | | | Hilbert curve visualization |
| bioconductor-hilda |
1.20.0 |
|
|
GPL-3 |
X | X | | | Conducting statistical inference on comparing the mutational exposures... |
| bioconductor-hipathia |
3.6.0 |
|
|
GPL-2 |
| | | X | HiPathia: High-throughput Pathway Analysis |
| bioconductor-hippo |
1.18.0 |
|
|
GPL |
| | | X | Heterogeneity-Induced Pre-Processing tOol |
| bioconductor-hireadsprocessor |
1.42.0 |
|
|
GPL-3 |
| | | X | Functions to process LM-PCR reads from 454/Illumina data |
| bioconductor-hireewas |
1.24.0 |
|
|
GPL |
X | X | | | Detection of cell-type-specific risk-CpG sites in epigenome-wide... |
| bioconductor-hitc |
1.50.0 |
|
|
Artistic-2.0 |
X | X | | X | High Throughput Chromosome Conformation Capture analysis |
| bioconductor-hivcdnavantwout03 |
1.46.0 |
|
|
GPL |
| | | X | T cell line infections with HIV-1 LAI (BRU) |
| bioconductor-hivprtplus2cdf |
2.18.0 |
|
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LGPL |
| | | X | hivprtplus2cdf |
| bioconductor-hmdbquery |
1.26.0 |
|
|
Artistic-2.0 |
| | | X | utilities for exploration of human metabolome database |
| bioconductor-hmmcopy |
1.48.0 |
|
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GPL-3 |
X | X | | | Copy number prediction with correction for GC and mappability bias for HTS data |
| bioconductor-hmp16sdata |
1.26.0 |
|
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Artistic-2.0 |
| | | X | 16S rRNA Sequencing Data from the Human Microbiome Project |
| bioconductor-hmp2data |
1.20.0 |
|
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Artistic-2.0 |
| | | X | 16s rRNA sequencing data from the Human Microbiome Project 2 |
| bioconductor-hmyrib36 |
1.26.0 |
|
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Artistic-2.0 |
| | | X | YRI hapmap + expression (GENEVAR), Build 36, r23a genotypes |
| bioconductor-holofoodr |
1.0.0 |
|
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Artistic-2.0 |
| | | X | R interface to EBI HoloFood resource |
| bioconductor-hom.at.inp.db |
3.1.3 |
|
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Artistic-2.0 |
| | | X | Homology information for Arabidopsis thaliana from Inparanoid |
| bioconductor-hom.ce.inp.db |
3.1.3 |
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Artistic-2.0 |
| | | X | Homology information for Caenorhabditis elegans from Inparanoid |
| bioconductor-hom.dm.inp.db |
3.1.3 |
|
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Artistic-2.0 |
| | | X | Homology information for Drosophila melanogaster from Inparanoid |
| bioconductor-hom.dr.inp.db |
3.1.3 |
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Artistic-2.0 |
| | | X | Homology information for Danio rerio from Inparanoid |
| bioconductor-hom.hs.inp.db |
3.1.3 |
|
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Artistic-2.0 |
X | X | | X | Homology information for Homo Sapiens from Inparanoid |
| bioconductor-hom.mm.inp.db |
3.1.3 |
|
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Artistic-2.0 |
| | | X | Homology information for Mus musculus from Inparanoid |
| bioconductor-hom.rn.inp.db |
3.1.3 |
|
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Artistic-2.0 |
| | | X | Homology information for Rattus norvegicus from Inparanoid |
| bioconductor-hom.sc.inp.db |
3.1.3 |
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Artistic-2.0 |
| | | X | Homology information for Saccharomyces cerevisiae from Inparanoid |
| bioconductor-homo.sapiens |
1.3.1 |
|
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Artistic-2.0 |
X | X | | X | Annotation package for the Homo.sapiens object |
| bioconductor-hoodscanr |
1.4.0 |
|
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GPL-3 |
X | X | | | Spatial cellular neighbourhood scanning in R |
| bioconductor-hopach |
2.66.0 |
|
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GPL |
X | X | | | Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH) |
| bioconductor-hpaanalyze |
1.24.0 |
|
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GPL-3 |
| | | X | Retrieve and analyze data from the Human Protein Atlas |
| bioconductor-hpannot |
1.1.0 |
|
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GPL-2 |
| | | X | Anotation package for Hipathia package |
| bioconductor-hpar |
1.48.0 |
|
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Artistic-2.0 |
X | X | | X | Human Protein Atlas in R |
| bioconductor-hpastainr |
1.9.0 |
|
|
Artistic-2.0 |
| | | X | Queries the Human Protein Atlas Staining Data for Multiple Proteins and Genes |
| bioconductor-hpip |
1.12.0 |
|
|
MIT |
| | | X | Host-Pathogen Interaction Prediction |
| bioconductor-hpo.db |
0.99.2 |
|
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Artistic-2.0 |
| | | X | A set of annotation maps describing the entire Human Phenotype Ontology |
| bioconductor-hs25kresogen.db |
2.5.0 |
|
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Artistic-2.0 |
| | | X | RNG_MRC Human Pangenomic 25k Set annotation data (chip hs25kresogen) |
| bioconductor-hs6ug171.db |
3.2.3 |
|
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Artistic-2.0 |
| | | X | A package containing metadata for Hs6UG171 arrays |
| bioconductor-hsagilentdesign026652.db |
3.2.3 |
|
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Artistic-2.0 |
| | | X | Agilent Chips that use Agilent design number 026652 annotation data... |
| bioconductor-hsmmsinglecell |
1.26.0 |
|
|
Artistic-2.0 |
X | X | | X | Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM) |
| bioconductor-hspec |
0.99.1 |
|
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LGPL |
| | | X | Hspec |
| bioconductor-hspeccdf |
0.99.1 |
|
|
LGPL |
| | | X | hspeccdf |
| bioconductor-hta20probeset.db |
8.8.0 |
|
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Artistic-2.0 |
| | | X | Affymetrix hta20 annotation data (chip hta20probeset) |
| bioconductor-hta20transcriptcluster.db |
8.8.0 |
|
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Artistic-2.0 |
| | | X | Affymetrix hta20 annotation data (chip hta20transcriptcluster) |
| bioconductor-hthgu133a.db |
3.13.0 |
|
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Artistic-2.0 |
| | | X | Affymetrix Affymetrix HT_HG-U133A Array annotation data (chip hthgu133a) |
| bioconductor-hthgu133acdf |
2.18.0 |
|
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LGPL |
| | | X | hthgu133acdf |
| bioconductor-hthgu133afrmavecs |
1.3.0 |
|
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GPL |
| | | X | Vectors used by frma for microarrays of type hthgu133a |
| bioconductor-hthgu133aprobe |
2.18.0 |
|
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LGPL |
| | | X | Probe sequence data for microarrays of type hthgu133a |
| bioconductor-hthgu133b.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix HT_HG-U133B Array annotation data (chip hthgu133b) |
| bioconductor-hthgu133bcdf |
2.18.0 |
|
|
LGPL |
| | | X | hthgu133bcdf |
| bioconductor-hthgu133bprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type hthgu133b |
| bioconductor-hthgu133plusa.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix HT_HG-U133_Plus_A Array annotation data (chip... |
| bioconductor-hthgu133plusb.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix HT_HG-U133_Plus_B Array annotation data (chip... |
| bioconductor-hthgu133pluspm.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix HT_HG-U133_Plus_PM Array annotation data (chip... |
| bioconductor-hthgu133pluspmcdf |
2.18.0 |
|
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LGPL |
| | | X | hthgu133pluspmcdf |
| bioconductor-hthgu133pluspmprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type hthgu133pluspm |
| bioconductor-htmg430a.db |
3.13.0 |
|
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Artistic-2.0 |
| | | X | Affymetrix Affymetrix HT_MG-430A Array annotation data (chip htmg430a) |
| bioconductor-htmg430acdf |
2.18.0 |
|
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LGPL |
| | | X | htmg430acdf |
| bioconductor-htmg430aprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type htmg430a |
| bioconductor-htmg430b.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix HT_MG-430B Array annotation data (chip htmg430b) |
| bioconductor-htmg430bcdf |
2.18.0 |
|
|
LGPL |
| | | X | htmg430bcdf |
| bioconductor-htmg430bprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type htmg430b |
| bioconductor-htmg430pm.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix HT_MG-430_PM Array annotation data (chip htmg430pm) |
| bioconductor-htmg430pmcdf |
2.18.0 |
|
|
LGPL |
| | | X | htmg430pmcdf |
| bioconductor-htmg430pmprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type htmg430pm |
| bioconductor-htqpcr |
1.56.0 |
|
|
Artistic-2.0 |
X | X | | X | Automated analysis of high-throughput qPCR data |
| bioconductor-htrat230pm.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix HT_Rat230_PM Array annotation data (chip htrat230pm) |
| bioconductor-htrat230pmcdf |
2.18.0 |
|
|
LGPL |
| | | X | htrat230pmcdf |
| bioconductor-htrat230pmprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type htrat230pm |
| bioconductor-htratfocus.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix HT_Rat-Focus Array annotation data (chip htratfocus) |
| bioconductor-htratfocuscdf |
2.18.0 |
|
|
LGPL |
| | | X | htratfocuscdf |
| bioconductor-htratfocusprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type htratfocus |
| bioconductor-htsanalyzer |
2.38.0 |
|
|
Artistic-2.0 |
| | | X | Gene set over-representation, enrichment and network analyses for... |
| bioconductor-htseqgenie |
4.32.0 |
|
|
Artistic-2.0 |
| | | X | A NGS analysis pipeline. |
| bioconductor-htseqtools |
1.31.0 |
|
|
GPL |
X | X | | X | We provide efficient, easy-to-use tools for High-Throughput Sequencing... |
| bioconductor-htsfilter |
1.46.0 |
|
|
Artistic-2.0 |
X | X | | X | Filter replicated high-throughput transcriptome sequencing data |
| bioconductor-hu35ksuba.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix Hu35KsubA Array annotation data (chip hu35ksuba) |
| bioconductor-hu35ksubacdf |
2.18.0 |
|
|
LGPL |
| | | X | hu35ksubacdf |
| bioconductor-hu35ksubaprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type hu35ksuba |
| bioconductor-hu35ksubb.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix Hu35KsubB Array annotation data (chip hu35ksubb) |
| bioconductor-hu35ksubbcdf |
2.18.0 |
|
|
LGPL |
| | | X | hu35ksubbcdf |
| bioconductor-hu35ksubbprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type hu35ksubb |
| bioconductor-hu35ksubc.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix Hu35KsubC Array annotation data (chip hu35ksubc) |
| bioconductor-hu35ksubccdf |
2.18.0 |
|
|
LGPL |
| | | X | hu35ksubccdf |
| bioconductor-hu35ksubcprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type hu35ksubc |
| bioconductor-hu35ksubd.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix Hu35KsubD Array annotation data (chip hu35ksubd) |
| bioconductor-hu35ksubdcdf |
2.18.0 |
|
|
LGPL |
| | | X | hu35ksubdcdf |
| bioconductor-hu35ksubdprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type hu35ksubd |
| bioconductor-hu6800.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix Hu6800 Array annotation data (chip hu6800) |
| bioconductor-hu6800cdf |
2.18.0 |
|
|
LGPL |
| | | X | hu6800cdf |
| bioconductor-hu6800probe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type hu6800 |
| bioconductor-hu6800subacdf |
2.18.0 |
|
|
LGPL |
| | | X | hu6800subacdf |
| bioconductor-hu6800subbcdf |
2.18.0 |
|
|
LGPL |
| | | X | hu6800subbcdf |
| bioconductor-hu6800subccdf |
2.18.0 |
|
|
LGPL |
| | | X | hu6800subccdf |
| bioconductor-hu6800subdcdf |
2.18.0 |
|
|
LGPL |
| | | X | hu6800subdcdf |
| bioconductor-hubmapr |
0.99.6 |
|
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Artistic-2.0 |
| | | X | Interface to 'HuBMAP' |
| bioconductor-hubpub |
1.14.0 |
|
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Artistic-2.0 |
| | | X | Utilities to create and use Bioconductor Hubs |
| bioconductor-huex.1.0.st.v2frmavecs |
1.1.0 |
|
|
GPL |
| | | X | Vectors used by frma for microarrays of type huex.1.0.st.v2 |
| bioconductor-huex10stprobeset.db |
8.8.0 |
|
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Artistic-2.0 |
| | | X | Affymetrix huex10 annotation data (chip huex10stprobeset) |
| bioconductor-huex10sttranscriptcluster.db |
8.8.0 |
|
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Artistic-2.0 |
| | | X | Affymetrix huex10 annotation data (chip huex10sttranscriptcluster) |
| bioconductor-huexexonprobesetlocation |
1.15.0 |
|
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LGPL |
| | | X | Probe sequence data for microarrays of type HuEx |
| bioconductor-huexexonprobesetlocationhg18 |
0.0.2 |
|
|
LGPL |
| | | X | Exon-level probeset chromosome location for microarrays of type HuEx |
| bioconductor-huexexonprobesetlocationhg19 |
0.0.3 |
|
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LGPL |
| | | X | Exon-level probeset chromosome location for microarrays of type HuEx |
| bioconductor-hugene.1.0.st.v1frmavecs |
1.1.0 |
|
|
GPL |
| | | X | Vectors used by frma for microarrays of type hugene.1.0.st.v1frmavecs |
| bioconductor-hugene10stprobeset.db |
8.8.0 |
|
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Artistic-2.0 |
| | | X | Affymetrix hugene10 annotation data (chip hugene10stprobeset) |
| bioconductor-hugene10sttranscriptcluster.db |
8.8.0 |
|
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Artistic-2.0 |
| | | X | Affymetrix hugene10 annotation data (chip hugene10sttranscriptcluster) |
| bioconductor-hugene10stv1cdf |
2.18.0 |
|
|
LGPL |
| | | X | hugene10stv1cdf |
| bioconductor-hugene10stv1probe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type hugene10stv1 |
| bioconductor-hugene11stprobeset.db |
8.8.0 |
|
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Artistic-2.0 |
| | | X | Affymetrix hugene11 annotation data (chip hugene11stprobeset) |
| bioconductor-hugene11sttranscriptcluster.db |
8.8.0 |
|
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Artistic-2.0 |
| | | X | Affymetrix hugene11 annotation data (chip hugene11sttranscriptcluster) |
| bioconductor-hugene20stprobeset.db |
8.8.0 |
|
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Artistic-2.0 |
| | | X | Affymetrix hugene20 annotation data (chip hugene20stprobeset) |
| bioconductor-hugene20sttranscriptcluster.db |
8.8.0 |
|
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Artistic-2.0 |
| | | X | Affymetrix hugene20 annotation data (chip hugene20sttranscriptcluster) |
| bioconductor-hugene21stprobeset.db |
8.8.0 |
|
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Artistic-2.0 |
| | | X | Affymetrix hugene21 annotation data (chip hugene21stprobeset) |
| bioconductor-hugene21sttranscriptcluster.db |
8.8.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix hugene21 annotation data (chip hugene21sttranscriptcluster) |
| bioconductor-human.db0 |
3.20.0 |
|
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Artistic-2.0 |
| | | X | Base Level Annotation databases for human |
| bioconductor-human1mduov3bcrlmm |
1.0.4 |
|
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Artistic-2.0 |
| | | X | Metadata for fast genotyping with the 'crlmm' package |
| bioconductor-human1mv1ccrlmm |
1.0.3 |
|
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Artistic-2.0 |
| | | X | Metadata for fast genotyping with the 'crlmm' package |
| bioconductor-human370quadv3ccrlmm |
1.0.3 |
|
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Artistic-2.0 |
| | | X | Metadata for fast genotyping with the 'crlmm' package |
| bioconductor-human370v1ccrlmm |
1.0.2 |
|
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Artistic-2.0 |
| | | X | Metadata for fast genotyping with the 'crlmm' package |
| bioconductor-human550v3bcrlmm |
1.0.4 |
|
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Artistic-2.0 |
| | | X | Metadata for fast genotyping with the 'crlmm' package |
| bioconductor-human610quadv1bcrlmm |
1.0.3 |
|
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Artistic-2.0 |
| | | X | Metadata for fast genotyping with the 'crlmm' package |
| bioconductor-human650v3acrlmm |
1.0.3 |
|
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Artistic-2.0 |
| | | X | Metadata for fast genotyping with the 'crlmm' package |
| bioconductor-human660quadv1acrlmm |
1.0.3 |
|
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Artistic-2.0 |
| | | X | Metadata for fast genotyping with the 'crlmm' package |
| bioconductor-humanaffydata |
1.32.0 |
|
|
Artistic-2.0 |
| | | X | GEO accession GSE64985 and ArrayExpress accession E-MTAB-62 as... |
| bioconductor-humanchrloc |
2.1.6 |
|
|
The |
| | | X | A data package containing annotation data for humanCHRLOC |
| bioconductor-humancytosnp12v2p1hcrlmm |
1.0.1 |
|
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Artistic-2.0 |
| | | X | Metadata for fast genotyping with the 'crlmm' package |
| bioconductor-humanomni1quadv1bcrlmm |
1.0.3 |
|
|
Artistic-2.0 |
| | | X | Metadata for fast genotyping with the 'crlmm' package |
| bioconductor-humanomni25quadv1bcrlmm |
1.0.2 |
|
|
Artistic-2.0 |
| | | X | Metadata for fast genotyping with the 'crlmm' package |
| bioconductor-humanomni5quadv1bcrlmm |
1.0.0 |
|
|
Artistic-2.0 |
| | | X | Metadata for fast genotyping with the 'crlmm' package |
| bioconductor-humanomniexpress12v1bcrlmm |
1.0.1 |
|
|
Artistic-2.0 |
| | | X | Metadata for fast genotyping with the 'crlmm' package |
| bioconductor-humanstemcell |
0.46.0 |
|
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Artistic-2.0 |
| | | X | Human Stem Cells time course experiment |
| bioconductor-humantranscriptomecompendium |
1.17.0 |
|
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Artistic-2.0 |
| | | X | Tools to work with a Compendium of 181000 human transcriptome sequencing studies |
| bioconductor-hummingbird |
1.16.0 |
|
|
GPL |
X | X | | | Bayesian Hidden Markov Model for the detection of differentially... |
| bioconductor-huo22.db |
3.2.3 |
|
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Artistic-2.0 |
| | | X | FHCRC Genomics Shared Resource HuO22 Annotation Data (HuO22) |
| bioconductor-hwgcod.db |
3.4.0 |
|
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Artistic-2.0 |
| | | X | Codelink Human Whole Genome Bioarray (~55 000 human genes) annotation... |
| bioconductor-hybridexpress |
1.2.0 |
|
|
GPL-3 |
| | | X | Comparative analysis of RNA-seq data for hybrids and their progenitors |
| bioconductor-hybridmtest |
1.50.0 |
|
|
GPL |
X | X | | X | Hybrid Multiple Testing |
| bioconductor-hyper |
2.4.0 |
|
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GPL-3 |
| | | X | An R Package For Geneset Enrichment Workflows |
| bioconductor-hyperdraw |
1.58.0 |
|
|
GPL |
X | X | | X | Visualizing Hypergaphs |
| bioconductor-hypergraph |
1.78.0 |
|
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Artistic-2.0 |
X | X | | X | A package providing hypergraph data structures |
| bioconductor-iaseq |
1.50.0 |
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GPL-2 |
X | X | | X | iASeq: integrating multiple sequencing datasets for detecting... |
| bioconductor-iasva |
1.24.0 |
|
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GPL-2 |
| | | X | Iteratively Adjusted Surrogate Variable Analysis |
| bioconductor-ibbig |
1.50.0 |
|
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Artistic-2.0 |
X | X | | | Iterative Binary Biclustering of Genesets |
| bioconductor-ibh |
1.54.0 |
|
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GPL |
X | X | | X | Interaction Based Homogeneity for Evaluating Gene Lists |
| bioconductor-ibmq |
1.46.0 |
|
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Artistic-2.0 |
X | X | | | integrated Bayesian Modeling of eQTL data |
| bioconductor-icare |
1.34.0 |
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GPL-3 |
X | X | | | Individualized Coherent Absolute Risk Estimation (iCARE) |
| bioconductor-icens |
1.78.0 |
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Artistic-2.0 |
X | X | | X | NPMLE for Censored and Truncated Data |
| bioconductor-icetea |
1.24.0 |
|
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GPL-3 |
| | | X | Integrating Cap Enrichment with Transcript Expression Analysis |
| bioconductor-icheck |
1.36.0 |
|
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GPL |
| | | X | QC Pipeline and Data Analysis Tools for High-Dimensional Illumina mRNA... |
| bioconductor-ichip |
1.60.0 |
|
|
GPL |
X | X | | | Bayesian Modeling of ChIP-chip Data Through Hidden Ising Models |
| bioconductor-iclusterplus |
1.38.0 |
|
|
GPL |
X | X | | | Integrative clustering of multi-type genomic data |
| bioconductor-icnv |
1.26.0 |
|
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GPL-2 |
| | | X | Integrated Copy Number Variation detection |
| bioconductor-icobra |
1.34.0 |
|
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GPL |
X | X | | X | Comparison and Visualization of Ranking and Assignment Methods |
| bioconductor-ideal |
2.0.0 |
|
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MIT |
X | X | | X | Interactive Differential Expression AnaLysis |
| bioconductor-ideoviz |
1.42.0 |
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GPL-2 |
X | X | | X | Plots data (continuous/discrete) along chromosomal ideogram |
| bioconductor-idiogram |
1.82.0 |
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GPL-2 |
X | X | | X | idiogram |
| bioconductor-idmappinganalysis |
1.30.0 |
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GPL-2 |
| | | X | ID Mapping Analysis |
| bioconductor-idmappingretrieval |
1.34.0 |
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GPL-2 |
| | | X | ID Mapping Data Retrieval |
| bioconductor-idpr |
1.16.0 |
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LGPL |
| | | X | Profiling and Analyzing Intrinsically Disordered Proteins in R |
| bioconductor-idr2d |
1.20.0 |
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MIT |
| | | X | Irreproducible Discovery Rate for Genomic Interactions Data |
| bioconductor-ifaa |
1.8.0 |
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GPL-2 |
| | | X | Robust Inference for Absolute Abundance in Microbiome Analysis |
| bioconductor-igc |
1.36.0 |
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GPL-2 |
| | | X | An integrated analysis package of Gene expression and Copy number alteration |
| bioconductor-iggeneusage |
1.20.0 |
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MIT |
X | X | | | Differential gene usage in immune repertoires |
| bioconductor-igvr |
1.26.0 |
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|
MIT |
| | | X | igvR: integrative genomics viewer |
| bioconductor-ihw |
1.34.0 |
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|
Artistic-2.0 |
X | X | | X | Independent Hypothesis Weighting |
| bioconductor-ihwpaper |
1.34.0 |
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|
Artistic-2.0 |
X | X | | | Reproduce figures in IHW paper |
| bioconductor-illumina450probevariants.db |
1.42.0 |
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GPL-3 |
| | | X | Annotation Package combining variant data from 1000 Genomes Project for... |
| bioconductor-illuminadatatestfiles |
1.44.0 |
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Artistic-2.0 |
| | | X | Illumina microarray files (IDAT) for testing |
| bioconductor-illuminahumanmethylation27k.db |
1.4.8 |
|
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Artistic-2.0 |
| | | X | Illumina Illumina Human Methylation 27k annotation data (chip... |
| bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19 |
0.6.0 |
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Artistic-2.0 |
| | | X | Annotation for Illumina's 27k methylation arrays |
| bioconductor-illuminahumanmethylation27kmanifest |
0.4.0 |
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Artistic-2.0 |
| | | X | Annotation for Illumina's 27k methylation arrays |
| bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 |
0.6.1 |
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|
Artistic-2.0 |
X | X | | X | Annotation for Illumina's 450k methylation arrays |
| bioconductor-illuminahumanmethylation450kmanifest |
0.4.0 |
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|
Artistic-2.0 |
X | X | | X | Annotation for Illumina's 450k methylation arrays |
| bioconductor-illuminahumanmethylation450kprobe |
2.0.6 |
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LGPL |
| | | X | Probe sequence data for microarrays of type IlluminaHumanMethylation450k |
| bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 |
0.6.0 |
|
|
Artistic-2.0 |
X | X | | X | Annotation for Illumina's EPIC methylation arrays |
| bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19 |
0.6.0 |
|
|
Artistic-2.0 |
X | X | | X | Annotation for Illumina's EPIC methylation arrays |
| bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 |
0.6.0 |
|
|
Artistic-2.0 |
X | X | | X | Annotation for Illumina's EPIC methylation arrays |
| bioconductor-illuminahumanmethylationepicmanifest |
0.3.0 |
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|
Artistic-2.0 |
X | X | | X | Manifest for Illumina's EPIC methylation arrays |
| bioconductor-illuminahumanv1.db |
1.26.0 |
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Artistic-2.0 |
| | | X | Illumina HumanWG6v1 annotation data (chip illuminaHumanv1) |
| bioconductor-illuminahumanv2.db |
1.26.0 |
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Artistic-2.0 |
| | | X | Illumina HumanWG6v2 annotation data (chip illuminaHumanv2) |
| bioconductor-illuminahumanv2beadid.db |
1.8.0 |
|
|
Artistic-2.0 |
| | | X | Illumina HumanWGv2 annotation data (chip illuminaHumanv2BeadID) |
| bioconductor-illuminahumanv3.db |
1.26.0 |
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Artistic-2.0 |
| | | X | Illumina HumanHT12v3 annotation data (chip illuminaHumanv3) |
| bioconductor-illuminahumanv4.db |
1.26.0 |
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Artistic-2.0 |
| | | X | Illumina HumanHT12v4 annotation data (chip illuminaHumanv4) |
| bioconductor-illuminahumanwgdaslv3.db |
1.26.0 |
|
|
Artistic-2.0 |
| | | X | Illumina HumanHT12WGDASLv3 annotation data (chip illuminaHumanWGDASLv3) |
| bioconductor-illuminahumanwgdaslv4.db |
1.26.0 |
|
|
Artistic-2.0 |
| | | X | Illumina HumanWGDASLv4 annotation data (chip illuminaHumanWGDASLv4) |
| bioconductor-illuminaio |
0.48.0 |
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|
GPL-2 |
X | X | | | Parsing Illumina Microarray Output Files |
| bioconductor-illuminamousev1.db |
1.26.0 |
|
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Artistic-2.0 |
| | | X | Illumina MouseWG6v1 annotation data (chip illuminaMousev1) |
| bioconductor-illuminamousev1p1.db |
1.26.0 |
|
|
Artistic-2.0 |
| | | X | Illumina MouseWG6v1p1 annotation data (chip illuminaMousev1p1) |
| bioconductor-illuminamousev2.db |
1.26.0 |
|
|
Artistic-2.0 |
X | X | | X | Illumina MouseWG6v2 annotation data (chip illuminaMousev2) |
| bioconductor-illuminaratv1.db |
1.26.0 |
|
|
Artistic-2.0 |
| | | X | Illumina Ratv1 annotation data (chip illuminaRatv1) |
| bioconductor-iloreg |
1.16.0 |
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GPL-3 |
| | | X | ILoReg: a tool for high-resolution cell population identification from... |
| bioconductor-imagehts |
1.48.0 |
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|
LGPL-2.1 |
X | X | | X | Analysis of high-throughput microscopy-based screens |
| bioconductor-imas |
1.30.0 |
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GPL-2 |
X | X | | X | Integrative analysis of Multi-omics data for Alternative Splicing |
| bioconductor-imcdatasets |
1.14.0 |
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GPL-3 |
| | | X | Collection of publicly available imaging mass cytometry (IMC) datasets |
| bioconductor-imcrtools |
1.12.0 |
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GPL-3 |
| | | X | Methods for imaging mass cytometry data analysis |
| bioconductor-imetagene |
1.18.0 |
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|
Artistic-2.0 |
| | | X | A graphical interface for the metagene package |
| bioconductor-imman |
1.26.0 |
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|
Artistic-2.0 |
| | | X | Interlog protein network reconstruction by Mapping and Mining ANalysis |
| bioconductor-immunespacer |
1.30.0 |
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GPL-2 |
| | | X | A Thin Wrapper around the ImmuneSpace Data and Tools Portal |
| bioconductor-immunoclust |
1.38.0 |
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Artistic-2.0 |
X | X | | | immunoClust - Automated Pipeline for Population Detection in Flow Cytometry |
| bioconductor-immunogenviewer |
1.0.0 |
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Apache |
| | | X | Visualization and evaluation of protein immunogens |
| bioconductor-immunotation |
1.14.0 |
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GPL-3 |
| | | X | Tools for working with diverse immune genes |
| bioconductor-impcdata |
1.42.0 |
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|
file |
| | | X | Retrieves data from IMPC database |
| bioconductor-impulsede |
1.13.0 |
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GPL-3 |
X | X | | X | Detection of DE genes in time series data using impulse models |
| bioconductor-impulsede2 |
1.11.0 |
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Artistic-2.0 |
| | | X | Differential expression analysis of longitudinal count data sets |
| bioconductor-impute |
1.80.0 |
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GPL-2 |
X | X | | | impute: Imputation for microarray data |
| bioconductor-indac.db |
3.2.3 |
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|
Artistic-2.0 |
| | | X | INDAC FlyChip_long_oligonucleotide_002 (FL002) annotation data (chip indac) |
| bioconductor-indeed |
2.20.0 |
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|
Artistic-2.0 |
| | | X | Interactive Visualization of Integrated Differential Expression and... |
| bioconductor-inetgrate |
1.4.0 |
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GPL-3 |
| | | X | Integrates DNA methylation data with gene expression in a single gene network |
| bioconductor-infercnv |
1.22.0 |
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BSD_3_clause |
| | | X | Infer Copy Number Variation from Single-Cell RNA-Seq Data |
| bioconductor-infinityflow |
1.12.0 |
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GPL-3 |
| | | X | Augmenting Massively Parallel Cytometry Experiments Using Multivariate... |
| bioconductor-informeasure |
1.16.0 |
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Artistic-2.0 |
| | | X | R implementation of information measures |
| bioconductor-inpas |
2.14.0 |
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|
GPL |
| | | X | Identify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data |
| bioconductor-inpower |
1.42.0 |
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GPL-2 |
X | X | | X | An R package for computing the number of susceptibility SNPs |
| bioconductor-inspect |
1.36.0 |
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GPL-2 |
X | X | | X | Modeling RNA synthesis, processing and degradation with RNA-seq data |
| bioconductor-intact |
1.6.0 |
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GPL-3 |
| | | X | Integrate TWAS and Colocalization Analysis for Gene Set Enrichment Analysis |
| bioconductor-intad |
1.26.0 |
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|
GPL |
| | | X | Search for correlation between epigenetic signals and gene expression in TADs |
| bioconductor-intansv |
1.46.0 |
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MIT |
| | | X | Integrative analysis of structural variations |
| bioconductor-interaccircos |
1.16.0 |
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GPL-3 |
| | | X | The Generation of Interactive Circos Plot |
| bioconductor-interactionset |
1.34.0 |
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GPL-3 |
X | X | | | Base Classes for Storing Genomic Interaction Data |
| bioconductor-interactivecomplexheatmap |
1.14.0 |
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MIT |
| | | X | Make Interactive Complex Heatmaps |
| bioconductor-interactivedisplay |
1.38.0 |
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Artistic-2.0 |
X | X | | X | Package for enabling powerful shiny web displays of Bioconductor objects |
| bioconductor-interactivedisplaybase |
1.44.0 |
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|
Artistic-2.0 |
X | X | | X | Base package for enabling powerful shiny web displays of Bioconductor objects |
| bioconductor-intercellar |
2.12.0 |
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MIT |
| | | X | InterCellar: an R-Shiny app for interactive analysis and exploration of... |
| bioconductor-interest |
1.30.0 |
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GPL-2 |
X | X | | X | Intron-Exon Retention Estimator |
| bioconductor-interminer |
1.24.0 |
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LGPL |
X | X | | X | R Interface with InterMine-Powered Databases |
| bioconductor-intomics |
1.2.0 |
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GPL-3 |
| | | X | Integrative analysis of multi-omics data to infer regulatory networks |
| bioconductor-intramirexplorer |
1.28.0 |
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GPL-2 |
| | | X | Predicting Targets for Drosophila Intragenic miRNAs |
| bioconductor-inversion |
1.42.0 |
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GPL |
X | X | | | Inversions in genotype data |
| bioconductor-ioniser |
2.30.0 |
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MIT |
X | X | | X | Quality Assessment Tools for Oxford Nanopore MinION data |
| bioconductor-iontreedata |
1.18.0 |
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GPL-2 |
| | | X | Raw MS2, MS3 scans from direct infusion mass spectrometry (DIMS) and a... |
| bioconductor-ipac |
1.46.0 |
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GPL-2 |
X | X | | X | Identification of Protein Amino acid Clustering |
| bioconductor-ipath |
1.12.0 |
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GPL-2 |
X | X | | | iPath pipeline for detecting perturbed pathways at individual level |
| bioconductor-ipddb |
1.24.0 |
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Artistic-2.0 |
| | | X | IPD IMGT/HLA and IPD KIR database for Homo sapiens |
| bioconductor-ipo |
1.32.0 |
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GPL |
X | X | | X | Automated Optimization of XCMS Data Processing parameters |
| bioconductor-ippd |
1.35.0 |
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|
GPL |
X | X | | | Isotopic peak pattern deconvolution for Protein Mass Spectrometry by... |
| bioconductor-iranges |
2.40.0 |
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Artistic-2.0 |
X | X | | | Foundation of integer range manipulation in Bioconductor |
| bioconductor-irisfgm |
1.8.0 |
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GPL-2 |
X | X | | | Comprehensive Analysis of Gene Interactivity Networks Based on... |
| bioconductor-isanalytics |
1.12.0 |
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|
CC |
| | | X | Analyze gene therapy vector insertion sites data identified from... |
| bioconductor-isee |
2.18.0 |
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MIT |
X | X | | X | Interactive SummarizedExperiment Explorer |
| bioconductor-iseede |
1.4.0 |
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|
Artistic-2.0 |
| | | X | iSEE extension for panels related to differential expression analysis |
| bioconductor-iseefier |
1.2.0 |
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MIT |
| | | X | Streamlining the creation of initial states for starting an iSEE instance |
| bioconductor-iseehex |
1.8.0 |
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Artistic-2.0 |
| | | X | iSEE extension for summarising data points in hexagonal bins |
| bioconductor-iseehub |
1.8.0 |
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Artistic-2.0 |
| | | X | iSEE for the Bioconductor ExperimentHub |
| bioconductor-iseeindex |
1.4.0 |
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Artistic-2.0 |
| | | X | iSEE extension for a landing page to a custom collection of data sets |
| bioconductor-iseepathways |
1.4.0 |
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Artistic-2.0 |
| | | X | iSEE extension for panels related to pathway analysis |
| bioconductor-iseetree |
1.0.0 |
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Artistic-2.0 |
| | | X | Interactive visualisation for microbiome data |
| bioconductor-iseeu |
1.18.0 |
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MIT |
| | | X | iSEE Universe |
| bioconductor-iseq |
1.58.0 |
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GPL |
X | X | | | Bayesian Hierarchical Modeling of ChIP-seq Data Through Hidden Ising Models |
| bioconductor-islet |
1.8.0 |
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GPL-2 |
| | | X | Individual-Specific ceLl typE referencing Tool |
| bioconductor-isobar |
1.52.0 |
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LGPL-2 |
| | | X | Analysis and quantitation of isobarically tagged MSMS proteomics data |
| bioconductor-isobayes |
1.4.0 |
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GPL-3 |
X | X | | | IsoBayes: Single Isoform protein inference Method via Bayesian Analyses |
| bioconductor-isocorrector |
1.24.0 |
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GPL-3 |
| | | X | Correction for natural isotope abundance and tracer purity in MS and... |
| bioconductor-isocorrectorgui |
1.22.0 |
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GPL-3 |
| | | X | Graphical User Interface for IsoCorrectoR |
| bioconductor-isoformswitchanalyzer |
2.6.0 |
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GPL |
X | X | | | Identify, Annotate and Visualize Isoform Switches with Functional... |
| bioconductor-isogenegui |
2.30.0 |
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GPL-2 |
X | X | | | A graphical user interface to conduct a dose-response analysis of... |
| bioconductor-isolde |
1.34.0 |
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|
GPL |
X | X | | | Integrative Statistics of alleLe Dependent Expression |
| bioconductor-isomirs |
1.34.0 |
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MIT |
X | X | | X | Analyze isomiRs and miRNAs from small RNA-seq |
| bioconductor-italics |
2.62.0 |
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GPL-2 |
| | | X | ITALICS |
| bioconductor-italicsdata |
2.44.0 |
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|
GPL |
| | | X | ITALICSData |
| bioconductor-iterativebma |
1.64.0 |
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|
GPL |
X | X | | X | The Iterative Bayesian Model Averaging (BMA) algorithm |
| bioconductor-iterativebmasurv |
1.64.0 |
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|
GPL |
X | X | | X | The Iterative Bayesian Model Averaging (BMA) Algorithm For Survival Analysis |
| bioconductor-iterclust |
1.24.0 |
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|
file |
| | | X | Iterative Clustering |
| bioconductor-iteremoval |
1.14.0 |
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GPL-2 |
| | | X | Iteration removal method for feature selection |
| bioconductor-ivas |
2.26.0 |
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GPL-2 |
X | X | | X | Identification of genetic Variants affecting Alternative Splicing |
| bioconductor-ivygapse |
1.28.0 |
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Artistic-2.0 |
| | | X | A SummarizedExperiment for Ivy-GAP data |
| bioconductor-iwtomics |
1.30.0 |
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GPL |
X | X | | X | Interval-Wise Testing for Omics Data |
| bioconductor-iyer517 |
1.48.0 |
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Artistic-2.0 |
| | | X | exprSets for Iyer, Eisen et all 1999 Science paper |
| bioconductor-jaspar2014 |
1.42.0 |
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GPL-2 |
X | X | | X | Data package for JASPAR |
| bioconductor-jaspar2016 |
1.34.0 |
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GPL-2 |
X | X | | X | Data package for JASPAR 2016 |
| bioconductor-jaspar2018 |
1.1.1 |
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GPL-2 |
X | X | | X | Data package for JASPAR 2018 |
| bioconductor-jaspar2020 |
0.99.10 |
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GPL-2 |
| | | X | Data package for JASPAR database (version 2020) |
| bioconductor-jaspar2022 |
0.99.8 |
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GPL-2 |
| | | X | Data package for JASPAR database (version 2022) |
| bioconductor-jaspar2024 |
0.99.6 |
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GPL-2 |
| | | X | Data package for JASPAR database (version 2024) |
| bioconductor-jazaerimetadata.db |
3.2.3 |
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Artistic-2.0 |
| | | X | A data package containing annotation data for JazaeriMetaData |
| bioconductor-jctseqdata |
1.20.0 |
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|
file |
| | | X | Example Junction Count data for use with JunctionSeq |
| bioconductor-jmosaics |
1.10.0 |
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GPL |
X | X | | | jmosaics detects enriched regions of ChIP-seq data sets jointly. |
| bioconductor-joda |
1.35.0 |
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GPL |
| | | X | JODA algorithm for quantifying gene deregulation using knowledge |
| bioconductor-junctionseq |
1.17.0 |
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|
file |
X | X | | | JunctionSeq: A Utility for Detection of Differential Exon and... |
| bioconductor-karyoploter |
1.32.0 |
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Artistic-2.0 |
| | | X | Plot customizable linear genomes displaying arbitrary data |
| bioconductor-katdetectr |
1.8.0 |
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GPL-3 |
| | | X | Detection, Characterization and Visualization of Kataegis in Sequencing Data |
| bioconductor-kboost |
1.14.0 |
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GPL-2 |
| | | X | Inference of gene regulatory networks from gene expression data |
| bioconductor-kcsmart |
2.64.0 |
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GPL-3 |
X | X | | X | Multi sample aCGH analysis package using kernel convolution |
| bioconductor-kebabs |
1.40.0 |
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|
GPL |
X | X | | | Kernel-Based Analysis of Biological Sequences |
| bioconductor-kegg.db |
3.2.4 |
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|
file |
X | X | | X | A set of annotation maps for KEGG |
| bioconductor-keggandmetacoredzpathwaysgeo |
1.26.0 |
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GPL-2 |
| | | X | Disease Datasets from GEO |
| bioconductor-keggdzpathwaysgeo |
1.44.0 |
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GPL-2 |
X | X | | X | KEGG Disease Datasets from GEO |
| bioconductor-kegggraph |
1.66.0 |
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GPL |
X | X | | X | KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor |
| bioconductor-kegglincs |
1.32.0 |
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GPL-3 |
X | X | | X | Visualize all edges within a KEGG pathway and overlay LINCS data |
| bioconductor-keggorthology |
2.58.0 |
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|
Artistic-2.0 |
X | X | | X | graph support for KO, KEGG Orthology |
| bioconductor-keggprofile |
1.32.0 |
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|
GPL |
| | | X | An annotation and visualization package for multi-types and... |
| bioconductor-keggrest |
1.46.0 |
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Artistic-2.0 |
X | X | | X | Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG) |
| bioconductor-kidpack |
1.48.0 |
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GPL-2 |
| | | X | DKFZ kidney package |
| bioconductor-kimod |
1.15.0 |
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GPL |
X | X | | X | A k-tables approach to integrate multiple Omics-Data |
| bioconductor-kinswingr |
1.24.0 |
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GPL-3 |
| | | X | KinSwingR: network-based kinase activity prediction |
| bioconductor-kissde |
1.20.0 |
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GPL |
| | | X | Retrieves Condition-Specific Variants in RNA-Seq Data |
| bioconductor-kmcut |
1.0.0 |
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Artistic-2.0 |
| | | X | Optimized Kaplan Meier analysis and identification and validation of... |
| bioconductor-knowseq |
1.20.0 |
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GPL |
| | | X | KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline |
| bioconductor-knowyourcg |
1.2.0 |
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MIT |
| | | X | Functional analysis of DNA methylome datasets |
| bioconductor-kodata |
1.32.0 |
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MIT |
X | X | | X | LINCS Knock-Out Data Package |
| bioconductor-koinar |
1.0.0 |
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Apache |
| | | X | KoinaR - Remote machine learning inference using Koina |
| bioconductor-lace |
2.10.0 |
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|
file |
| | | X | Longitudinal Analysis of Cancer Evolution (LACE) |
| bioconductor-lapmix |
1.72.0 |
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GPL |
X | X | | X | Laplace Mixture Model in Microarray Experiments |
| bioconductor-lapointe.db |
3.2.3 |
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Artistic-2.0 |
| | | X | A package containing metadata for LAPOINTE arrays |
| bioconductor-lbe |
1.74.0 |
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GPL-2 |
X | X | | X | Estimation of the false discovery rate |
| bioconductor-ldblock |
1.36.0 |
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Artistic-2.0 |
| | | X | data structures for linkage disequilibrium measures in populations |
| bioconductor-lea |
3.18.0 |
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GPL-3 |
X | X | | | LEA: an R package for Landscape and Ecological Association Studies |
| bioconductor-ledpred |
1.40.0 |
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MIT |
| | | X | Learning from DNA to Predict Enhancers |
| bioconductor-leebamviews |
1.42.0 |
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Artistic |
| | | X | leeBamViews -- multiple yeast RNAseq samples excerpted from Lee 2009 |
| bioconductor-lefser |
1.16.0 |
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Artistic-2.0 |
| | | X | R implementation of the LEfSE method for microbiome biomarker discovery |
| bioconductor-lemur |
1.4.0 |
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MIT |
X | X | | | Latent Embedding Multivariate Regression |
| bioconductor-les |
1.56.0 |
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GPL-3 |
X | X | | X | Identifying Differential Effects in Tiling Microarray Data |
| bioconductor-leukemiaseset |
1.42.0 |
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GPL |
| | | X | Leukemia's microarray gene expression data (expressionSet). |
| bioconductor-levi |
1.24.0 |
|
|
GPL |
X | X | | | Landscape Expression Visualization Interface |
| bioconductor-lfa |
2.6.0 |
|
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GPL |
X | X | | | Logistic Factor Analysis for Categorical Data |
| bioconductor-liebermanaidenhic2009 |
0.44.0 |
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LGPL |
| | | X | Selected data from the HiC paper of E. Lieberman-Aiden et al. in Science (2009) |
| bioconductor-limma |
3.62.1 |
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|
GPL |
X | X | | | Linear Models for Microarray and Omics Data |
| bioconductor-limmagui |
1.82.0 |
|
|
GPL |
| | | X | GUI for limma Package With Two Color Microarrays |
| bioconductor-limpca |
1.2.0 |
|
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Artistic-2.0 |
| | | X | An R package for the linear modeling of high-dimensional designed data... |
| bioconductor-linc |
1.15.0 |
|
|
Artistic-2.0 |
X | X | | | co-expression of lincRNAs and protein-coding genes |
| bioconductor-lineagepulse |
1.21.0 |
|
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Artistic-2.0 |
| | | X | Differential expression analysis and model fitting for single-cell RNA-seq data |
| bioconductor-lineagespot |
1.10.0 |
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MIT |
| | | X | Detection of SARS-CoV-2 lineages in wastewater samples using... |
| bioconductor-linkhd |
1.20.0 |
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GPL-3 |
| | | X | LinkHD: a versatile framework to explore and integrate heterogeneous data |
| bioconductor-linnorm |
2.30.0 |
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MIT |
X | X | | | Linear model and normality based normalization and transformation... |
| bioconductor-lintind |
1.10.0 |
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MIT |
| | | X | Lineage tracing by indels |
| bioconductor-lionessr |
1.20.0 |
|
|
MIT |
| | | X | Modeling networks for individual samples using LIONESS |
| bioconductor-lipidr |
2.20.0 |
|
|
MIT |
| | | X | Data Mining and Analysis of Lipidomics Datasets |
| bioconductor-liquidassociation |
1.60.0 |
|
|
GPL |
X | X | | X | LiquidAssociation |
| bioconductor-lisaclust |
1.14.0 |
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|
GPL |
| | | X | lisaClust: Clustering of Local Indicators of Spatial Association |
| bioconductor-listeretalbsseq |
1.38.0 |
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Artistic |
| | | X | BS-seq data of H1 and IMR90 cell line excerpted from Lister et al. 2009 |
| bioconductor-lmdme |
1.48.0 |
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|
GPL |
X | X | | X | Linear Model decomposition for Designed Multivariate Experiments |
| bioconductor-lmgene |
2.43.0 |
|
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LGPL |
X | X | | X | LMGene Software for Data Transformation and Identification of... |
| bioconductor-lobstahs |
1.32.0 |
|
|
GPL |
X | X | | X | Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences |
| bioconductor-loci2path |
1.26.0 |
|
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Artistic-2.0 |
| | | X | Loci2path: regulatory annotation of genomic intervals based on... |
| bioconductor-logicfs |
2.26.0 |
|
|
LGPL |
| | | X | Identification of SNP Interactions |
| bioconductor-logitt |
1.58.0 |
|
|
GPL |
X | X | | | logit-t Package |
| bioconductor-logolas |
1.11.0 |
|
|
GPL |
| | | X | EDLogo Plots Featuring String Logos and Adaptive Scaling of... |
| bioconductor-lol |
1.34.0 |
|
|
GPL-2 |
X | X | | X | Lots Of Lasso |
| bioconductor-lola |
1.36.0 |
|
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GPL-3 |
X | X | | X | Locus overlap analysis for enrichment of genomic ranges |
| bioconductor-loomexperiment |
1.24.0 |
|
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Artistic-2.0 |
| | | X | LoomExperiment container |
| bioconductor-lowmaca |
1.28.0 |
|
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GPL-3 |
| | | X | LowMACA - Low frequency Mutation Analysis via Consensus Alignment |
| bioconductor-lowmacaannotation |
0.99.3 |
|
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GPL-3 |
| | | X | LowMACAAnnotation |
| bioconductor-lpe |
1.80.0 |
|
|
LGPL |
X | X | | X | Methods for analyzing microarray data using Local Pooled Error (LPE) method |
| bioconductor-lpeadj |
1.62.0 |
|
|
LGPL |
X | X | | X | A correction of the local pooled error (LPE) method to replace the... |
| bioconductor-lpnet |
2.38.0 |
|
|
Artistic |
X | X | | X | Linear Programming Model for Network Inference |
| bioconductor-lpsymphony |
1.34.0 |
|
|
EPL |
X | X | | | Symphony integer linear programming solver in R |
| bioconductor-lrbase.ath.eg.db |
2.0.0 |
|
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Artistic-2.0 |
| | | X | Ligand-Receptor list for Arabidopsis thaliana (Ath, Thale cress,... |
| bioconductor-lrbase.bta.eg.db |
2.0.0 |
|
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Artistic-2.0 |
| | | X | Ligand-Receptor list for Bos taurus (Bta, Cow, Taxonomy ID: 9913) |
| bioconductor-lrbase.cel.eg.db |
2.0.0 |
|
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Artistic-2.0 |
| | | X | Ligand-Receptor list for Caenorhabditis elegans (Cel, Worm, Taxonomy ID: 6239) |
| bioconductor-lrbase.dme.eg.db |
2.0.0 |
|
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Artistic-2.0 |
| | | X | Ligand-Receptor list for Drosophila melanogaster (Dme, Fruit fly,... |
| bioconductor-lrbase.dre.eg.db |
2.0.0 |
|
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Artistic-2.0 |
| | | X | Ligand-Receptor list for Danio rerio (Dre, Zebrafish, Taxonomy ID: 7955) |
| bioconductor-lrbase.gga.eg.db |
2.0.0 |
|
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Artistic-2.0 |
| | | X | Ligand-Receptor list for Gallus gallus (Gga, Chicken, Taxonomy ID: 9031) |
| bioconductor-lrbase.hsa.eg.db |
2.0.0 |
|
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Artistic-2.0 |
| | | X | Ligand-Receptor list for Homo sapiens (Hsa, Human, Taxonomy ID: 9606) |
| bioconductor-lrbase.mmu.eg.db |
2.0.0 |
|
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Artistic-2.0 |
| | | X | Ligand-Receptor list for Mus musculus (Mmu, Mouse, Taxonomy ID: 10090) |
| bioconductor-lrbase.pab.eg.db |
2.0.0 |
|
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Artistic-2.0 |
| | | X | Ligand-Receptor list for Pongo abelii (Pab, Orangutan, Taxonomy ID: 9601) |
| bioconductor-lrbase.rno.eg.db |
2.0.0 |
|
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Artistic-2.0 |
| | | X | Ligand-Receptor list for Rattus norvegicus (Rno, Rat, Taxonomy ID: 10116) |
| bioconductor-lrbase.ssc.eg.db |
2.0.0 |
|
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Artistic-2.0 |
| | | X | Ligand-Receptor list for Sus scrofa (Ssc, Pig, Taxonomy ID: 9823) |
| bioconductor-lrbase.xtr.eg.db |
2.0.0 |
|
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Artistic-2.0 |
| | | X | Ligand-Receptor list for Xenopus tropicalis (Xtr, Tropical clawed frog,... |
| bioconductor-lrbasedbi |
2.16.0 |
|
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Artistic-2.0 |
| | | X | DBI to construct LRBase-related package |
| bioconductor-lrcell |
1.14.0 |
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|
MIT |
| | | X | Differential cell type change analysis using Logistic/linear Regression |
| bioconductor-lrcelltypemarkers |
1.14.0 |
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|
MIT |
| | | X | Marker gene information for LRcell R Bioconductor package |
| bioconductor-lumi |
2.58.0 |
|
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LGPL |
X | X | | X | BeadArray Specific Methods for Illumina Methylation and Expression Microarrays |
| bioconductor-lumibarnes |
1.46.0 |
|
|
LGPL |
| | | X | Barnes Benchmark Illumina Tissues Titration Data |
| bioconductor-lumihumanall.db |
1.22.0 |
|
|
Artistic-2.0 |
X | X | | X | Illumina Human Illumina expression annotation data (chip lumiHumanAll) |
| bioconductor-lumihumanidmapping |
1.10.1 |
|
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The |
| | | X | Illumina Identifier mapping for Human |
| bioconductor-lumimouseall.db |
1.22.0 |
|
|
Artistic-2.0 |
| | | X | Illumina Mouse Illumina expression annotation data (chip lumiMouseAll) |
| bioconductor-lumimouseidmapping |
1.10.0 |
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The |
| | | X | Illumina Identifier mapping for Mouse |
| bioconductor-lumiratall.db |
1.22.0 |
|
|
Artistic-2.0 |
| | | X | Illumina Rat Illumina expression annotation data (chip lumiRatAll) |
| bioconductor-lumiratidmapping |
1.10.0 |
|
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The |
| | | X | Illumina Identifier mapping for Rat |
| bioconductor-lungcanceracvssccgeo |
1.42.0 |
|
|
GPL-2 |
X | X | | X | A lung cancer dataset that can be used with maPredictDSC package for... |
| bioconductor-lungcancerlines |
0.44.0 |
|
|
Artistic-2.0 |
| | | X | Reads from Two Lung Cancer Cell Lines |
| bioconductor-lungexpression |
0.44.0 |
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|
GPL |
| | | X | ExpressionSets for Parmigiani et al., 2004 Clinical Cancer Research paper |
| bioconductor-lute |
1.2.0 |
|
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Artistic-2.0 |
| | | X | Framework for cell size scale factor normalized bulk transcriptomics... |
| bioconductor-lvsmirna |
1.36.0 |
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GPL-2 |
X | X | | | LVS normalization for Agilent miRNA data |
| bioconductor-lydata |
1.32.0 |
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MIT |
| | | X | Example Dataset for crossmeta Package |
| bioconductor-lymphoseq |
1.34.0 |
|
|
Artistic-2.0 |
| | | X | Analyze high-throughput sequencing of T and B cell receptors |
| bioconductor-lymphoseqdb |
0.99.2 |
|
|
Artistic-2.0 |
| | | X | LymphoSeq annotation databases |
| bioconductor-m10kcod.db |
3.4.0 |
|
|
Artistic-2.0 |
| | | X | Codelink UniSet Mouse I Bioarray (~10 000 mouse gene targets)... |
| bioconductor-m20kcod.db |
3.4.0 |
|
|
Artistic-2.0 |
| | | X | Codelink UniSet Mouse 20k I Bioarray annotation data (chip m20kcod) |
| bioconductor-m3c |
1.28.0 |
|
|
AGPL-3 |
| | | X | Monte Carlo Reference-based Consensus Clustering |
| bioconductor-m3d |
1.22.0 |
|
|
Artistic |
X | X | | | Identifies differentially methylated regions across testing groups |
| bioconductor-m3dexampledata |
1.32.0 |
|
|
GPL |
| | | X | M3Drop Example Data |
| bioconductor-m3drop |
1.32.0 |
|
|
GPL |
X | X | | X | Michaelis-Menten Modelling of Dropouts in single-cell RNASeq |
| bioconductor-m6aboost |
1.12.0 |
|
|
Artistic-2.0 |
| | | X | m6Aboost |
| bioconductor-maanova |
1.68.0 |
|
|
GPL |
X | X | | | Tools for analyzing Micro Array experiments |
| bioconductor-maaslin2 |
1.18.0 |
|
|
MIT |
| | | X | "Multivariable Association Discovery in Population-scale Meta-omics... |
| bioconductor-macarron |
1.6.0 |
|
|
MIT |
| | | X | Prioritization of potentially bioactive metabolic features from... |
| bioconductor-macat |
1.76.0 |
|
|
Artistic-2.0 |
X | X | | X | MicroArray Chromosome Analysis Tool |
| bioconductor-macorrplot |
1.76.0 |
|
|
GPL |
X | X | | X | Visualize artificial correlation in microarray data |
| bioconductor-macpet |
1.14.0 |
|
|
GPL-3 |
X | X | | | Model based analysis for paired-end data |
| bioconductor-macrophage |
1.22.0 |
|
|
GPL |
| | | X | Human macrophage immune response |
| bioconductor-macsdata |
1.14.0 |
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|
file |
| | | X | Test datasets for the MACSr package |
| bioconductor-macsquantifyr |
1.20.0 |
|
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Artistic-2.0 |
| | | X | Fast treatment of MACSQuantify FACS data |
| bioconductor-macsr |
1.14.0 |
|
|
BSD_3_clause |
| | | X | MACS: Model-based Analysis for ChIP-Seq |
| bioconductor-made4 |
1.80.0 |
|
|
Artistic-2.0 |
X | X | | X | Multivariate analysis of microarray data using ADE4 |
| bioconductor-madseq |
1.32.0 |
|
|
GPL(>=2) |
X | X | | X | Mosaic Aneuploidy Detection and Quantification using Massive Parallel... |
| bioconductor-mafdb.1kgenomes.phase1.grch38 |
3.10.0 |
|
|
Artistic-2.0 |
| | | X | Minor allele frequency data from 1000 Genomes Phase 1 for GRCh38 |
| bioconductor-mafdb.1kgenomes.phase1.hs37d5 |
3.10.0 |
|
|
Artistic-2.0 |
| | | X | Minor allele frequency data from 1000 Genomes Phase 1 for hs37d5 |
| bioconductor-mafdb.1kgenomes.phase3.grch38 |
3.10.0 |
|
|
Artistic-2.0 |
| | | X | Minor allele frequency data from 1000 Genomes Phase 3 for GRCh38 |
| bioconductor-mafdb.1kgenomes.phase3.hs37d5 |
3.10.0 |
|
|
Artistic-2.0 |
| | | X | Minor allele frequency data from 1000 Genomes Phase 3 for hs37d5 |
| bioconductor-mafdb.esp6500si.v2.ssa137.grch38 |
3.10.0 |
|
|
Artistic-2.0 |
| | | X | Minor allele frequency data from NHLBI ESP for GRCh38 |
| bioconductor-mafdb.esp6500si.v2.ssa137.hs37d5 |
3.10.0 |
|
|
Artistic-2.0 |
| | | X | Minor allele frequency data from NHLBI ESP for hs37d5 |
| bioconductor-mafdb.exac.r1.0.grch38 |
3.10.0 |
|
|
Artistic-2.0 |
| | | X | Minor allele frequency data from ExAC release 1.0 for GRCh38 |
| bioconductor-mafdb.exac.r1.0.hs37d5 |
3.10.0 |
|
|
Artistic-2.0 |
| | | X | Minor allele frequency data from ExAC release 1.0 for hs37d5 |
| bioconductor-mafdb.exac.r1.0.nontcga.grch38 |
3.10.0 |
|
|
Artistic-2.0 |
| | | X | Minor allele frequency data from ExAC release 1.0 subset of nonTCGA... |
| bioconductor-mafdb.exac.r1.0.nontcga.hs37d5 |
3.10.0 |
|
|
Artistic-2.0 |
| | | X | Minor allele frequency data from ExAC release 1.0 subset of nonTCGA... |
| bioconductor-mafdb.gnomad.r2.0.1.grch38 |
3.9.0 |
|
|
Artistic-2.0 |
| | | X | Store minor allele frequency data from the Genome Aggregation Database... |
| bioconductor-mafdb.gnomad.r2.0.1.hs37d5 |
3.8.0 |
|
|
Artistic-2.0 |
| | | X | Store minor allele frequency data from the Genome Aggregation Database... |
| bioconductor-mafdb.gnomad.r2.1.grch38 |
3.10.0 |
|
|
Artistic-2.0 |
| | | X | Minor allele frequency data from gnomAD release 2.1 for GRCh38 |
| bioconductor-mafdb.gnomad.r2.1.hs37d5 |
3.10.0 |
|
|
Artistic-2.0 |
| | | X | Minor allele frequency data from gnomAD release 2.1 for hs37d5 |
| bioconductor-mafdb.gnomad.r3.0.grch38 |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Minor allele frequency data from gnomAD release 3.0 for GRCh38 |
| bioconductor-mafdb.gnomadex.r2.0.1.grch38 |
3.9.0 |
|
|
Artistic-2.0 |
| | | X | Store minor allele frequency data from the Genome Aggregation Database... |
| bioconductor-mafdb.gnomadex.r2.0.1.hs37d5 |
3.8.0 |
|
|
Artistic-2.0 |
| | | X | Store minor allele frequency data from the Genome Aggregation Database... |
| bioconductor-mafdb.gnomadex.r2.1.grch38 |
3.10.0 |
|
|
Artistic-2.0 |
| | | X | Minor allele frequency data from gnomAD exomes release 2.1 for GRCh38 |
| bioconductor-mafdb.gnomadex.r2.1.hs37d5 |
3.10.0 |
|
|
Artistic-2.0 |
| | | X | Minor allele frequency data from gnomAD exomes release 2.1 for hs37d5 |
| bioconductor-mafdb.topmed.freeze5.hg19 |
3.10.0 |
|
|
Artistic-2.0 |
| | | X | Minor allele frequency data from TOPMed for hg19 |
| bioconductor-mafdb.topmed.freeze5.hg38 |
3.10.0 |
|
|
Artistic-2.0 |
| | | X | Minor allele frequency data from TOPMed for hg38 |
| bioconductor-mafh5.gnomad.r3.0.grch38 |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Minor allele frequency data from gnomAD release 3.0 for GRCh38 stored... |
| bioconductor-mafh5.gnomad.v3.1.1.grch38 |
3.13.1 |
|
|
Artistic-2.0 |
| | | X | Minor allele frequency data from gnomAD version 3.1.1 for GRCh38 |
| bioconductor-mafh5.gnomad.v3.1.2.grch38 |
3.15.0 |
|
|
Artistic-2.0 |
| | | X | Minor allele frequency data from gnomAD version 3.1.2 for GRCh38 |
| bioconductor-maftools |
2.22.0 |
|
|
MIT |
X | X | | X | Summarize, Analyze and Visualize MAF Files |
| bioconductor-magar |
1.14.0 |
|
|
GPL-3 |
| | | X | MAGAR: R-package to compute methylation Quantitative Trait Loci... |
| bioconductor-mageckflute |
2.9.0 |
|
|
GPL |
| | | X | Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens |
| bioconductor-magpie |
1.6.0 |
|
|
MIT |
| | | X | MeRIP-Seq data Analysis for Genomic Power Investigation and Evaluation |
| bioconductor-magrene |
1.8.0 |
|
|
GPL-3 |
| | | X | Motif Analysis In Gene Regulatory Networks |
| bioconductor-mai |
1.12.0 |
|
|
GPL-3 |
| | | X | Mechanism-Aware Imputation |
| bioconductor-maigespack |
1.64.0 |
|
|
GPL-3.0-or-later |
X | X | | | Functions to handle cDNA microarray data, including several methods of... |
| bioconductor-mait |
1.40.0 |
|
|
GPL-2 |
X | X | | | Statistical Analysis of Metabolomic Data |
| bioconductor-maizecdf |
2.18.0 |
|
|
LGPL |
| | | X | maizecdf |
| bioconductor-maizeprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type maize |
| bioconductor-makecdfenv |
1.82.0 |
|
|
GPL |
X | X | | | CDF Environment Maker |
| bioconductor-malaria.db0 |
3.20.0 |
|
|
Artistic-2.0 |
| | | X | Base Level Annotation databases for malaria |
| bioconductor-mammaprintdata |
1.42.0 |
|
|
Artistic-2.0 |
| | | X | RGLists from the Glas and Buyse breast cancer studies |
| bioconductor-manor |
1.78.0 |
|
|
GPL-2 |
X | X | | | CGH Micro-Array NORmalization |
| bioconductor-manta |
1.32.0 |
|
|
Artistic-2.0 |
X | X | | X | Microbial Assemblage Normalized Transcript Analysis |
| bioconductor-mantelcorr |
1.76.0 |
|
|
GPL |
X | X | | X | Compute Mantel Cluster Correlations |
| bioconductor-mapkl |
1.28.0 |
|
|
GPL |
X | | | X | A Hybrid Feature Selection method for gene expression data |
| bioconductor-mapkldata |
1.34.0 |
|
|
Artistic-2.0 |
| | | X | Gene expression data for testing of the package mAPKL. |
| bioconductor-mapredictdsc |
1.44.0 |
|
|
GPL-2 |
X | X | | X | Phenotype prediction using microarray data: approach of the best... |
| bioconductor-mapscape |
1.30.0 |
|
|
GPL-3 |
| | | X | mapscape |
| bioconductor-maqcexpression4plex |
1.50.0 |
|
|
GPL |
| | | X | Sample Expression Data - MAQC / HG18 - NimbleGen |
| bioconductor-maqcsubset |
1.44.0 |
|
|
Artistic-2.0 |
| | | X | Experimental Data Package: MAQCsubset |
| bioconductor-maqcsubsetafx |
1.30.0 |
|
|
Artistic-2.0 |
| | | X | MAQC data subset for the Affymetrix platform |
| bioconductor-maqcsubsetilm |
1.40.0 |
|
|
Artistic-2.0 |
| | | X | MAQC data subset for the Illumina platform |
| bioconductor-mariner |
1.6.0 |
|
|
GPL-3 |
| | | X | Mariner: Explore the Hi-Cs |
| bioconductor-marinerdata |
1.6.0 |
|
|
GPL-3 |
| | | X | ExperimentHub data for the mariner package |
| bioconductor-marr |
1.16.0 |
|
|
GPL |
X | X | | | Maximum rank reproducibility |
| bioconductor-marray |
1.84.0 |
|
|
LGPL |
X | X | | X | Exploratory analysis for two-color spotted microarray data |
| bioconductor-martini |
1.26.0 |
|
|
GPL-3 |
X | X | | | GWAS Incorporating Networks |
| bioconductor-maser |
1.24.0 |
|
|
MIT |
| | | X | Mapping Alternative Splicing Events to pRoteins |
| bioconductor-masigpro |
1.78.0 |
|
|
GPL |
X | X | | X | Significant Gene Expression Profile Differences in Time Course Gene... |
| bioconductor-maskbad |
1.50.0 |
|
|
GPL |
X | X | | X | Masking probes with binding affinity differences |
| bioconductor-massarray |
1.58.0 |
|
|
GPL |
X | X | | X | Analytical Tools for MassArray Data |
| bioconductor-massir |
1.42.0 |
|
|
GPL-3 |
X | X | | X | massiR: MicroArray Sample Sex Identifier |
| bioconductor-massspecwavelet |
1.72.0 |
|
|
LGPL |
X | X | | | Peak Detection for Mass Spectrometry data using wavelet-based algorithms |
| bioconductor-mast |
1.32.0 |
|
|
GPL(>= |
X | X | | X | Model-based Analysis of Single Cell Transcriptomics |
| bioconductor-mastr |
1.6.0 |
|
|
MIT |
| | | X | Markers Automated Screening Tool in R |
| bioconductor-matchbox |
1.48.0 |
|
|
Artistic-2.0 |
| | | X | Utilities to compute, compare, and plot the agreement between ordered... |
| bioconductor-matrixgenerics |
1.18.0 |
|
|
Artistic-2.0 |
| | | X | S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects |
| bioconductor-matrixqcvis |
1.14.0 |
|
|
GPL-3 |
| | | X | Shiny-based interactive data-quality exploration for omics data |
| bioconductor-matrixrider |
1.38.0 |
|
|
GPL-3 |
X | X | | | Obtain total affinity and occupancies for binding site matrices on a... |
| bioconductor-matter |
2.8.0 |
|
|
Artistic-2.0 |
X | X | | | Out-of-core statistical computing and signal processing |
| bioconductor-maxcontrastprojection |
1.11.0 |
|
|
Artistic-2.0 |
| | | X | Perform a maximum contrast projection of 3D images along the z-dimension into 2D |
| bioconductor-mbamethyl |
1.40.0 |
|
|
Artistic-2.0 |
X | X | | X | Model-based analysis of DNA methylation data |
| bioconductor-mbased |
1.40.0 |
|
|
Artistic-2.0 |
X | X | | X | Package containing functions for ASE analysis using Meta-analysis Based... |
| bioconductor-mbcb |
1.60.0 |
|
|
GPL |
| | | X | MBCB (Model-based Background Correction for Beadarray) |
| bioconductor-mbecs |
1.10.0 |
|
|
Artistic-2.0 |
| | | X | Evaluation and correction of batch effects in microbiome data-sets |
| bioconductor-mbkmeans |
1.22.0 |
|
|
MIT |
X | X | | | Mini-batch K-means Clustering for Single-Cell RNA-seq |
| bioconductor-mbomic |
1.3.0 |
|
|
Artistic-2.0 |
| | | X | Integrative analysis of the microbiome and metabolome |
| bioconductor-mbpcr |
1.60.0 |
|
|
GPL |
| | | X | Bayesian Piecewise Constant Regression for DNA copy number estimation |
| bioconductor-mbqn |
2.18.0 |
|
|
GPL-3 |
| | | X | Mean/Median-balanced quantile normalization |
| bioconductor-mbqtl |
1.2.0 |
|
|
MIT |
| | | X | mbQTL: A package for SNP-Taxa mGWAS analysis |
| bioconductor-mbttest |
1.34.0 |
|
|
GPL-3 |
X | X | | X | Multiple Beta t-Tests |
| bioconductor-mcagui |
1.37.0 |
|
|
GPL |
| | | X | Microbial Community Analysis GUI |
| bioconductor-mcbiclust |
1.30.0 |
|
|
GPL-2 |
| | | X | Massive correlating biclusters for gene expression data and associated methods |
| bioconductor-mcrestimate |
2.42.0 |
|
|
GPL |
X | X | | X | Misclassification error estimation with cross-validation |
| bioconductor-mcsea |
1.22.0 |
|
|
GPL-2 |
| | | X | Methylated CpGs Set Enrichment Analysis |
| bioconductor-mcseadata |
1.26.1 |
|
|
GPL-2 |
| | | X | Data package for mCSEA package |
| bioconductor-mcsurvdata |
1.24.0 |
|
|
GPL |
| | | X | Meta cohort survival data |
| bioconductor-mdgsa |
1.22.0 |
|
|
GPL |
X | X | | X | Multi Dimensional Gene Set Analysis. |
| bioconductor-mdp |
1.26.0 |
|
|
GPL-3 |
| | | X | Molecular Degree of Perturbation calculates scores for transcriptome... |
| bioconductor-mdqc |
1.68.0 |
|
|
LGPL |
X | X | | X | Mahalanobis Distance Quality Control for microarrays |
| bioconductor-mdts |
1.26.0 |
|
|
Artistic-2.0 |
| | | X | Detection of de novo deletion in targeted sequencing trios |
| bioconductor-meal |
1.28.0 |
|
|
Artistic-2.0 |
| | | X | Perform methylation analysis |
| bioconductor-measurementerror.cor |
1.78.0 |
|
|
LGPL |
X | X | | X | Measurement Error model estimate for correlation coefficient |
| bioconductor-meat |
1.18.0 |
|
|
MIT |
| | | X | Muscle Epigenetic Age Test |
| bioconductor-meb |
1.20.0 |
|
|
GPL-2 |
| | | X | A normalization-invariant minimum enclosing ball method to detect... |
| bioconductor-medicagocdf |
2.18.0 |
|
|
LGPL |
| | | X | medicagocdf |
| bioconductor-medicagoprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type medicago |
| bioconductor-medips |
1.58.0 |
|
|
GPL |
X | X | | X | DNA IP-seq data analysis |
| bioconductor-medipsdata |
1.42.0 |
|
|
GPL |
| | | X | Example data for MEDIPS and QSEA packages |
| bioconductor-medme |
1.66.0 |
|
|
GPL |
X | X | | | Modelling Experimental Data from MeDIP Enrichment |
| bioconductor-meebodata |
1.44.0 |
|
|
LGPL |
| | | X | MEEBO set and MEEBO controls. |
| bioconductor-megadepth |
1.16.0 |
|
|
Artistic-2.0 |
| | | X | megadepth: BigWig and BAM related utilities |
| bioconductor-meigor |
1.40.0 |
|
|
GPL-3 |
X | X | | X | MEIGOR - MEtaheuristics for bIoinformatics Global Optimization |
| bioconductor-melissa |
1.22.0 |
|
|
GPL-3 |
| | | X | Bayesian clustering and imputationa of single cell methylomes |
| bioconductor-memes |
1.14.0 |
|
|
MIT |
| | | X | motif matching, comparison, and de novo discovery using the MEME Suite |
| bioconductor-merfishdata |
1.8.0 |
|
|
Artistic-2.0 |
| | | X | Collection of public MERFISH datasets |
| bioconductor-mergemaid |
2.59.0 |
|
|
GPL |
X | X | | X | Merge Maid |
| bioconductor-mergeomics |
1.34.0 |
|
|
GPL |
X | X | | X | Integrative network analysis of omics data |
| bioconductor-mesh.aca.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Anolis carolinensis Gene ID to MeSH |
| bioconductor-mesh.aga.pest.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Anopheles gambiae str. PEST Gene ID to MeSH |
| bioconductor-mesh.ame.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Ailuropoda melanoleuca Gene ID to MeSH |
| bioconductor-mesh.aml.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Apis mellifera Gene ID to MeSH |
| bioconductor-mesh.ana.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Filamentos cyanobacteria Gene ID to MeSH |
| bioconductor-mesh.ani.fgsc.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Aspergillus nidulans FGSC A4 Gene ID to MeSH |
| bioconductor-mesh.aor.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | A set of annotation maps describing the entire MeSH |
| bioconductor-mesh.ath.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Arabidopsis thaliana Gene ID to MeSH |
| bioconductor-mesh.bfl.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Branchiostoma floridae Gene ID to MeSH |
| bioconductor-mesh.bsu.168.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Bacillus subtilis subsp. spizizenii str. 168 Gene ID to MeSH |
| bioconductor-mesh.bta.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Bos taurus Gene ID to MeSH |
| bioconductor-mesh.cal.sc5314.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Candida albicans SC5314 Gene ID to MeSH |
| bioconductor-mesh.cbr.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Caenorhabditis briggsae Gene ID to MeSH |
| bioconductor-mesh.cel.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Caenorhabditis elegans Gene ID to MeSH |
| bioconductor-mesh.cfa.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Canis familiaris Gene ID to MeSH |
| bioconductor-mesh.cin.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Ciona intestinalis Gene ID to MeSH |
| bioconductor-mesh.cja.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Callithrix jacchus Gene ID to MeSH |
| bioconductor-mesh.cpo.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Cavia porcellus Gene ID to MeSH |
| bioconductor-mesh.cre.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Caenorhabditis remani Gene ID to MeSH |
| bioconductor-mesh.dan.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Drosophila ananassae Gene ID to MeSH |
| bioconductor-mesh.db |
1.15.0 |
|
|
Artistic-2.0 |
X | X | | X | A set of annotation maps describing the entire MeSH |
| bioconductor-mesh.dda.3937.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Dickeya dadantii 3937 Gene ID to MeSH |
| bioconductor-mesh.ddi.ax4.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Dictyostelium discoideum AX4 Gene ID to MeSH |
| bioconductor-mesh.der.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Drosophila eracta Gene ID to MeSH |
| bioconductor-mesh.dgr.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Drosophila grimshawi Gene ID to MeSH |
| bioconductor-mesh.dme.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Drosophila melanogaster Gene ID to MeSH |
| bioconductor-mesh.dmo.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Drosophila mojavensis Gene ID to MeSH |
| bioconductor-mesh.dpe.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Drosophila persimilis Gene ID to MeSH |
| bioconductor-mesh.dre.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Danio rerio Gene ID to MeSH |
| bioconductor-mesh.dse.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Drosophila sechellia Gene ID to MeSH |
| bioconductor-mesh.dsi.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Drosophila simulans Gene ID to MeSH |
| bioconductor-mesh.dvi.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Drosophila virllis Gene ID to MeSH |
| bioconductor-mesh.dya.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Drosophila yakuba Gene ID to MeSH |
| bioconductor-mesh.eca.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Equus caballus Gene ID to MeSH |
| bioconductor-mesh.eco.55989.eg.db |
1.13.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Escherichia coli 55989 Gene ID to MeSH |
| bioconductor-mesh.eco.ed1a.eg.db |
1.13.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Escherichia coli ED1a Gene ID to MeSH |
| bioconductor-mesh.eco.iai39.eg.db |
1.13.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Escherichia coli IAI39 Gene ID to MeSH |
| bioconductor-mesh.eco.k12.mg1655.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Escherichia coli str K-12 substr. MG1655 Gene ID to MeSH |
| bioconductor-mesh.eco.o157.h7.sakai.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Escherichia coli O157:H7 Sakai Gene ID to MeSH |
| bioconductor-mesh.eco.umn026.eg.db |
1.13.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Escherichia coli UMN026 Gene ID to MeSH |
| bioconductor-mesh.eqc.eg.db |
1.13.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Equus caballus Gene ID to MeSH |
| bioconductor-mesh.gga.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Gallus gallus Gene ID to MeSH |
| bioconductor-mesh.gma.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Glycine max Gene ID to MeSH |
| bioconductor-mesh.hsa.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Homo sapiens Gene ID to MeSH |
| bioconductor-mesh.laf.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Loxodonta africana Gene ID to MeSH |
| bioconductor-mesh.lma.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Leishmania major strain Friedlin Gene ID to MeSH |
| bioconductor-mesh.mdo.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Monodelphis domestica Gene ID to MeSH |
| bioconductor-mesh.mes.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for NA Gene ID to MeSH |
| bioconductor-mesh.mga.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Meleagris gallopavo Gene ID to MeSH |
| bioconductor-mesh.miy.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Lotus japonicus Gene ID to MeSH |
| bioconductor-mesh.mml.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Macaca mulatta Gene ID to MeSH |
| bioconductor-mesh.mmu.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Mus musculus Gene ID to MeSH |
| bioconductor-mesh.mtr.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Medicago truncatula Gene ID to MeSH |
| bioconductor-mesh.nle.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Nomascus leucogenys Gene ID to MeSH |
| bioconductor-mesh.oan.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Ornithorhynchus anatinus Gene ID to MeSH |
| bioconductor-mesh.ocu.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Oryctolagus cuniculus Gene ID to MeSH |
| bioconductor-mesh.oni.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Oreochromis niloticus Gene ID to MeSH |
| bioconductor-mesh.osa.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Oryza sativa Japonica Gene ID to MeSH |
| bioconductor-mesh.pab.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Pongo abelii Gene ID to MeSH |
| bioconductor-mesh.pae.pao1.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Pseudomonas aeruginosa PAO1 Gene ID to MeSH |
| bioconductor-mesh.pcr.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | A set of annotation maps describing the entire MeSH |
| bioconductor-mesh.pfa.3d7.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Plasmodium falciparum 3D7 Gene ID to MeSH |
| bioconductor-mesh.pto.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Pan troglodytes Gene ID to MeSH |
| bioconductor-mesh.ptr.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Populus trichocarpa Gene ID to MeSH |
| bioconductor-mesh.rno.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Rattus norvegicus Gene ID to MeSH |
| bioconductor-mesh.sce.s288c.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Saccharomyces cerevisiae S288c Gene ID to MeSH |
| bioconductor-mesh.sco.a32.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Streptomyces coelicolor A3(2) Gene ID to MeSH |
| bioconductor-mesh.sil.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Bombyx mori Gene ID to MeSH |
| bioconductor-mesh.spu.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Strongylocentrotus purpuratus Gene ID to MeSH |
| bioconductor-mesh.ssc.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Sus scrofa Gene ID to MeSH |
| bioconductor-mesh.syn.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Cyanobacteria Gene ID to MeSH |
| bioconductor-mesh.tbr.9274.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Trypanosoma brucei brucei strain 927_4 GUTat10.1 Gene... |
| bioconductor-mesh.tgo.me49.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Toxoplasma gondii ME49 Gene ID to MeSH |
| bioconductor-mesh.tgu.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Taeniopygia guttata Gene ID to MeSH |
| bioconductor-mesh.vvi.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Vitis vinifera Gene ID to MeSH |
| bioconductor-mesh.xla.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Xenopus tropicalis Gene ID to MeSH |
| bioconductor-mesh.xtr.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Xenopus tropicalis Gene ID to MeSH |
| bioconductor-mesh.zma.eg.db |
1.15.0 |
|
|
Artistic-2.0 |
| | | X | Mapping table for Zea mays Gene ID to MeSH |
| bioconductor-meshdbi |
1.42.0 |
|
|
Artistic-2.0 |
X | X | | X | DBI to construct MeSH-related package from sqlite file |
| bioconductor-meshes |
1.32.0 |
|
|
Artistic-2.0 |
X | X | | X | MeSH Enrichment and Semantic analyses |
| bioconductor-meshr |
2.12.0 |
|
|
Artistic-2.0 |
| | | X | Tools for conducting enrichment analysis of MeSH |
| bioconductor-meshsim |
1.7.0 |
|
|
GPL-2 |
X | X | | | Provide for measuring semantic similarity over MeSH headings and... |
| bioconductor-meskit |
1.16.0 |
|
|
GPL-3 |
| | | X | A tool kit for dissecting cancer evolution from multi-region derived... |
| bioconductor-messina |
1.42.0 |
|
|
EPL |
X | X | | | Single-gene classifiers and outlier-resistant detection of differential... |
| bioconductor-metaarray |
1.66.0 |
|
|
LGPL-2 |
X | X | | | Integration of Microarray Data for Meta-analysis |
| bioconductor-metab |
1.33.0 |
|
|
GPL |
X | X | | X | Metab: An R Package for a High-Throughput Analysis of Metabolomics Data... |
| bioconductor-metabcombiner |
1.16.0 |
|
|
GPL-3 |
X | X | | | Method for Combining LC-MS Metabolomics Feature Measurements |
| bioconductor-metabinr |
1.8.0 |
|
|
GPL-3 |
| | | X | Abundance and Compositional Based Binning of Metagenomes |
| bioconductor-metaboannotation |
1.10.0 |
|
|
Artistic-2.0 |
| | | X | Utilities for Annotation of Metabolomics Data |
| bioconductor-metabocoreutils |
1.14.0 |
|
|
Artistic-2.0 |
| | | X | Core Utils for Metabolomics Data |
| bioconductor-metaboliteidmapping |
1.0.0 |
|
|
GPL-3 |
| | | X | Mapping of Metabolite IDs from Different Sources |
| bioconductor-metabolomicsworkbenchr |
1.16.0 |
|
|
GPL-3 |
| | | X | Metabolomics Workbench in R |
| bioconductor-metabomxtr |
1.40.0 |
|
|
GPL-2 |
| | | X | A package to run mixture models for truncated metabolomics data with... |
| bioconductor-metabosignal |
1.32.0 |
|
|
GPL-3 |
X | X | | X | MetaboSignal: a network-based approach to overlay and explore metabolic... |
| bioconductor-metacca |
1.34.0 |
|
|
MIT |
X | X | | X | Summary Statistics-Based Multivariate Meta-Analysis of Genome-Wide... |
| bioconductor-metacyto |
1.28.0 |
|
|
GPL |
| | | X | MetaCyto: A package for meta-analysis of cytometry data |
| bioconductor-metagene |
2.31.0 |
|
|
Artistic-2.0 |
| | | X | A package to produce metagene plots |
| bioconductor-metagene2 |
1.22.0 |
|
|
Artistic-2.0 |
| | | X | A package to produce metagene plots |
| bioconductor-metagenomefeatures |
2.10.0 |
|
|
Artistic-2.0 |
| | | X | Exploration of marker-gene sequence taxonomic annotations |
| bioconductor-metagenomeseq |
1.43.0 |
|
|
Artistic-2.0 |
X | X | | X | Statistical analysis for sparse high-throughput sequencing |
| bioconductor-metagxbreast |
1.26.0 |
|
|
Apache |
| | | X | Transcriptomic Breast Cancer Datasets |
| bioconductor-metagxovarian |
1.26.0 |
|
|
Artistic-2.0 |
| | | X | Transcriptomic Ovarian Cancer Datasets |
| bioconductor-metagxpancreas |
1.26.0 |
|
|
Artistic-2.0 |
| | | X | Transcriptomic Pancreatic Cancer Datasets |
| bioconductor-metahdep |
1.64.0 |
|
|
GPL-3 |
X | X | | | Hierarchical Dependence in Meta-Analysis |
| bioconductor-metams |
1.42.0 |
|
|
GPL |
X | X | | X | MS-based metabolomics annotation pipeline |
| bioconductor-metamsdata |
1.42.0 |
|
|
GPL |
| | | X | Example CDF data for the metaMS package |
| bioconductor-metaneighbor |
1.26.0 |
|
|
MIT |
X | X | | X | Single cell replicability analysis |
| bioconductor-metaphor |
1.8.0 |
|
|
Artistic-2.0 |
| | | X | Metabolic Pathway Analysis of RNA |
| bioconductor-metapod |
1.14.0 |
|
|
GPL-3 |
X | X | | | Meta-Analyses on P-Values of Differential Analyses |
| bioconductor-metapone |
1.12.0 |
|
|
Artistic-2.0 |
| | | X | Conducts pathway test of metabolomics data using a weighted permutation test |
| bioconductor-metascope |
1.2.0 |
|
|
GPL |
| | | X | Tools and functions for preprocessing 16S and metagenomic sequencing... |
| bioconductor-metaseq |
1.46.0 |
|
|
Artistic-2.0 |
X | X | | | Meta-analysis of RNA-Seq count data in multiple studies |
| bioconductor-metaseqr |
1.28.0 |
|
|
GPL |
| | | X | An R package for the analysis and result reporting of RNA-Seq data by... |
| bioconductor-metaseqr2 |
1.18.0 |
|
|
GPL |
X | X | | X | An R package for the analysis and result reporting of RNA-Seq data by... |
| bioconductor-metavizr |
1.21.0 |
|
|
MIT |
X | X | | X | R Interface to the metaviz web app for interactive metagenomics data... |
| bioconductor-metavolcanor |
1.14.0 |
|
|
GPL-3 |
| | | X | Gene Expression Meta-analysis Visualization Tool |
| bioconductor-metcirc |
1.36.0 |
|
|
GPL |
X | X | | X | Navigating mass spectral similarity in high-resolution MS/MS... |
| bioconductor-methcp |
1.11.0 |
|
|
Artistic-2.0 |
| | | X | Differential methylation anlsysis for bisulfite sequencing data |
| bioconductor-methimpute |
1.28.0 |
|
|
Artistic-2.0 |
X | X | | | Imputation-guided re-construction of complete methylomes from WGBS data |
| bioconductor-methinheritsim |
1.28.0 |
|
|
Artistic-2.0 |
| | | X | Simulating Whole-Genome Inherited Bisulphite Sequencing Data |
| bioconductor-methped |
1.34.0 |
|
|
GPL-2 |
X | X | | X | A DNA methylation classifier tool for the identification of pediatric... |
| bioconductor-methreg |
1.12.0 |
|
|
GPL-3 |
| | | X | Assessing the regulatory potential of DNA methylation regions or sites... |
| bioconductor-methrix |
1.20.0 |
|
|
MIT |
| | | X | Fast and efficient summarization of generic bedGraph files from... |
| bioconductor-methtargetedngs |
1.38.0 |
|
|
Artistic-2.0 |
X | X | | X | Perform Methylation Analysis on Next Generation Sequencing Data |
| bioconductor-methvisual |
1.39.0 |
|
|
GPL |
| | | X | Methods for visualization and statistics on DNA methylation data |
| bioconductor-methyanalysis |
1.32.0 |
|
|
Artistic-2.0 |
X | X | | X | DNA methylation data analysis and visualization |
| bioconductor-methylaid |
1.40.0 |
|
|
GPL |
| | | X | Visual and interactive quality control of large Illumina DNA... |
| bioconductor-methylaiddata |
1.38.0 |
|
|
GPL |
| | | X | MethylAid-summarized data for 2800 Illumina 450k array samples and 2620... |
| bioconductor-methylcc |
1.20.0 |
|
|
GPL-3 |
| | | X | Estimate the cell composition of whole blood in DNA methylation samples |
| bioconductor-methylclock |
1.12.0 |
|
|
MIT |
X | X | | | Methylclock - DNA methylation-based clocks |
| bioconductor-methylclockdata |
1.14.0 |
|
|
MIT |
| | | X | Data for methylclock package |
| bioconductor-methylgsa |
1.16.0 |
|
|
GPL-2 |
| | | X | Gene Set Analysis Using the Outcome of Differential Methylation |
| bioconductor-methylimp2 |
1.2.0 |
|
|
GPL-3 |
| | | X | Missing value estimation of DNA methylation data |
| bioconductor-methylinheritance |
1.30.0 |
|
|
Artistic-2.0 |
| | | X | Permutation-Based Analysis associating Conserved Differentially... |
| bioconductor-methylkit |
1.32.0 |
|
|
Artistic-2.0 |
X | X | | | DNA methylation analysis from high-throughput bisulfite sequencing results |
| bioconductor-methylmix |
2.36.0 |
|
|
GPL-2 |
| | | X | MethylMix: Identifying methylation driven cancer genes |
| bioconductor-methylmnm |
1.44.0 |
|
|
GPL-3 |
X | X | | | detect different methylation level (DMR) |
| bioconductor-methylpipe |
1.40.0 |
|
|
GPL(>=2) |
X | X | | | Base resolution DNA methylation data analysis |
| bioconductor-methylscaper |
1.14.0 |
|
|
GPL-2 |
| | | X | Visualization of Methylation Data |
| bioconductor-methylseekr |
1.46.0 |
|
|
GPL |
X | X | | X | Segmentation of Bis-seq data |
| bioconductor-methylseqdata |
1.16.0 |
|
|
CC0 |
| | | X | Collection of Public DNA Methylation Sequencing Datasets |
| bioconductor-methylsig |
1.18.0 |
|
|
GPL-3 |
| | | X | MethylSig: Differential Methylation Testing for WGBS and RRBS Data |
| bioconductor-methylumi |
2.52.0 |
|
|
GPL-2 |
X | X | | X | Handle Illumina methylation data |
| bioconductor-methyvim |
1.11.0 |
|
|
file |
| | | X | Targeted, Robust, and Model-free Differential Methylation Analysis |
| bioconductor-methyvimdata |
1.12.0 |
|
|
file |
| | | X | Example experimental data for use with the methyvim package |
| bioconductor-metid |
1.24.0 |
|
|
Artistic-2.0 |
| | | X | Network-based prioritization of putative metabolite IDs |
| bioconductor-metmashr |
1.0.0 |
|
|
GPL-3 |
| | | X | Metabolite Mashing with R |
| bioconductor-metnet |
1.24.0 |
|
|
GPL |
| | | X | Inferring metabolic networks from untargeted high-resolution mass... |
| bioconductor-mfa |
1.28.0 |
|
|
GPL |
X | X | | | Bayesian hierarchical mixture of factor analyzers for modelling genomic... |
| bioconductor-mfuzz |
2.66.0 |
|
|
GPL-2 |
| | | X | Soft clustering of omics time series data |
| bioconductor-mgfm |
1.40.0 |
|
|
GPL-3 |
X | X | | X | Marker Gene Finder in Microarray gene expression data |
| bioconductor-mgfr |
1.32.0 |
|
|
GPL-3 |
X | X | | X | Marker Gene Finder in RNA-seq data |
| bioconductor-mgnifyr |
1.2.0 |
|
|
Artistic-2.0 |
| | | X | R interface to EBI MGnify metagenomics resource |
| bioconductor-mgsa |
1.54.0 |
|
|
Artistic-2.0 |
X | X | | | Model-based gene set analysis |
| bioconductor-mgu74a.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix MG_U74A Array annotation data (chip mgu74a) |
| bioconductor-mgu74acdf |
2.18.0 |
|
|
LGPL |
| | | X | mgu74acdf |
| bioconductor-mgu74aprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type mgu74a |
| bioconductor-mgu74av2.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix MG_U74Av2 Array annotation data (chip mgu74av2) |
| bioconductor-mgu74av2cdf |
2.18.0 |
|
|
LGPL |
| | | X | mgu74av2cdf |
| bioconductor-mgu74av2probe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type mgu74av2 |
| bioconductor-mgu74b.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix MG_U74B Array annotation data (chip mgu74b) |
| bioconductor-mgu74bcdf |
2.18.0 |
|
|
LGPL |
| | | X | mgu74bcdf |
| bioconductor-mgu74bprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type mgu74b |
| bioconductor-mgu74bv2.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix MG_U74Bv2 Array annotation data (chip mgu74bv2) |
| bioconductor-mgu74bv2cdf |
2.18.0 |
|
|
LGPL |
| | | X | mgu74bv2cdf |
| bioconductor-mgu74bv2probe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type mgu74bv2 |
| bioconductor-mgu74c.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix MG_U74C Array annotation data (chip mgu74c) |
| bioconductor-mgu74ccdf |
2.18.0 |
|
|
LGPL |
| | | X | mgu74ccdf |
| bioconductor-mgu74cprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type mgu74c |
| bioconductor-mgu74cv2.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix MG_U74Cv2 Array annotation data (chip mgu74cv2) |
| bioconductor-mgu74cv2cdf |
2.18.0 |
|
|
LGPL |
| | | X | mgu74cv2cdf |
| bioconductor-mgu74cv2probe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type mgu74cv2 |
| bioconductor-mguatlas5k.db |
3.2.3 |
|
|
Artistic-2.0 |
| | | X | Clontech BD Atlas Long Oligos Mouse 5K annotation data (chip mguatlas5k) |
| bioconductor-mgug4104a.db |
3.2.3 |
|
|
Artistic-2.0 |
| | | X | Agilent annotation data (chip mgug4104a) |
| bioconductor-mgug4120a.db |
3.2.3 |
|
|
Artistic-2.0 |
| | | X | Agilent annotation data (chip mgug4120a) |
| bioconductor-mgug4121a.db |
3.2.3 |
|
|
Artistic-2.0 |
| | | X | Agilent Mouse annotation data (chip mgug4121a) |
| bioconductor-mgug4122a.db |
3.2.3 |
|
|
Artistic-2.0 |
X | X | | X | Agilent "Mouse Genome, Whole" annotation data (chip mgug4122a) |
| bioconductor-mi16cod.db |
3.4.0 |
|
|
Artistic-2.0 |
| | | X | Codelink Mouse Inflammation 16 Bioarray annotation data (chip mi16cod) |
| bioconductor-mia |
1.14.0 |
|
|
Artistic-2.0 |
| | | X | Microbiome analysis |
| bioconductor-miasim |
1.12.0 |
|
|
Artistic-2.0 |
| | | X | Microbiome Data Simulation |
| bioconductor-miaviz |
1.14.0 |
|
|
Artistic-2.0 |
| | | X | Microbiome Analysis Plotting and Visualization |
| bioconductor-michip |
1.60.0 |
|
|
GPL |
X | X | | X | MiChip Parsing and Summarizing Functions |
| bioconductor-microbiome |
1.28.0 |
|
|
BSD_2_clause |
X | X | | X | Microbiome Analytics |
| bioconductor-microbiomebenchmarkdata |
1.8.0 |
|
|
Artistic-2.0 |
| | | X | Datasets for benchmarking in microbiome research |
| bioconductor-microbiomedasim |
1.16.0 |
|
|
MIT |
| | | X | Microbiome Differential Abundance Simulation |
| bioconductor-microbiomedatasets |
1.14.0 |
|
|
CC0 |
| | | X | Experiment Hub based microbiome datasets |
| bioconductor-microbiomeexplorer |
1.12.0 |
|
|
MIT |
| | | X | Microbiome Exploration App |
| bioconductor-microbiomemarker |
1.8.0 |
|
|
GPL-3 |
| | | X | microbiome biomarker analysis toolkit |
| bioconductor-microbiomeprofiler |
1.12.0 |
|
|
GPL-2 |
| | | X | An R/shiny package for microbiome functional enrichment analysis |
| bioconductor-microbiotaprocess |
1.18.0 |
|
|
GPL |
| | | X | A comprehensive R package for managing and analyzing microbiome and... |
| bioconductor-microrna |
1.64.0 |
|
|
Artistic-2.0 |
X | X | | | Data and functions for dealing with microRNAs |
| bioconductor-micrornaome |
1.28.0 |
|
|
GPL |
| | | X | SummarizedExperiment for the microRNAome project |
| bioconductor-microstasis |
1.6.0 |
|
|
GPL-3 |
| | | X | Microbiota STability ASsessment via Iterative cluStering |
| bioconductor-micsqtl |
1.4.0 |
|
|
GPL-3 |
| | | X | MICSQTL (Multi-omic deconvolution, Integration and Cell-type-specific... |
| bioconductor-midashla |
1.14.0 |
|
|
MIT |
| | | X | R package for immunogenomics data handling and association analysis |
| bioconductor-migsa |
1.21.0 |
|
|
GPL |
| | | X | Massive and Integrative Gene Set Analysis |
| bioconductor-migsadata |
1.24.0 |
|
|
GPL |
| | | X | MIGSA vignette data |
| bioconductor-milor |
2.2.0 |
|
|
GPL-3 |
X | X | | X | Differential neighbourhood abundance testing on a graph |
| bioconductor-mimager |
1.30.0 |
|
|
MIT |
| | | X | mimager: The Microarray Imager |
| bioconductor-mimosa |
1.37.0 |
|
|
MIT |
X | X | | | Mixture Models for Single-Cell Assays |
| bioconductor-mina |
1.14.0 |
|
|
GPL |
X | X | | | Microbial community dIversity and Network Analysis |
| bioconductor-mineica |
1.46.0 |
|
|
GPL-2 |
X | X | | X | Analysis of an ICA decomposition obtained on genomics data |
| bioconductor-minet |
3.64.0 |
|
|
Artistic-2.0 |
X | X | | | Mutual Information NETworks |
| bioconductor-minfi |
1.52.0 |
|
|
Artistic-2.0 |
X | X | | X | Analyze Illumina Infinium DNA methylation arrays |
| bioconductor-minfidata |
0.52.0 |
|
|
Artistic-2.0 |
| | | X | Example data for the Illumina Methylation 450k array |
| bioconductor-minfidataepic |
1.32.0 |
|
|
Artistic-2.0 |
| | | X | Example data for the Illumina Methylation EPIC array |
| bioconductor-minimumdistance |
1.50.0 |
|
|
Artistic-2.0 |
X | X | | X | A Package for De Novo CNV Detection in Case-Parent Trios |
| bioconductor-minionsummarydata |
1.36.0 |
|
|
MIT |
| | | X | Summarised MinION sequencing data published by Ashton et al. 2015 |
| bioconductor-mipp |
1.78.0 |
|
|
GPL |
X | X | | X | Misclassification Penalized Posterior Classification |
| bioconductor-miqc |
1.14.0 |
|
|
BSD_3_clause |
| | | X | Flexible, probabilistic metrics for quality control of scRNA-seq data |
| bioconductor-mira |
1.28.0 |
|
|
GPL-3 |
| | | X | Methylation-Based Inference of Regulatory Activity |
| bioconductor-mirage |
1.48.0 |
|
|
GPL |
X | X | | X | MiRNA Ranking by Gene Expression |
| bioconductor-mirbase.db |
1.2.0 |
|
|
file |
| | | X | miRBase: the microRNA database |
| bioconductor-mirbaseconverter |
1.30.0 |
|
|
GPL |
| | | X | A comprehensive and high-efficiency tool for converting and retrieving... |
| bioconductor-mirbaseversions.db |
1.1.0 |
|
|
Artistic-2.0 |
X | X | | X | Collection of mature miRNA names of 22 different miRBase release versions |
| bioconductor-mircomp |
1.36.0 |
|
|
GPL-3 |
| | | X | Tools to assess and compare miRNA expression estimatation methods |
| bioconductor-mircompdata |
1.36.0 |
|
|
GPL-3 |
| | | X | Data used in the miRcomp package |
| bioconductor-mirintegrator |
1.36.0 |
|
|
GPL |
X | X | | X | Integrating microRNA expression into signaling pathways for pathway analysis |
| bioconductor-mirlab |
1.36.0 |
|
|
GPL |
| | | X | Dry lab for exploring miRNA-mRNA relationships |
| bioconductor-mirmine |
1.22.0 |
|
|
GPL |
| | | X | Data package with miRNA-seq datasets from miRmine database as... |
| bioconductor-mirna102xgaincdf |
2.18.0 |
|
|
LGPL |
| | | X | mirna102xgaincdf |
| bioconductor-mirna10cdf |
2.18.0 |
|
|
LGPL |
| | | X | mirna10cdf |
| bioconductor-mirna10probe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type mirna10 |
| bioconductor-mirna20cdf |
2.18.0 |
|
|
LGPL |
| | | X | mirna20cdf |
| bioconductor-mirnameconverter |
1.34.0 |
|
|
Artistic-2.0 |
X | X | | X | Convert miRNA Names to Different miRBase Versions |
| bioconductor-mirnapath |
1.66.0 |
|
|
LGPL-2.1 |
X | X | | X | miRNApath: Pathway Enrichment for miRNA Expression Data |
| bioconductor-mirnatap |
1.40.0 |
|
|
GPL-2 |
X | X | | X | miRNAtap: microRNA Targets - Aggregated Predictions |
| bioconductor-mirnatap.db |
0.99.10 |
|
|
GPL-2 |
X | X | | X | Data for miRNAtap |
| bioconductor-mirnatarget |
1.44.0 |
|
|
GPL |
| | | X | gene target tabale of miRNA for human/mouse used for MiRaGE package |
| bioconductor-mirsm |
1.18.0 |
|
|
GPL-3 |
X | X | | | Inferring miRNA sponge modules in heterogeneous data |
| bioconductor-mirsponge |
1.10.0 |
|
|
GPL-3 |
X | X | | | The name of the miRsponge package has been changed into... |
| bioconductor-mirsponger |
2.10.0 |
|
|
GPL-3 |
X | X | | | Identification and analysis of miRNA sponge regulation |
| bioconductor-mirsynergy |
1.23.0 |
|
|
GPL-2 |
X | X | | X | Mirsynergy |
| bioconductor-mirtarrnaseq |
1.14.0 |
|
|
MIT |
| | | X | mirTarRnaSeq |
| bioconductor-missmethyl |
1.32.0 |
|
|
GPL-2 |
X | X | | X | Analysing Illumina HumanMethylation BeadChip Data |
| bioconductor-missrows |
1.26.0 |
|
|
Artistic-2.0 |
| | | X | Handling Missing Individuals in Multi-Omics Data Integration |
| bioconductor-mistyr |
1.14.0 |
|
|
GPL-3 |
| | | X | Multiview Intercellular SpaTial modeling framework |
| bioconductor-mitch |
1.14.0 |
|
|
CC |
| | | X | Multi-Contrast Gene Set Enrichment Analysis |
| bioconductor-mitoclone2 |
1.12.0 |
|
|
GPL-3 |
X | X | | | Clonal Population Identification in Single-Cell RNA-Seq Data using... |
| bioconductor-mitoode |
1.25.0 |
|
|
LGPL |
X | X | | | Implementation of the differential equation model described in... |
| bioconductor-mitoodedata |
1.26.0 |
|
|
LGPL |
| | | X | Experimental data associated to the paper "Dynamical modelling of... |
| bioconductor-mixomics |
6.30.0 |
|
|
GPL |
| | | X | Omics Data Integration Project |
| bioconductor-mlinterfaces |
1.86.0 |
|
|
LGPL |
X | X | | X | Uniform interfaces to R machine learning procedures for data in... |
| bioconductor-mlm4omics |
1.2.0 |
|
|
GPL-3 |
X | X | | | To conduct Bayesian inference regression for responses with multilevel... |
| bioconductor-mlp |
1.54.0 |
|
|
GPL-3 |
X | X | | X | Mean Log P Analysis |
| bioconductor-mlseq |
2.24.0 |
|
|
GPL(>=2) |
X | X | | X | Machine Learning Interface for RNA-Seq Data |
| bioconductor-mm24kresogen.db |
2.5.0 |
|
|
Artistic-2.0 |
| | | X | RNG_MRC Mouse Pangenomic 24k Set annotation data (chip mm24kresogen) |
| bioconductor-mmagilentdesign026655.db |
3.2.3 |
|
|
Artistic-2.0 |
| | | X | Agilent Chips that use Agilent design number 026655 annotation data... |
| bioconductor-mmappr2 |
1.14.0 |
|
|
GPL-3 |
| | | X | Mutation Mapping Analysis Pipeline for Pooled RNA-Seq |
| bioconductor-mmappr2data |
1.16.0 |
|
|
GPL-3 |
| | | X | Sample Data for MMAPPR2 |
| bioconductor-mmdiff |
1.10.0 |
|
|
Artistic-2.0 |
X | | | | This package detects statistically significant difference between read... |
| bioconductor-mmdiff2 |
1.34.0 |
|
|
Artistic-2.0 |
X | X | | X | Statistical Testing for ChIP-Seq data sets |
| bioconductor-mmdiffbamsubset |
1.42.0 |
|
|
LGPL |
| | | X | Example ChIP-Seq data for the MMDiff package |
| bioconductor-mmnet |
1.13.0 |
|
|
GPL |
X | X | | | This package gives the implementations microbiome metabolic network... |
| bioconductor-mmpalatemirna |
1.37.0 |
|
|
GPL-3 |
| | | X | Murine Palate miRNA Expression Analysis |
| bioconductor-mmuphin |
1.16.0 |
|
|
MIT |
| | | X | Meta-analysis Methods with Uniform Pipeline for Heterogeneity in... |
| bioconductor-mnem |
1.22.0 |
|
|
GPL-3 |
X | X | | | Mixture Nested Effects Models |
| bioconductor-moanin |
1.14.0 |
|
|
BSD |
| | | X | An R Package for Time Course RNASeq Data Analysis |
| bioconductor-mobilitytransformr |
1.6.0 |
|
|
Artistic-2.0 |
| | | X | Effective mobility scale transformation of CE-MS(/MS) data |
| bioconductor-moda |
1.28.0 |
|
|
GPL |
| | | X | MODA: MOdule Differential Analysis for weighted gene co-expression network |
| bioconductor-modcon |
1.14.0 |
|
|
GPL-3 |
| | | X | Modifying splice site usage by changing the mRNP code, while... |
| bioconductor-modstrings |
1.22.0 |
|
|
Artistic-2.0 |
| | | X | Working with modified nucleotide sequences |
| bioconductor-moe430a.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix MOE430A Array annotation data (chip moe430a) |
| bioconductor-moe430acdf |
2.18.0 |
|
|
LGPL |
| | | X | moe430acdf |
| bioconductor-moe430aprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type moe430a |
| bioconductor-moe430b.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix MOE430B Array annotation data (chip moe430b) |
| bioconductor-moe430bcdf |
2.18.0 |
|
|
LGPL |
| | | X | moe430bcdf |
| bioconductor-moe430bprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type moe430b |
| bioconductor-moex10stprobeset.db |
8.8.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix moex10 annotation data (chip moex10stprobeset) |
| bioconductor-moex10sttranscriptcluster.db |
8.8.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix moex10 annotation data (chip moex10sttranscriptcluster) |
| bioconductor-moexexonprobesetlocation |
1.15.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type MoEx |
| bioconductor-mofa |
1.6.1 |
|
|
LGPL-3 |
| | | X | Multi-Omics Factor Analysis (MOFA) |
| bioconductor-mofa2 |
1.16.0 |
|
|
file |
X | X | | | Multi-Omics Factor Analysis v2 |
| bioconductor-mofadata |
1.22.0 |
|
|
LGPL-3 |
| | | X | Data package for Multi-Omics Factor Analysis (MOFA) |
| bioconductor-mogamun |
1.16.0 |
|
|
GPL-3 |
| | | X | MOGAMUN: A Multi-Objective Genetic Algorithm to Find Active Modules in... |
| bioconductor-mogene.1.0.st.v1frmavecs |
1.1.0 |
|
|
GPL |
| | | X | Vectors used by frma for microarrays of type mogene.1.0.st.v1frmavecs |
| bioconductor-mogene10stprobeset.db |
8.8.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix mogene10 annotation data (chip mogene10stprobeset) |
| bioconductor-mogene10sttranscriptcluster.db |
8.8.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix mogene10 annotation data (chip mogene10sttranscriptcluster) |
| bioconductor-mogene10stv1cdf |
2.18.0 |
|
|
LGPL |
| | | X | mogene10stv1cdf |
| bioconductor-mogene10stv1probe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type mogene10stv1 |
| bioconductor-mogene11stprobeset.db |
8.8.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix mogene11 annotation data (chip mogene11stprobeset) |
| bioconductor-mogene11sttranscriptcluster.db |
8.8.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix mogene11 annotation data (chip mogene11sttranscriptcluster) |
| bioconductor-mogene20stprobeset.db |
8.8.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix mogene20 annotation data (chip mogene20stprobeset) |
| bioconductor-mogene20sttranscriptcluster.db |
8.8.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix mogene20 annotation data (chip mogene20sttranscriptcluster) |
| bioconductor-mogene21stprobeset.db |
8.8.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix mogene21 annotation data (chip mogene21stprobeset) |
| bioconductor-mogene21sttranscriptcluster.db |
8.8.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix mogene21 annotation data (chip mogene21sttranscriptcluster) |
| bioconductor-mogsa |
1.40.0 |
|
|
GPL-2 |
| | | X | Multiple omics data integrative clustering and gene set analysis |
| bioconductor-moleculeexperiment |
1.6.0 |
|
|
MIT |
| | | X | Prioritising a molecule-level storage of Spatial Transcriptomics Data |
| bioconductor-moma |
1.18.0 |
|
|
GPL-3 |
| | | X | Multi Omic Master Regulator Analysis |
| bioconductor-monalisa |
1.12.0 |
|
|
GPL |
| | | X | Binned Motif Enrichment Analysis and Visualization |
| bioconductor-monocle |
2.34.0 |
|
|
Artistic-2.0 |
X | X | | | Clustering, differential expression, and trajectory analysis for... |
| bioconductor-moonlight2r |
1.4.0 |
|
|
GPL-3 |
| | | X | Identify oncogenes and tumor suppressor genes from omics data |
| bioconductor-moonlightr |
1.32.0 |
|
|
GPL |
| | | X | Identify oncogenes and tumor suppressor genes from omics data |
| bioconductor-mops |
1.21.0 |
|
|
GPL-3 |
X | X | | X | MoPS - Model-based Periodicity Screening |
| bioconductor-mosaics |
2.44.0 |
|
|
GPL |
X | X | | | MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq) |
| bioconductor-mosaicsexample |
1.44.0 |
|
|
GPL |
| | | X | Example data for the mosaics package, which implements MOSAiCS and... |
| bioconductor-mosbi |
1.12.0 |
|
|
AGPL-3 |
X | X | | | Molecular Signature identification using Biclustering |
| bioconductor-mosdef |
1.2.0 |
|
|
MIT |
| | | X | MOSt frequently used and useful Differential Expression Functions |
| bioconductor-mosim |
2.2.0 |
|
|
GPL-3 |
X | X | | X | Multi-Omics Simulation (MOSim) |
| bioconductor-motif2site |
1.10.0 |
|
|
GPL-2 |
| | | X | Detect binding sites from motifs and ChIP-seq experiments, and compare... |
| bioconductor-motifbreakr |
2.16.0 |
|
|
GPL-2 |
X | X | | X | A Package For Predicting The Disruptiveness Of Single Nucleotide... |
| bioconductor-motifcounter |
1.30.0 |
|
|
GPL-2 |
X | X | | | R package for analysing TFBSs in DNA sequences |
| bioconductor-motifdb |
1.48.0 |
|
|
Artistic-2.0 |
X | X | | X | An Annotated Collection of Protein-DNA Binding Sequence Motifs |
| bioconductor-motifmatchr |
1.28.0 |
|
|
GPL-3 |
X | X | | | Fast Motif Matching in R |
| bioconductor-motifrg |
1.31.0 |
|
|
Artistic-2.0 |
X | X | | X | A package for discriminative motif discovery, designed for high... |
| bioconductor-motifstack |
1.50.0 |
|
|
GPL |
X | X | | X | Plot stacked logos for single or multiple DNA, RNA and amino acid sequence |
| bioconductor-motiftestr |
1.2.1 |
|
|
GPL-3 |
| | | X | Perform key tests for binding motifs in sequence data |
| bioconductor-motiv |
1.43.0 |
|
|
GPL-2 |
X | X | | | Motif Identification and Validation |
| bioconductor-mouse.db0 |
3.20.0 |
|
|
Artistic-2.0 |
| | | X | Base Level Annotation databases for mouse |
| bioconductor-mouse4302.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix Mouse430_2 Array annotation data (chip mouse4302) |
| bioconductor-mouse4302barcodevecs |
1.44.0 |
|
|
GPL |
| | | X | mouse4302 data for barcode |
| bioconductor-mouse4302cdf |
2.18.0 |
|
|
LGPL |
| | | X | mouse4302cdf |
| bioconductor-mouse4302frmavecs |
1.5.0 |
|
|
GPL |
| | | X | Vectors used by frma for microarrays of type mouse4302 |
| bioconductor-mouse4302probe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type mouse4302 |
| bioconductor-mouse430a2.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix Mouse430A_2 Array annotation data (chip mouse430a2) |
| bioconductor-mouse430a2cdf |
2.18.0 |
|
|
LGPL |
| | | X | mouse430a2cdf |
| bioconductor-mouse430a2frmavecs |
1.3.0 |
|
|
GPL |
| | | X | Vectors used by frma for microarrays of type mouse430a2 |
| bioconductor-mouse430a2probe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type mouse430a2 |
| bioconductor-mousechrloc |
2.1.6 |
|
|
The |
| | | X | A data package containing annotation data for mouseCHRLOC |
| bioconductor-mousefm |
1.16.0 |
|
|
GPL-3 |
| | | X | In-silico methods for genetic finemapping in inbred mice |
| bioconductor-mousegastrulationdata |
1.16.0 |
|
|
GPL-3 |
| | | X | Single-Cell -omics Data across Mouse Gastrulation and Early Organogenesis |
| bioconductor-mousethymusageing |
1.10.0 |
|
|
GPL-3 |
| | | X | Single-cell Transcriptomics Data of the Ageing Mouse Thymus |
| bioconductor-mpac |
1.0.0 |
|
|
GPL-3 |
| | | X | Multi-omic Pathway Analysis of Cancer |
| bioconductor-mpedbarray.db |
3.2.3 |
|
|
Artistic-2.0 |
| | | X | FHCRC Nelson Lab mpedbarray Annotation Data (mpedbarray) |
| bioconductor-mpfe |
1.42.0 |
|
|
GPL |
X | X | | X | Estimation of the amplicon methylation pattern distribution from... |
| bioconductor-mpo.db |
0.99.8 |
|
|
Artistic-2.0 |
| | | X | A set of annotation maps describing the Mouse Phenotype Ontology |
| bioconductor-mpra |
1.28.0 |
|
|
Artistic-2.0 |
| | | X | Analyze massively parallel reporter assays |
| bioconductor-mpranalyze |
1.24.0 |
|
|
GPL-3 |
| | | X | Statistical Analysis of MPRA data |
| bioconductor-mqmetrics |
1.10.0 |
|
|
GPL-3 |
| | | X | Quality Control of Protemics Data |
| bioconductor-mqtl.nmr |
1.14.0 |
|
|
Artistic-2.0 |
X | X | | | mQTL.NMR provides a complete mQTL analysis pipeline for 1H NMR data.... |
| bioconductor-msa |
1.38.0 |
|
|
GPL |
X | X | | | Multiple Sequence Alignment |
| bioconductor-msa2dist |
1.10.0 |
|
|
GPL-3 |
X | X | | | MSA2dist calculates pairwise distances between all sequences of a... |
| bioconductor-msbackendmassbank |
1.14.0 |
|
|
Artistic-2.0 |
| | | X | Mass Spectrometry Data Backend for MassBank record Files |
| bioconductor-msbackendmetabolights |
1.0.0 |
|
|
Artistic-2.0 |
| | | X | Retrieve Mass Spectrometry Data from MetaboLights |
| bioconductor-msbackendmgf |
1.14.0 |
|
|
Artistic-2.0 |
| | | X | Mass Spectrometry Data Backend for Mascot Generic Format (mgf) Files |
| bioconductor-msbackendmsp |
1.10.0 |
|
|
Artistic-2.0 |
| | | X | Mass Spectrometry Data Backend for NIST msp Files |
| bioconductor-msbackendrawfilereader |
1.8.1 |
|
|
GPL-3 |
| | | X | Mass Spectrometry Backend for Reading Thermo Fisher Scientific raw Files |
| bioconductor-msbackendsql |
1.6.0 |
|
|
Artistic-2.0 |
| | | X | SQL-based Mass Spectrometry Data Backend |
| bioconductor-mscoreutils |
1.18.0 |
|
|
Artistic-2.0 |
X | X | | | Core Utils for Mass Spectrometry Data |
| bioconductor-msd16s |
1.22.0 |
|
|
Artistic-2.0 |
| | | X | Healthy and moderate to severe diarrhea 16S expression data |
| bioconductor-msdata |
0.46.0 |
|
|
GPL |
| | | X | Various Mass Spectrometry raw data example files |
| bioconductor-msdatahub |
1.6.0 |
|
|
Artistic-2.0 |
| | | X | Mass Spectrometry Data on ExperimentHub |
| bioconductor-mseadbi |
1.2.0 |
|
|
Artistic-2.0 |
| | | X | DBI to construct MSEA-related package |
| bioconductor-msexperiment |
1.8.0 |
|
|
Artistic-2.0 |
| | | X | Infrastructure for Mass Spectrometry Experiments |
| bioconductor-msfeatures |
1.14.0 |
|
|
Artistic-2.0 |
| | | X | Functionality for Mass Spectrometry Features |
| bioconductor-msgbsr |
1.30.0 |
|
|
GPL-2 |
| | | X | msgbsR: methylation sensitive genotyping by sequencing (MS-GBS) R functions |
| bioconductor-msgfgui |
1.28.0 |
|
|
GPL |
| | | X | A shiny GUI for MSGFplus |
| bioconductor-msgfplus |
1.28.0 |
|
|
GPL |
| | | X | An interface between R and MS-GF+ |
| bioconductor-msigdb |
1.14.0 |
|
|
CC |
| | | X | An ExperimentHub Package for the Molecular Signatures Database (MSigDB) |
| bioconductor-msimpute |
1.16.0 |
|
|
GPL |
| | | X | Imputation of label-free mass spectrometry peptides |
| bioconductor-mslp |
1.8.0 |
|
|
GPL-3 |
| | | X | Predict synthetic lethal partners of tumour mutations |
| bioconductor-msmb |
1.24.0 |
|
|
LGPL |
| | | X | Data sets for the book 'Modern Statistics for Biology' |
| bioconductor-msmseda |
1.44.0 |
|
|
GPL-2 |
X | X | | X | Exploratory Data Analysis of LC-MS/MS data by spectral counts |
| bioconductor-msmstests |
1.44.0 |
|
|
GPL-2 |
| | | X | LC-MS/MS Differential Expression Tests |
| bioconductor-msnbase |
2.32.0 |
|
|
Artistic-2.0 |
X | X | | | Base Functions and Classes for Mass Spectrometry and Proteomics |
| bioconductor-msnid |
1.40.0 |
|
|
Artistic-2.0 |
X | X | | | Utilities for Exploration and Assessment of Confidence of LC-MSn... |
| bioconductor-msprep |
1.16.0 |
|
|
GPL-3 |
| | | X | Package for Summarizing, Filtering, Imputing, and Normalizing Metabolomics Data |
| bioconductor-mspurity |
1.32.0 |
|
|
GPL-3 |
X | X | | | Automated Evaluation of Precursor Ion Purity for Mass Spectrometry... |
| bioconductor-mspuritydata |
1.34.0 |
|
|
GPL |
X | X | | X | Fragmentation spectral libraries and data to test the msPurity package |
| bioconductor-msqc1 |
1.34.0 |
|
|
GPL |
| | | X | Sigma mix MSQC1 data |
| bioconductor-msqrob2 |
1.14.0 |
|
|
Artistic-2.0 |
| | | X | Robust statistical inference for quantitative LC-MS proteomics |
| bioconductor-msquality |
1.6.0 |
|
|
GPL-3 |
| | | X | MsQuality - Quality metric calculation from Spectra and MsExperiment objects |
| bioconductor-msstats |
4.14.0 |
|
|
Artistic-2.0 |
X | X | | X | Protein Significance Analysis in DDA, SRM and DIA for Label-free or... |
| bioconductor-msstatsbig |
1.4.0 |
|
|
Artistic-2.0 |
| | | X | MSstats Preprocessing for Larger than Memory Data |
| bioconductor-msstatsbiodata |
1.13.0 |
|
|
Artistic-2.0 |
| | | X | Datasets of published biological studies with DDA or SRM experiments |
| bioconductor-msstatsconvert |
1.16.0 |
|
|
Artistic-2.0 |
| | | X | Import Data from Various Mass Spectrometry Signal Processing Tools to... |
| bioconductor-msstatslip |
1.8.1 |
|
|
Artistic-2.0 |
X | X | | | LiP Significance Analysis in shotgun mass spectrometry-based proteomic... |
| bioconductor-msstatslobd |
1.14.0 |
|
|
Artistic-2.0 |
X | X | | | Assay characterization: estimation of limit of blanc(LoB) and limit of... |
| bioconductor-msstatsptm |
2.4.1 |
|
|
Artistic-2.0 |
X | X | | X | Statistical Characterization of Post-translational Modifications |
| bioconductor-msstatsqc |
2.24.0 |
|
|
Artistic |
| | | X | Longitudinal system suitability monitoring and quality control for... |
| bioconductor-msstatsqcgui |
1.26.0 |
|
|
Artistic |
| | | X | A graphical user interface for MSstatsQC package |
| bioconductor-msstatssamplesize |
1.13.0 |
|
|
Artistic-2.0 |
| | | X | Simulation tool for optimal design of high-dimensional MS-based... |
| bioconductor-msstatsshiny |
1.4.1 |
|
|
Artistic-2.0 |
| | | X | MSstats GUI for Statistical Anaylsis of Proteomics Experiments |
| bioconductor-msstatstmt |
2.10.0 |
|
|
Artistic-2.0 |
| | | X | Protein Significance Analysis in shotgun mass spectrometry-based... |
| bioconductor-msstatstmtptm |
1.1.2 |
|
|
Artistic-2.0 |
X | X | | X | Post Translational Modification (PTM) Significance Analysis in shotgun... |
| bioconductor-mta10probeset.db |
8.8.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix mta10 annotation data (chip mta10probeset) |
| bioconductor-mta10transcriptcluster.db |
8.8.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix mta10 annotation data (chip mta10transcriptcluster) |
| bioconductor-mtbls2 |
1.36.0 |
|
|
CC0 |
| | | X | MetaboLights MTBLS2: Comparative LC/MS-based profiling of silver... |
| bioconductor-mtseeker |
1.3.0 |
|
|
GPL-3 |
| | | X | Bioconductor Tools for Human Mitochondrial Variant Analysis |
| bioconductor-mtseekerdata |
1.3.0 |
|
|
Artistic-2.0 |
| | | X | Supporting Data for the MTseeker Package |
| bioconductor-mu11ksuba.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix Mu11KsubA Array annotation data (chip mu11ksuba) |
| bioconductor-mu11ksubacdf |
2.18.0 |
|
|
LGPL |
| | | X | mu11ksubacdf |
| bioconductor-mu11ksubaprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type mu11ksuba |
| bioconductor-mu11ksubb.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix Mu11KsubB Array annotation data (chip mu11ksubb) |
| bioconductor-mu11ksubbcdf |
2.18.0 |
|
|
LGPL |
| | | X | mu11ksubbcdf |
| bioconductor-mu11ksubbprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type mu11ksubb |
| bioconductor-mu15v1.db |
3.2.3 |
|
|
Artistic-2.0 |
| | | X | FHCRC Genomics Shared Resource Mu15v1 Annotation Data (Mu15v1) |
| bioconductor-mu19ksuba.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix Mu19KsubA Array annotation data (chip mu19ksuba) |
| bioconductor-mu19ksubacdf |
2.18.0 |
|
|
LGPL |
| | | X | mu19ksubacdf |
| bioconductor-mu19ksubb.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix Mu19KsubB Array annotation data (chip mu19ksubb) |
| bioconductor-mu19ksubbcdf |
2.18.0 |
|
|
LGPL |
| | | X | mu19ksubbcdf |
| bioconductor-mu19ksubc.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix Mu19KsubC Array annotation data (chip mu19ksubc) |
| bioconductor-mu19ksubccdf |
2.18.0 |
|
|
LGPL |
| | | X | mu19ksubccdf |
| bioconductor-mu22v3.db |
3.2.3 |
|
|
Artistic-2.0 |
| | | X | FHCRC Genomics Shared Resource Mu22v3 Annotation Data (Mu22v3) |
| bioconductor-mu6500subacdf |
2.18.0 |
|
|
LGPL |
| | | X | mu6500subacdf |
| bioconductor-mu6500subbcdf |
2.18.0 |
|
|
LGPL |
| | | X | mu6500subbcdf |
| bioconductor-mu6500subccdf |
2.18.0 |
|
|
LGPL |
| | | X | mu6500subccdf |
| bioconductor-mu6500subdcdf |
2.18.0 |
|
|
LGPL |
| | | X | mu6500subdcdf |
| bioconductor-mudata |
1.10.0 |
|
|
GPL-3 |
| | | X | Serialization for MultiAssayExperiment Objects |
| bioconductor-mugaexampledata |
1.26.0 |
|
|
GPL-3 |
| | | X | Example {M}ouse {U}niversal {G}enotyping {A}rray data for genome... |
| bioconductor-mulcom |
1.56.0 |
|
|
GPL-2 |
X | X | | | Calculates Mulcom test |
| bioconductor-mulder2012 |
0.26.0 |
|
|
Artistic-2.0 |
| | | X | Predicting functional networks and modules of chromatin factors... |
| bioconductor-multiassayexperiment |
1.32.0 |
|
|
Artistic-2.0 |
X | X | | X | Software for the integration of multi-omics experiments in Bioconductor |
| bioconductor-multibac |
1.16.0 |
|
|
GPL-3 |
| | | X | Multiomic Batch effect Correction |
| bioconductor-multiclust |
1.36.0 |
|
|
GPL |
X | X | | X | multiClust: An R-package for Identifying Biologically Relevant Clusters... |
| bioconductor-multicrispr |
1.16.0 |
|
|
GPL-2 |
| | | X | Multi-locus multi-purpose Crispr/Cas design |
| bioconductor-multidataset |
1.34.0 |
|
|
file |
X | X | | X | Implementation of MultiDataSet and ResultSet |
| bioconductor-multigsea |
1.16.0 |
|
|
GPL-3 |
| | | X | Combining GSEA-based pathway enrichment with multi omics data integration |
| bioconductor-multihiccompare |
1.24.0 |
|
|
MIT |
| | | X | Normalize and detect differences between Hi-C datasets when replicates... |
| bioconductor-multimed |
2.28.0 |
|
|
GPL |
X | X | | X | Testing multiple biological mediators simultaneously |
| bioconductor-multimir |
1.28.0 |
|
|
MIT |
| | | X | Integration of multiple microRNA-target databases with their disease... |
| bioconductor-multimodalexperiment |
1.6.0 |
|
|
Artistic-2.0 |
| | | X | Integrative Bulk and Single-Cell Experiment Container |
| bioconductor-multiomicsviz |
1.24.0 |
|
|
LGPL |
X | X | | X | Plot the effect of one omics data on other omics data along the chromosome |
| bioconductor-multirnaflow |
1.4.0 |
|
|
GPL-3 |
| | | X | An R package for integrated analysis of temporal RNA-seq data with... |
| bioconductor-multiscan |
1.66.0 |
|
|
GPL |
X | X | | | R package for combining multiple scans |
| bioconductor-multisight |
1.7.0 |
|
|
CeCILL |
| | | X | Multi-omics Classification, Functional Enrichment and Network Inference analysis |
| bioconductor-multistateqtl |
1.2.0 |
|
|
GPL-3 |
| | | X | Toolkit for the analysis of multi-state QTL data |
| bioconductor-multiwgcna |
1.4.0 |
|
|
GPL-3 |
| | | X | multiWGCNA |
| bioconductor-multtest |
2.62.0 |
|
|
LGPL |
X | X | | | Resampling-based multiple hypothesis testing |
| bioconductor-mumosa |
1.14.0 |
|
|
GPL-3 |
| | | X | Multi-Modal Single-Cell Analysis Methods |
| bioconductor-mungesumstats |
1.14.1 |
|
|
Artistic-2.0 |
| | | X | Standardise summary statistics from GWAS |
| bioconductor-mus.musculus |
1.3.1 |
|
|
Artistic-2.0 |
| | | X | Annotation package for the Mus.musculus object |
| bioconductor-muscat |
1.16.0 |
|
|
GPL-3 |
| | | X | Multi-sample multi-group scRNA-seq data analysis tools |
| bioconductor-muscdata |
1.20.0 |
|
|
MIT |
| | | X | Multi-sample multi-group scRNA-seq data |
| bioconductor-muscle |
3.48.0 |
|
|
Unlimited |
X | X | | | Multiple Sequence Alignment with MUSCLE |
| bioconductor-musicatk |
1.12.0 |
|
|
LGPL-3 |
| | | X | Mutational Signature Comprehensive Analysis Toolkit |
| bioconductor-mutationalpatterns |
3.16.0 |
|
|
MIT |
X | X | | X | Comprehensive genome-wide analysis of mutational processes |
| bioconductor-mvcclass |
1.80.0 |
|
|
LGPL |
X | X | | X | Model-View-Controller (MVC) Classes |
| bioconductor-mvgst |
1.12.0 |
|
|
GPL-3 |
X | X | | | mvGST provides platform-independent tools to identify GO terms (gene... |
| bioconductor-mvoutdata |
1.42.0 |
|
|
Artistic-2.0 |
| | | X | affy and illumina raw data for assessing outlier detector performance |
| bioconductor-mwastools |
1.30.0 |
|
|
CC |
X | X | | X | MWASTools: an integrated pipeline to perform metabolome-wide association studies |
| bioconductor-mwgcod.db |
3.4.0 |
|
|
Artistic-2.0 |
| | | X | Codelink Mouse Whole Genome Bioarray (~36 000 mouse gene targets)... |
| bioconductor-mygene |
1.42.0 |
|
|
Artistic-2.0 |
X | X | | X | Access MyGene.Info_ services |
| bioconductor-myvariant |
1.36.0 |
|
|
Artistic-2.0 |
X | X | | X | Accesses MyVariant.info variant query and annotation services |
| bioconductor-mzid |
1.44.0 |
|
|
GPL |
X | X | | X | An mzIdentML parser for R |
| bioconductor-mzr |
2.40.0 |
|
|
Artistic-2.0 |
X | X | | | parser for netCDF, mzXML and mzML and mzIdentML files (mass spectrometry data) |
| bioconductor-nadfinder |
1.30.0 |
|
|
GPL |
X | X | | X | Call wide peaks for sequencing data |
| bioconductor-nanomethviz |
3.2.0 |
|
|
Apache |
X | X | | | Visualise methylation data from Oxford Nanopore sequencing |
| bioconductor-nanoporernaseq |
1.12.0 |
|
|
GPL-3 |
| | | X | Nanopore RNA-Seq Example data |
| bioconductor-nanostringdiff |
1.36.0 |
|
|
GPL |
X | X | | | Differential Expression Analysis of NanoString nCounter Data |
| bioconductor-nanostringnctools |
1.14.0 |
|
|
MIT |
| | | X | NanoString nCounter Tools |
| bioconductor-nanostringqcpro |
1.32.0 |
|
|
Artistic-2.0 |
| | | X | Quality metrics and data processing methods for NanoString mRNA gene... |
| bioconductor-nanotator |
1.18.0 |
|
|
file |
| | | X | Next generation structural variant annotation and classification |
| bioconductor-nanotube |
1.12.0 |
|
|
GPL-3 |
| | | X | An Easy Pipeline for NanoString nCounter Data Analysis |
| bioconductor-nanotubes |
1.22.0 |
|
|
GPL-3 |
| | | X | Mouse nanotube CAGE data |
| bioconductor-narrowpeaks |
1.31.0 |
|
|
Artistic-2.0 |
X | X | | | Shape-based Analysis of Variation in ChIP-seq using Functional PCA |
| bioconductor-nbamseq |
1.22.0 |
|
|
GPL-2 |
| | | X | Negative Binomial Additive Model for RNA-Seq Data |
| bioconductor-nbsplice |
1.15.0 |
|
|
GPL |
| | | X | Negative Binomial Models to detect Differential Splicing |
| bioconductor-ncdfflow |
2.52.0 |
|
|
AGPL-3.0-only |
X | X | | | ncdfFlow: A package that provides HDF5 based storage for flow cytometry data. |
| bioconductor-ncgtw |
1.20.0 |
|
|
GPL-2 |
X | X | | | Alignment of LC-MS Profiles by Neighbor-wise Compound-specific... |
| bioconductor-ncigraph |
1.54.0 |
|
|
GPL-3 |
X | X | | X | Pathways from the NCI Pathways Database |
| bioconductor-ncigraphdata |
1.42.0 |
|
|
GPL-3 |
| | | X | Data for the NCIgraph software package |
| bioconductor-ncrnatools |
1.16.0 |
|
|
GPL-3 |
| | | X | An R toolkit for non-coding RNA |
| bioconductor-ndexr |
1.28.0 |
|
|
BSD_3_clause |
X | X | | X | NDEx R client library |
| bioconductor-nearbynding |
1.16.0 |
|
|
Artistic-2.0 |
| | | X | Discern RNA structure proximal to protein binding |
| bioconductor-nebulosa |
1.16.0 |
|
|
GPL-3 |
| | | X | Single-Cell Data Visualisation Using Kernel Gene-Weighted Density Estimation |
| bioconductor-neighbornet |
1.18.0 |
|
|
CC |
| | | X | Neighbor_net analysis |
| bioconductor-nem |
2.60.0 |
|
|
GPL |
X | X | | | (Dynamic) Nested Effects Models and Deterministic Effects Propagation... |
| bioconductor-nempi |
1.10.0 |
|
|
GPL-3 |
| | | X | Inferring unobserved perturbations from gene expression data |
| bioconductor-nestlink |
1.22.0 |
|
|
GPL |
| | | X | NestLink an R data package to guide through Engineered Peptide Barcodes... |
| bioconductor-netactivity |
1.8.0 |
|
|
MIT |
| | | X | Compute gene set scores from a deep learning framework |
| bioconductor-netactivitydata |
1.8.0 |
|
|
MIT |
| | | X | Data required for getting the gene set scores with NetActivity package |
| bioconductor-netbenchmark |
1.19.0 |
|
|
CC |
X | X | | | Benchmarking of several gene network inference methods |
| bioconductor-netbiov |
1.31.0 |
|
|
GPL |
X | X | | X | A package for visualizing complex biological network |
| bioconductor-netboost |
2.6.0 |
|
|
GPL-3 |
X | X | | | Network Analysis Supported by Boosting |
| bioconductor-netboxr |
1.9.0 |
|
|
LGPL-3 |
| | | X | netboxr |
| bioconductor-netdx |
1.14.0 |
|
|
MIT |
| | | X | Network-based patient classifier |
| bioconductor-netdx.examples |
0.99.3 |
|
|
MIT |
| | | X | Companion data package to netDx |
| bioconductor-nethet |
1.38.0 |
|
|
GPL-2 |
X | X | | | A bioconductor package for high-dimensional exploration of biological... |
| bioconductor-netomics |
1.8.0 |
|
|
GPL-3 |
| | | X | Multi-Omics (time-course) network-based integration and interpretation |
| bioconductor-netpathminer |
1.42.0 |
|
|
GPL |
X | X | | | NetPathMiner for Biological Network Construction, Path Mining and Visualization |
| bioconductor-netprior |
1.32.0 |
|
|
GPL-3 |
| | | X | A model for network-based prioritisation of genes |
| bioconductor-netreg |
1.13.1 |
|
|
GPL-3 |
X | X | | | Network-Regularized Regression Models |
| bioconductor-netresponse |
1.66.0 |
|
|
GPL |
X | X | | | Functional Network Analysis |
| bioconductor-netsam |
1.46.0 |
|
|
LGPL |
| | | X | Network Seriation And Modularization |
| bioconductor-netsmooth |
1.26.0 |
|
|
GPL-3 |
| | | X | Network smoothing for scRNAseq |
| bioconductor-networkbma |
2.34.0 |
|
|
GPL |
X | X | | | Regression-based network inference using Bayesian Model Averaging |
| bioconductor-netzoor |
1.10.0 |
|
|
GPL-3 |
| | | X | Unified methods for the inference and analysis of gene regulatory networks |
| bioconductor-neuca |
1.6.0 |
|
|
GPL-2 |
| | | X | NEUral network-based single-Cell Annotation tool |
| bioconductor-neve2006 |
0.44.0 |
|
|
Artistic-2.0 |
| | | X | expression and CGH data on breast cancer cell lines |
| bioconductor-newwave |
1.16.0 |
|
|
GPL-3 |
| | | X | Negative binomial model for scRNA-seq |
| bioconductor-ngscopy |
1.17.1 |
|
|
GPL |
| | | X | NGScopy provides a quantitative caller for detecting copy number... |
| bioconductor-ngscopydata |
1.26.0 |
|
|
GPL |
| | | X | Subset of BAM files of human tumor and pooled normal sequencing data... |
| bioconductor-ngsreports |
2.8.0 |
|
|
LGPL-3 |
| | | X | Load FastqQC reports and other NGS related files |
| bioconductor-nipalsmcia |
1.4.0 |
|
|
GPL-3 |
| | | X | Multiple Co-Inertia Analysis via the NIPALS Method |
| bioconductor-nnnorm |
2.70.0 |
|
|
LGPL |
X | X | | X | Spatial and intensity based normalization of cDNA microarray data based... |
| bioconductor-nnsvg |
1.10.0 |
|
|
MIT |
| | | X | Scalable identification of spatially variable genes in... |
| bioconductor-noiseq |
2.50.0 |
|
|
Artistic-2.0 |
X | X | | X | Exploratory analysis and differential expression for RNA-seq data |
| bioconductor-nondetects |
2.32.0 |
|
|
GPL-3 |
X | X | | X | Non-detects in qPCR data |
| bioconductor-norce |
1.18.0 |
|
|
MIT |
| | | X | NoRCE: Noncoding RNA Sets Cis Annotation and Enrichment |
| bioconductor-normalize450k |
1.34.0 |
|
|
BSD_2_clause |
| | | X | Preprocessing of Illumina Infinium 450K data |
| bioconductor-normalyzerde |
1.24.0 |
|
|
Artistic-2.0 |
| | | X | Evaluation of normalization methods and calculation of differential... |
| bioconductor-normqpcr |
1.52.0 |
|
|
LGPL-3 |
| | | X | Functions for normalisation of RT-qPCR data |
| bioconductor-normr |
1.32.0 |
|
|
GPL-2 |
X | X | | | Normalization and difference calling in ChIP-seq data |
| bioconductor-norway981.db |
3.2.3 |
|
|
Artistic-2.0 |
| | | X | Norway981 http://genome-www5.stanford.edu/ Annotation Data (Norway981) |
| bioconductor-nparc |
1.18.0 |
|
|
GPL-3 |
| | | X | Non-parametric analysis of response curves for thermal proteome... |
| bioconductor-npgsea |
1.42.0 |
|
|
Artistic-2.0 |
X | X | | X | Permutation approximation methods for gene set enrichment analysis... |
| bioconductor-ntw |
1.56.0 |
|
|
GPL-2 |
X | X | | X | Predict gene network using an Ordinary Differential Equation (ODE) based method |
| bioconductor-nucleosim |
1.34.0 |
|
|
Artistic-2.0 |
X | X | | X | Generate synthetic nucleosome maps |
| bioconductor-nucler |
2.38.0 |
|
|
LGPL |
X | X | | X | Nucleosome positioning package for R |
| bioconductor-nucpos |
1.24.0 |
|
|
GPL-2 |
X | X | | X | An R package for prediction of nucleosome positions |
| bioconductor-nudge |
1.46.0 |
|
|
GPL-2 |
X | X | | | Package for normalizing microarray data in single and multiple... |
| bioconductor-nugohs1a520180.db |
3.4.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix nugohs1a520180 annotation data (chip nugohs1a520180) |
| bioconductor-nugohs1a520180cdf |
3.4.0 |
|
|
LGPL |
| | | X | nugohs1a520180cdf |
| bioconductor-nugohs1a520180probe |
3.4.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type nugohs1a520180 |
| bioconductor-nugomm1a520177.db |
3.4.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix nugomm1a520177 annotation data (chip nugomm1a520177) |
| bioconductor-nugomm1a520177cdf |
3.4.0 |
|
|
LGPL |
| | | X | nugomm1a520177cdf |
| bioconductor-nugomm1a520177probe |
3.4.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type nugomm1a520177 |
| bioconductor-nullranges |
1.12.0 |
|
|
GPL-3 |
| | | X | Generation of null ranges via bootstrapping or covariate matching |
| bioconductor-nullrangesdata |
1.12.0 |
|
|
GPL-3 |
| | | X | ExperimentHub datasets for the nullranges package |
| bioconductor-nupop |
2.14.0 |
|
|
GPL-2 |
X | X | | | An R package for nucleosome positioning prediction |
| bioconductor-nxtirfcore |
1.6.0 |
|
|
MIT |
X | X | | | Core Engine for NxtIRF: a User-Friendly Intron Retention and... |
| bioconductor-nxtirfdata |
1.12.0 |
|
|
MIT |
| | | X | Data for NxtIRF |
| bioconductor-obmiti |
1.14.0 |
|
|
GPL-3 |
| | | X | Ob/ob Mice Data on Normal and High Fat Diet |
| bioconductor-occugene |
1.66.0 |
|
|
GPL |
X | X | | X | Functions for Multinomial Occupancy Distribution |
| bioconductor-ocplus |
1.80.0 |
|
|
LGPL |
| | | X | Operating characteristics plus sample size and local fdr for microarray... |
| bioconductor-oct4 |
1.22.0 |
|
|
GPL |
| | | X | Conditional knockdown of OCT4 in mouse ESCs |
| bioconductor-octad |
1.8.0 |
|
|
Artistic-2.0 |
| | | X | Open Cancer TherApeutic Discovery (OCTAD) |
| bioconductor-octad.db |
1.8.0 |
|
|
Artistic-2.0 |
| | | X | Open Cancer TherApeutic Discovery (OCTAD) database |
| bioconductor-oder |
1.6.0 |
|
|
Artistic-2.0 |
| | | X | Optimising the Definition of Expressed Regions |
| bioconductor-odseq |
1.34.0 |
|
|
MIT |
| | | X | Outlier detection in multiple sequence alignments |
| bioconductor-ogre |
1.10.0 |
|
|
Artistic-2.0 |
| | | X | Calculate, visualize and analyse overlap between genomic regions |
| bioconductor-ogsa |
1.17.0 |
|
|
GPL |
X | X | | X | Outlier Gene Set Analysis |
| bioconductor-oligo |
1.70.0 |
|
|
LGPL |
X | X | | | Preprocessing tools for oligonucleotide arrays |
| bioconductor-oligoclasses |
1.68.0 |
|
|
GPL |
X | X | | X | Classes for high-throughput arrays supported by oligo and crlmm |
| bioconductor-oligodata |
1.8.0 |
|
|
LGPL |
| | | X | Dataset samples for the oligo package |
| bioconductor-olin |
1.84.0 |
|
|
GPL-2 |
X | X | | X | Optimized local intensity-dependent normalisation of two-color microarrays |
| bioconductor-olingui |
1.80.0 |
|
|
GPL-2 |
| | | X | Graphical user interface for OLIN |
| bioconductor-omada |
1.8.0 |
|
|
GPL-3 |
X | X | | | Machine learning tools for automated transcriptome clustering analysis |
| bioconductor-omadb |
2.22.0 |
|
|
GPL-3 |
| | | X | R wrapper for the OMA REST API |
| bioconductor-omicade4 |
1.46.0 |
|
|
GPL-2 |
X | X | | X | Multiple co-inertia analysis of omics datasets |
| bioconductor-omiccircos |
1.44.0 |
|
|
GPL-2 |
X | X | | X | High-quality circular visualization of omics data |
| bioconductor-omicplotr |
1.26.0 |
|
|
MIT |
| | | X | Visual Exploration of Omic Datasets Using a Shiny App |
| bioconductor-omicrexposome |
1.28.0 |
|
|
MIT |
| | | X | Exposome and omic data associatin and integration analysis |
| bioconductor-omicslonda |
1.14.0 |
|
|
MIT |
| | | X | Omics Longitudinal Differential Analysis |
| bioconductor-omicsmarker |
1.19.0 |
|
|
GPL-3 |
| | | X | Classification and Feature Selection for 'Omics' Datasets |
| bioconductor-omicsmlrepor |
1.0.0 |
|
|
Artistic-2.0 |
| | | X | Search harmonized metadata created under the OmicsMLRepo project |
| bioconductor-omicspca |
1.24.0 |
|
|
GPL-3 |
| | | X | An R package for quantitative integration and analysis of multiple... |
| bioconductor-omicspcadata |
1.24.0 |
|
|
GPL-3 |
| | | X | Supporting data for package OMICsPCA |
| bioconductor-omicsprint |
1.26.0 |
|
|
GPL |
| | | X | Cross omic genetic fingerprinting |
| bioconductor-omicsviewer |
1.10.0 |
|
|
GPL-2 |
| | | X | Interactive and explorative visualization of SummarizedExperssionSet or... |
| bioconductor-omixer |
1.16.0 |
|
|
MIT |
| | | X | Omixer: multivariate and reproducible sample randomization to... |
| bioconductor-omnipathr |
3.10.1 |
|
|
MIT |
| | | X | OmniPath web service client and more |
| bioconductor-ompbam |
1.10.0 |
|
|
MIT |
X | X | | | C++ Library for OpenMP-based multi-threaded sequential profiling of... |
| bioconductor-omxplore |
1.0.0 |
|
|
Artistic-2.0 |
| | | X | Vizualization tools for 'omics' datasets with R |
| bioconductor-onassis |
1.12.0 |
|
|
GPL-2 |
| | | X | OnASSIs Ontology Annotation and Semantic SImilarity software |
| bioconductor-onassisjavalibs |
1.28.0 |
|
|
GPL-2 |
| | | X | OnassisJavaLibs, java libraries to run conceptmapper and semantic similarity |
| bioconductor-oncomix |
1.28.0 |
|
|
GPL-3 |
| | | X | Identifying Genes Overexpressed in Subsets of Tumors from Tumor-Normal... |
| bioconductor-oncoscanr |
1.8.0 |
|
|
MIT |
| | | X | Secondary analyses of CNV data (HRD and more) |
| bioconductor-oncoscore |
1.34.0 |
|
|
file |
| | | X | A tool to identify potentially oncogenic genes |
| bioconductor-oncosimulr |
4.8.0 |
|
|
GPL |
X | X | | | Forward Genetic Simulation of Cancer Progression with Epistasis |
| bioconductor-onesense |
1.20.0 |
|
|
GPL |
| | | X | One-Dimensional Soli-Expression by Nonlinear Stochastic Embedding (OneSENSE) |
| bioconductor-onlinefdr |
2.14.0 |
|
|
GPL-3 |
X | X | | X | Online error rate control |
| bioconductor-ontoproc |
2.0.0 |
|
|
Artistic-2.0 |
| | | X | processing of ontologies of anatomy, cell lines, and so on |
| bioconductor-ontoprocdata |
0.99.9901 |
|
|
Artistic-2.0 |
| | | X | A data package for ontoProc |
| bioconductor-opencyto |
2.18.0 |
|
|
AGPL-3.0-only |
X | X | | | Hierarchical Gating Pipeline for flow cytometry data |
| bioconductor-openprimer |
1.28.0 |
|
|
GPL-2 |
| | | X | Multiplex PCR Primer Design and Analysis |
| bioconductor-openprimerui |
1.24.0 |
|
|
GPL-2 |
| | | X | Shiny Application for Multiplex PCR Primer Design and Analysis |
| bioconductor-openstats |
1.18.0 |
|
|
GPL |
| | | X | A Robust and Scalable Software Package for Reproducible Analysis of... |
| bioconductor-operonhumanv3.db |
3.2.3 |
|
|
Artistic-2.0 |
| | | X | FHCRC Nelson Lab OperonHumanV3 Annotation Data (OperonHumanV3) |
| bioconductor-opossom |
2.24.0 |
|
|
GPL |
X | X | | | Comprehensive analysis of transcriptome data |
| bioconductor-oppar |
1.34.0 |
|
|
GPL-2 |
X | X | | | Outlier profile and pathway analysis in R |
| bioconductor-oppti |
1.20.0 |
|
|
MIT |
| | | X | Outlier Protein and Phosphosite Target Identifier |
| bioconductor-optimalflow |
1.18.0 |
|
|
Artistic-2.0 |
| | | X | optimalFlow |
| bioconductor-optimalflowdata |
1.18.0 |
|
|
Artistic-2.0 |
| | | X | optimalFlowData |
| bioconductor-opweight |
1.28.0 |
|
|
Artistic-2.0 |
| | | X | Optimal p-value weighting with independent information |
| bioconductor-orderedlist |
1.78.0 |
|
|
GPL |
X | X | | X | Similarities of Ordered Gene Lists |
| bioconductor-orfhunter |
1.14.0 |
|
|
MIT |
X | X | | | Predict open reading frames in nucleotide sequences |
| bioconductor-orfik |
1.26.0 |
|
|
MIT |
X | X | | | Open Reading Frames in Genomics |
| bioconductor-org.ag.eg.db |
3.20.0 |
|
|
Artistic-2.0 |
| | | X | Genome wide annotation for Anopheles |
| bioconductor-org.at.tair.db |
3.20.0 |
|
|
Artistic-2.0 |
| | | X | Genome wide annotation for Arabidopsis |
| bioconductor-org.bt.eg.db |
3.20.0 |
|
|
Artistic-2.0 |
X | X | | X | Genome wide annotation for Bovine |
| bioconductor-org.ce.eg.db |
3.20.0 |
|
|
Artistic-2.0 |
X | X | | X | Genome wide annotation for Worm |
| bioconductor-org.cf.eg.db |
3.20.0 |
|
|
Artistic-2.0 |
X | X | | X | Genome wide annotation for Canine |
| bioconductor-org.dm.eg.db |
3.20.0 |
|
|
Artistic-2.0 |
X | X | | X | Genome wide annotation for Fly |
| bioconductor-org.dr.eg.db |
3.20.0 |
|
|
Artistic-2.0 |
X | X | | X | Genome wide annotation for Zebrafish |
| bioconductor-org.eck12.eg.db |
3.20.0 |
|
|
Artistic-2.0 |
| | | X | Genome wide annotation for E coli strain K12 |
| bioconductor-org.ecsakai.eg.db |
3.20.0 |
|
|
Artistic-2.0 |
| | | X | Genome wide annotation for E coli strain Sakai |
| bioconductor-org.gg.eg.db |
3.20.0 |
|
|
Artistic-2.0 |
X | X | | X | Genome wide annotation for Chicken |
| bioconductor-org.hs.eg.db |
3.20.0 |
|
|
Artistic-2.0 |
X | X | | X | Genome wide annotation for Human |
| bioconductor-org.mm.eg.db |
3.20.0 |
|
|
Artistic-2.0 |
X | X | | X | Genome wide annotation for Mouse |
| bioconductor-org.mmu.eg.db |
3.20.0 |
|
|
Artistic-2.0 |
| | | X | Genome wide annotation for Rhesus |
| bioconductor-org.mxanthus.db |
1.0.27 |
|
|
Artistic-2.0 |
| | | X | Genome wide annotation for Myxococcus xanthus DK 1622 |
| bioconductor-org.pf.plasmo.db |
3.14.0 |
|
|
Artistic-2.0 |
| | | X | Genome wide annotation for Malaria |
| bioconductor-org.pt.eg.db |
3.20.0 |
|
|
Artistic-2.0 |
| | | X | Genome wide annotation for Chimp |
| bioconductor-org.rn.eg.db |
3.20.0 |
|
|
Artistic-2.0 |
X | X | | X | Genome wide annotation for Rat |
| bioconductor-org.sc.sgd.db |
3.20.0 |
|
|
Artistic-2.0 |
X | X | | X | Genome wide annotation for Yeast |
| bioconductor-org.ss.eg.db |
3.20.0 |
|
|
Artistic-2.0 |
X | X | | X | Genome wide annotation for Pig |
| bioconductor-org.xl.eg.db |
3.20.0 |
|
|
Artistic-2.0 |
| | | X | Genome wide annotation for Xenopus |
| bioconductor-organism.dplyr |
1.34.0 |
|
|
Artistic-2.0 |
| | | X | dplyr-based Access to Bioconductor Annotation Resources |
| bioconductor-organismdbi |
1.48.0 |
|
|
Artistic-2.0 |
X | X | | X | Software to enable the smooth interfacing of different database packages |
| bioconductor-orthogene |
1.12.0 |
|
|
GPL-3 |
| | | X | Interspecies gene mapping |
| bioconductor-orthology.eg.db |
3.20.0 |
|
|
Artistic-2.0 |
| | | X | Orthology mapping package |
| bioconductor-orthos |
1.4.0 |
|
|
MIT |
| | | X | `orthos` is an R package for variance decomposition using conditional... |
| bioconductor-orthosdata |
1.4.0 |
|
|
MIT |
| | | X | Data for the orthos package |
| bioconductor-osat |
1.54.0 |
|
|
Artistic-2.0 |
X | X | | X | OSAT: Optimal Sample Assignment Tool |
| bioconductor-oscope |
1.36.0 |
|
|
Artistic-2.0 |
X | X | | X | Oscope - A statistical pipeline for identifying oscillatory genes in... |
| bioconductor-otubase |
1.56.0 |
|
|
Artistic-2.0 |
X | X | | X | Provides structure and functions for the analysis of OTU data |
| bioconductor-outlierd |
1.53.0 |
|
|
GPL |
X | X | | X | Outlier detection using quantile regression on the M-A scatterplots of... |
| bioconductor-outrider |
1.24.0 |
|
|
MIT |
X | X | | | OUTRIDER - OUTlier in RNA-Seq fInDER |
| bioconductor-outsplice |
1.6.0 |
|
|
GPL-2 |
| | | X | Comparison of Splicing Events between Tumor and Normal Samples |
| bioconductor-oveseg |
1.22.0 |
|
|
GPL-2 |
X | X | | | OVESEG-test to detect tissue/cell-specific markers |
| bioconductor-paa |
1.40.0 |
|
|
BSD_3_clause |
X | X | | | PAA (Protein Array Analyzer) |
| bioconductor-packfinder |
1.18.0 |
|
|
GPL-2 |
| | | X | de novo Annotation of Pack-TYPE Transposable Elements |
| bioconductor-padma |
1.16.0 |
|
|
GPL |
| | | X | Individualized Multi-Omic Pathway Deviation Scores Using Multiple... |
| bioconductor-padog |
1.48.0 |
|
|
GPL |
X | X | | X | Pathway Analysis with Down-weighting of Overlapping Genes (PADOG) |
| bioconductor-paeg1acdf |
2.18.0 |
|
|
LGPL |
| | | X | paeg1acdf |
| bioconductor-paeg1aprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type paeg1a |
| bioconductor-pagerank |
1.16.0 |
|
|
GPL-2 |
| | | X | Temporal and Multiplex PageRank for Gene Regulatory Network Analysis |
| bioconductor-pairadise |
1.22.0 |
|
|
MIT |
| | | X | PAIRADISE: Paired analysis of differential isoform expression |
| bioconductor-paircompviz |
1.44.0 |
|
|
GPL |
X | X | | X | Multiple comparison test visualization |
| bioconductor-pairedgsea |
1.6.0 |
|
|
MIT |
| | | X | Paired DGE and DGS analysis for gene set enrichment analysis |
| bioconductor-pairkat |
1.12.0 |
|
|
GPL-3 |
| | | X | PaIRKAT |
| bioconductor-pandar |
1.38.0 |
|
|
GPL-2 |
X | X | | X | PANDA Algorithm |
| bioconductor-panelcn.mops |
1.28.0 |
|
|
LGPL |
| | | X | CNV detection tool for targeted NGS panel data |
| bioconductor-pannbuilder |
1.43.0 |
|
|
LGPL |
X | X | | | Processing annotation data from public data repositories and building... |
| bioconductor-panomir |
1.10.0 |
|
|
MIT |
| | | X | Detection of miRNAs that regulate interacting groups of pathways |
| bioconductor-panp |
1.76.0 |
|
|
GPL |
X | X | | X | Presence-Absence Calls from Negative Strand Matching Probesets |
| bioconductor-panr |
1.52.0 |
|
|
Artistic-2.0 |
X | X | | X | Posterior association networks and functional modules inferred from... |
| bioconductor-panther.db |
1.0.12 |
|
|
Artistic-2.0 |
X | X | | X | A set of annotation maps describing the entire PANTHER Gene Ontology |
| bioconductor-panviz |
1.4.0 |
|
|
Artistic-2.0 |
| | | X | Integrating Multi-Omic Network Data With Summay-Level GWAS Data |
| bioconductor-panvizgenerator |
1.22.0 |
|
|
GPL |
| | | X | Generate PanViz visualisations from your pangenome |
| bioconductor-papi |
1.26.0 |
|
|
GPL(>= |
X | X | | X | Predict metabolic pathway activity based on metabolomics data |
| bioconductor-parathyroidse |
1.40.0 |
|
|
LGPL |
| | | X | RangedSummarizedExperiment for RNA-Seq of primary cultures of... |
| bioconductor-pareg |
1.6.0 |
|
|
GPL-3 |
| | | X | Pathway enrichment using a regularized regression approach |
| bioconductor-parglms |
1.38.0 |
|
|
Artistic-2.0 |
| | | X | support for parallelized estimation of GLMs/GEEs |
| bioconductor-parody |
1.64.0 |
|
|
Artistic-2.0 |
X | X | | X | Parametric And Resistant Outlier DYtection |
| bioconductor-partcnv |
1.4.0 |
|
|
GPL-2 |
| | | X | Infer locally aneuploid cells using single cell RNA-seq data |
| bioconductor-partheenmetadata.db |
3.2.3 |
|
|
Artistic-2.0 |
| | | X | PartheenMetaData http://swegene.onk.lu.se Annotation Data (PartheenMetaData) |
| bioconductor-pasilla |
1.34.0 |
|
|
LGPL |
| | | X | Data package with per-exon and per-gene read counts of RNA-seq samples... |
| bioconductor-pasillabamsubset |
0.44.0 |
|
|
LGPL |
| | | X | Subset of BAM files from "Pasilla" experiment |
| bioconductor-pasillatranscriptexpr |
1.30.0 |
|
|
GPL |
| | | X | Data package with transcript expression obtained with kallisto from... |
| bioconductor-past |
1.22.0 |
|
|
GPL |
| | | X | Pathway Association Study Tool (PAST) |
| bioconductor-path2ppi |
1.36.0 |
|
|
GPL |
X | X | | X | Prediction of pathway-related protein-protein interaction networks |
| bioconductor-pathifier |
1.44.0 |
|
|
Artistic-1.0 |
X | X | | X | Quantify deregulation of pathways in cancer |
| bioconductor-pathnet |
1.46.0 |
|
|
GPL-3 |
X | X | | X | An R package for pathway analysis using topological information |
| bioconductor-pathnetdata |
1.42.0 |
|
|
GPL-3 |
| | | X | Experimental data for the PathNet package |
| bioconductor-pathostat |
1.32.0 |
|
|
GPL |
X | X | | X | PathoStat Statistical Microbiome Analysis Package |
| bioconductor-pathprint |
1.17.0 |
|
|
GPL |
X | X | | X | Pathway fingerprinting for analysis of gene expression arrays |
| bioconductor-pathprintgeodata |
1.20.0 |
|
|
GPL |
| | | X | Pathway fingerprint vectors representing a subsection of arrays from... |
| bioconductor-pathrender |
1.74.0 |
|
|
LGPL |
X | X | | X | Render molecular pathways |
| bioconductor-pathvar |
1.30.0 |
|
|
LGPL |
X | X | | X | Methods to Find Pathways with Significantly Different Variability |
| bioconductor-pathview |
1.46.0 |
|
|
GPL |
X | X | | X | a tool set for pathway based data integration and visualization |
| bioconductor-pathwaypca |
1.22.0 |
|
|
GPL-3 |
| | | X | Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection |
| bioconductor-pathwaysplice |
1.10.0 |
|
|
LGPL(>=2) |
| | | X | An R Package for Unbiased Splicing Pathway Analysis |
| bioconductor-paxtoolsr |
1.36.0 |
|
|
LGPL-3 |
| | | X | Access Pathways from Multiple Databases Through BioPAX and Pathway Commons |
| bioconductor-pbase |
0.26.0 |
|
|
GPL-3 |
X | X | | | Manipulating and exploring protein and proteomics data |
| bioconductor-pbcmc |
1.8.0 |
|
|
GPL |
X | X | | | The pbcmc package characterizes uncertainty assessment on gene... |
| bioconductor-pcaexplorer |
3.0.0 |
|
|
MIT |
X | X | | X | Interactive Visualization of RNA-seq Data Using a Principal Components Approach |
| bioconductor-pcagopromoter |
1.30.0 |
|
|
GPL |
X | X | | X | pcaGoPromoter is used to analyze DNA micro array data |
| bioconductor-pcagopromoter.hs.hg19 |
1.26.0 |
|
|
GPL |
| | | X | pcaGoPromoter.Hs.hg19 is a data package used by pcaGoPromoter |
| bioconductor-pcagopromoter.mm.mm9 |
1.26.0 |
|
|
GPL |
| | | X | pcaGoPromoter.Mm.mm9 is a data package used by pcaGoPromoter |
| bioconductor-pcagopromoter.rn.rn4 |
1.26.0 |
|
|
GPL |
| | | X | pcaGoPromoter.Rn.rn4 is a data package used by pcaGoPromoter |
| bioconductor-pcamethods |
1.98.0 |
|
|
GPL |
X | X | | | A collection of PCA methods |
| bioconductor-pcan |
1.34.0 |
|
|
CC |
X | X | | X | Phenotype Consensus ANalysis (PCAN) |
| bioconductor-pcatools |
2.18.0 |
|
|
GPL-3 |
X | X | | X | PCAtools: Everything Principal Components Analysis |
| bioconductor-pchicdata |
1.34.0 |
|
|
Artistic-2.0 |
X | X | | X | Promoter Capture Hi-C data |
| bioconductor-pcot2 |
1.58.0 |
|
|
GPL |
X | X | | X | Principal Coordinates and Hotelling's T-Square method |
| bioconductor-pcpheno |
1.50.0 |
|
|
Artistic-2.0 |
X | X | | X | Phenotypes and cellular organizational units |
| bioconductor-pcxn |
2.24.0 |
|
|
MIT |
| | | X | Exploring, analyzing and visualizing functions utilizing the pcxnData package |
| bioconductor-pcxndata |
2.24.0 |
|
|
MIT |
| | | X | Correlation coefficients and p values between pre-defined pathway/gene sets |
| bioconductor-pd.081229.hg18.promoter.medip.hx1 |
0.99.4 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for NimbleGen 081229_hg18_promoter_medip_hx1 |
| bioconductor-pd.2006.07.18.hg18.refseq.promoter |
1.8.1 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for NimbleGen 2006-07-18_hg18_refseq_promoter |
| bioconductor-pd.2006.07.18.mm8.refseq.promoter |
0.99.3 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for NimbleGen 2006-07-18_mm8_refseq_promoter |
| bioconductor-pd.2006.10.31.rn34.refseq.promoter |
0.99.3 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for NimbleGen 2006-10-31_rn34_refseq_promoter |
| bioconductor-pd.ag |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name AG |
| bioconductor-pd.aragene.1.0.st |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix AraGene-1_0-st |
| bioconductor-pd.aragene.1.1.st |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix AraGene-1_1-st |
| bioconductor-pd.atdschip.tiling |
0.44.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix Atdschip_tiling |
| bioconductor-pd.ath1.121501 |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name ATH1-121501 |
| bioconductor-pd.barley1 |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name Barley1 |
| bioconductor-pd.bovgene.1.0.st |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix BovGene-1_0-st |
| bioconductor-pd.bovgene.1.1.st |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix BovGene-1_1-st |
| bioconductor-pd.bovine |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name Bovine |
| bioconductor-pd.bsubtilis |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name Bsubtilis |
| bioconductor-pd.cangene.1.0.st |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix CanGene-1_0-st |
| bioconductor-pd.cangene.1.1.st |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix CanGene-1_1-st |
| bioconductor-pd.canine |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name Canine |
| bioconductor-pd.canine.2 |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name Canine_2 |
| bioconductor-pd.celegans |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name Celegans |
| bioconductor-pd.charm.hg18.example |
0.99.4 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for NimbleGen charm_hg18_example |
| bioconductor-pd.chicken |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name Chicken |
| bioconductor-pd.chigene.1.0.st |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix ChiGene-1_0-st |
| bioconductor-pd.chigene.1.1.st |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix ChiGene-1_1-st |
| bioconductor-pd.chogene.2.0.st |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix CHOGene-2_0-st |
| bioconductor-pd.chogene.2.1.st |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix CHOGene-2_1-st |
| bioconductor-pd.citrus |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name Citrus |
| bioconductor-pd.clariom.d.human |
3.14.1 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix Clariom_D_Human |
| bioconductor-pd.clariom.s.human |
3.14.1 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix Clariom_S_Human |
| bioconductor-pd.clariom.s.human.ht |
3.14.1 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix Clariom_S_Human_HT |
| bioconductor-pd.clariom.s.mouse |
3.14.1 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix Clariom_S_Mouse |
| bioconductor-pd.clariom.s.mouse.ht |
3.14.1 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix Clariom_S_Mouse_HT |
| bioconductor-pd.clariom.s.rat |
3.14.1 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix Clariom_S_Rat |
| bioconductor-pd.clariom.s.rat.ht |
3.14.1 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix Clariom_S_Rat_HT |
| bioconductor-pd.cotton |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name Cotton |
| bioconductor-pd.cyngene.1.0.st |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix CynGene-1_0-st |
| bioconductor-pd.cyngene.1.1.st |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix CynGene-1_1-st |
| bioconductor-pd.cyrgene.1.0.st |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix CyRGene-1_0-st |
| bioconductor-pd.cyrgene.1.1.st |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix CyRGene-1_1-st |
| bioconductor-pd.cytogenetics.array |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix Cytogenetics_Array |
| bioconductor-pd.drogene.1.0.st |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix DroGene-1_0-st |
| bioconductor-pd.drogene.1.1.st |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix DroGene-1_1-st |
| bioconductor-pd.drosgenome1 |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name DrosGenome1 |
| bioconductor-pd.drosophila.2 |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name Drosophila_2 |
| bioconductor-pd.e.coli.2 |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name E_coli_2 |
| bioconductor-pd.ecoli |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name Ecoli |
| bioconductor-pd.ecoli.asv2 |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name Ecoli_ASv2 |
| bioconductor-pd.elegene.1.0.st |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix EleGene-1_0-st |
| bioconductor-pd.elegene.1.1.st |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix EleGene-1_1-st |
| bioconductor-pd.equgene.1.0.st |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix EquGene-1_0-st |
| bioconductor-pd.equgene.1.1.st |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix EquGene-1_1-st |
| bioconductor-pd.feinberg.hg18.me.hx1 |
0.99.3 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for NimbleGen feinberg_hg18_me_hx1 |
| bioconductor-pd.feinberg.mm8.me.hx1 |
0.99.3 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for NimbleGen feinberg_mm8_me_hx1 |
| bioconductor-pd.felgene.1.0.st |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix FelGene-1_0-st |
| bioconductor-pd.felgene.1.1.st |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix FelGene-1_1-st |
| bioconductor-pd.fingene.1.0.st |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix FinGene-1_0-st |
| bioconductor-pd.fingene.1.1.st |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix FinGene-1_1-st |
| bioconductor-pd.genomewidesnp.5 |
3.14.1 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix GenomeWideSNP_5 |
| bioconductor-pd.genomewidesnp.6 |
3.14.1 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix GenomeWideSNP_6 |
| bioconductor-pd.guigene.1.0.st |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix GuiGene-1_0-st |
| bioconductor-pd.guigene.1.1.st |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix GuiGene-1_1-st |
| bioconductor-pd.hc.g110 |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name HC_G110 |
| bioconductor-pd.hg.focus |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name HG-Focus |
| bioconductor-pd.hg.u133.plus.2 |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name HG-U133_Plus_2 |
| bioconductor-pd.hg.u133a |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name HG-U133A |
| bioconductor-pd.hg.u133a.2 |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name HG-U133A_2 |
| bioconductor-pd.hg.u133a.tag |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name HG-U133A_tag |
| bioconductor-pd.hg.u133b |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name HG-U133B |
| bioconductor-pd.hg.u219 |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name HG-U219 |
| bioconductor-pd.hg.u95a |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name HG U95A |
| bioconductor-pd.hg.u95av2 |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name HG U95Av2 |
| bioconductor-pd.hg.u95b |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name HG U95B |
| bioconductor-pd.hg.u95c |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name HG U95C |
| bioconductor-pd.hg.u95d |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name HG U95D |
| bioconductor-pd.hg.u95e |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name HG U95E |
| bioconductor-pd.hg18.60mer.expr |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for NimbleGen hg18_60mer_expr |
| bioconductor-pd.ht.hg.u133.plus.pm |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name HT_HG-U133_Plus_PM |
| bioconductor-pd.ht.hg.u133a |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name HT_HG-U133A |
| bioconductor-pd.ht.mg.430a |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name HT_MG-430A |
| bioconductor-pd.hta.2.0 |
3.12.2 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix HTA-2_0 |
| bioconductor-pd.hu6800 |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name Hu6800 |
| bioconductor-pd.huex.1.0.st.v2 |
3.14.1 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix HuEx-1_0-st-v2 |
| bioconductor-pd.hugene.1.0.st.v1 |
3.14.1 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix HuGene-1_0-st-v1 |
| bioconductor-pd.hugene.1.1.st.v1 |
3.14.1 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix HuGene-1_1-st-v1 |
| bioconductor-pd.hugene.2.0.st |
3.14.1 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix HuGene-2_0-st |
| bioconductor-pd.hugene.2.1.st |
3.14.1 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix HuGene-2_1-st |
| bioconductor-pd.maize |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name Maize |
| bioconductor-pd.mapping250k.nsp |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix Mapping250K_Nsp |
| bioconductor-pd.mapping250k.sty |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix Mapping250K_Sty |
| bioconductor-pd.mapping50k.hind240 |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix Mapping50K_Hind240 |
| bioconductor-pd.mapping50k.xba240 |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix Mapping50K_Xba240 |
| bioconductor-pd.margene.1.0.st |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix MarGene-1_0-st |
| bioconductor-pd.margene.1.1.st |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix MarGene-1_1-st |
| bioconductor-pd.medgene.1.0.st |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix MedGene-1_0-st |
| bioconductor-pd.medgene.1.1.st |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix MedGene-1_1-st |
| bioconductor-pd.medicago |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name Medicago |
| bioconductor-pd.mg.u74a |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name MG_U74A |
| bioconductor-pd.mg.u74av2 |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name MG_U74Av2 |
| bioconductor-pd.mg.u74b |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name MG_U74B |
| bioconductor-pd.mg.u74bv2 |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name MG_U74Bv2 |
| bioconductor-pd.mg.u74c |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name MG_U74C |
| bioconductor-pd.mg.u74cv2 |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name MG_U74Cv2 |
| bioconductor-pd.mirna.1.0 |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name miRNA-1_0 |
| bioconductor-pd.mirna.2.0 |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix miRNA-2_0 |
| bioconductor-pd.mirna.3.0 |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix miRNA-3_0 |
| bioconductor-pd.mirna.3.1 |
3.8.1 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix miRNA-3_1 |
| bioconductor-pd.mirna.4.0 |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix miRNA-4_0 |
| bioconductor-pd.moe430a |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name MOE430A |
| bioconductor-pd.moe430b |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name MOE430B |
| bioconductor-pd.moex.1.0.st.v1 |
3.14.1 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix MoEx-1_0-st-v1 |
| bioconductor-pd.mogene.1.0.st.v1 |
3.14.1 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix MoGene-1_0-st-v1 |
| bioconductor-pd.mogene.1.1.st.v1 |
3.14.1 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix MoGene-1_1-st-v1 |
| bioconductor-pd.mogene.2.0.st |
3.14.1 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix MoGene-2_0-st |
| bioconductor-pd.mogene.2.1.st |
3.14.1 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix MoGene-2_1-st |
| bioconductor-pd.mouse430.2 |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name Mouse430_2 |
| bioconductor-pd.mouse430a.2 |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name Mouse430A_2 |
| bioconductor-pd.mta.1.0 |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix MTA-1_0 |
| bioconductor-pd.mu11ksuba |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name Mu11KsubA |
| bioconductor-pd.mu11ksubb |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name Mu11KsubB |
| bioconductor-pd.nugo.hs1a520180 |
3.4.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name NuGO_Hs1a520180 |
| bioconductor-pd.nugo.mm1a520177 |
3.4.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name NuGO_Mm1a520177 |
| bioconductor-pd.ovigene.1.0.st |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix OviGene-1_0-st |
| bioconductor-pd.ovigene.1.1.st |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix OviGene-1_1-st |
| bioconductor-pd.pae.g1a |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name Pae_G1a |
| bioconductor-pd.plasmodium.anopheles |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name Plasmodium_Anopheles |
| bioconductor-pd.poplar |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name Poplar |
| bioconductor-pd.porcine |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name Porcine |
| bioconductor-pd.porgene.1.0.st |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix PorGene-1_0-st |
| bioconductor-pd.porgene.1.1.st |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix PorGene-1_1-st |
| bioconductor-pd.rabgene.1.0.st |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix RabGene-1_0-st |
| bioconductor-pd.rabgene.1.1.st |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix RabGene-1_1-st |
| bioconductor-pd.rae230a |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name RAE230A |
| bioconductor-pd.rae230b |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name RAE230B |
| bioconductor-pd.raex.1.0.st.v1 |
3.14.1 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix RaEx-1_0-st-v1 |
| bioconductor-pd.ragene.1.0.st.v1 |
3.14.1 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix RaGene-1_0-st-v1 |
| bioconductor-pd.ragene.1.1.st.v1 |
3.14.1 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix RaGene-1_1-st-v1 |
| bioconductor-pd.ragene.2.0.st |
3.14.1 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix RaGene-2_0-st |
| bioconductor-pd.ragene.2.1.st |
3.14.1 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix RaGene-2_1-st |
| bioconductor-pd.rat230.2 |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name Rat230_2 |
| bioconductor-pd.rcngene.1.0.st |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix RCnGene-1_0-st |
| bioconductor-pd.rcngene.1.1.st |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix RCnGene-1_1-st |
| bioconductor-pd.rg.u34a |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name RG_U34A |
| bioconductor-pd.rg.u34b |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name RG_U34B |
| bioconductor-pd.rg.u34c |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name RG_U34C |
| bioconductor-pd.rhegene.1.0.st |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix RheGene-1_0-st |
| bioconductor-pd.rhegene.1.1.st |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix RheGene-1_1-st |
| bioconductor-pd.rhesus |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name Rhesus |
| bioconductor-pd.rice |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name Rice |
| bioconductor-pd.rjpgene.1.0.st |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix RJpGene-1_0-st |
| bioconductor-pd.rjpgene.1.1.st |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix RJpGene-1_1-st |
| bioconductor-pd.rn.u34 |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name RN_U34 |
| bioconductor-pd.rta.1.0 |
3.12.2 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix RTA-1_0 |
| bioconductor-pd.rusgene.1.0.st |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix RUSGene-1_0-st |
| bioconductor-pd.rusgene.1.1.st |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix RUSGene-1_1-st |
| bioconductor-pd.s.aureus |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name S_aureus |
| bioconductor-pd.soybean |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name Soybean |
| bioconductor-pd.soygene.1.0.st |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix SoyGene-1_0-st |
| bioconductor-pd.soygene.1.1.st |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix SoyGene-1_1-st |
| bioconductor-pd.sugar.cane |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name Sugar_Cane |
| bioconductor-pd.tomato |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name Tomato |
| bioconductor-pd.u133.x3p |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name U133_X3P |
| bioconductor-pd.vitis.vinifera |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name Vitis_Vinifera |
| bioconductor-pd.wheat |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name wheat |
| bioconductor-pd.x.laevis.2 |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name X_laevis_2 |
| bioconductor-pd.x.tropicalis |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name X_tropicalis |
| bioconductor-pd.xenopus.laevis |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name Xenopus_laevis |
| bioconductor-pd.yeast.2 |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name Yeast_2 |
| bioconductor-pd.yg.s98 |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name YG_S98 |
| bioconductor-pd.zebgene.1.0.st |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix ZebGene-1_0-st |
| bioconductor-pd.zebgene.1.1.st |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for Affymetrix ZebGene-1_1-st |
| bioconductor-pd.zebrafish |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Platform Design Info for The Manufacturer's Name Zebrafish |
| bioconductor-pdatk |
1.8.0 |
|
|
MIT |
| | | X | Pancreatic Ductal Adenocarcinoma Tool-Kit |
| bioconductor-pdinfobuilder |
1.70.0 |
|
|
Artistic-2.0 |
X | X | | | Platform Design Information Package Builder |
| bioconductor-peacoqc |
1.16.0 |
|
|
GPL |
| | | X | Peak-based selection of high quality cytometry data |
| bioconductor-peakpanther |
1.20.0 |
|
|
GPL-3 |
| | | X | Peak Picking and Annotation of High Resolution Experiments |
| bioconductor-peca |
1.42.0 |
|
|
GPL |
X | X | | X | Probe-level Expression Change Averaging |
| bioconductor-peco |
1.18.0 |
|
|
GPL |
| | | X | A Supervised Approach for **P**r**e**dicting **c**ell Cycle... |
| bioconductor-pedbarrayv10.db |
3.2.3 |
|
|
Artistic-2.0 |
| | | X | FHCRC Nelson Lab pedbarrayv10 Annotation Data (pedbarrayv10) |
| bioconductor-pedbarrayv9.db |
3.2.3 |
|
|
Artistic-2.0 |
| | | X | FHCRC Nelson Lab pedbarrayv9 Annotation Data (pedbarrayv9) |
| bioconductor-pedixplorer |
1.2.0 |
|
|
Artistic-2.0 |
| | | X | Pedigree Functions |
| bioconductor-pengls |
1.12.0 |
|
|
GPL-2 |
| | | X | Fit Penalised Generalised Least Squares models |
| bioconductor-pepdat |
1.26.0 |
|
|
Artistic-2.0 |
| | | X | Peptide microarray data package |
| bioconductor-pepsettest |
1.0.0 |
|
|
GPL |
| | | X | Peptide Set Test |
| bioconductor-pepsnmr |
1.24.0 |
|
|
GPL-2 |
| | | X | Pre-process 1H-NMR FID signals |
| bioconductor-pepsnmrdata |
1.24.0 |
|
|
GPL-2 |
| | | X | Datasets for the PepsNMR package |
| bioconductor-pepstat |
1.40.0 |
|
|
Artistic-2.0 |
X | X | | X | Statistical analysis of peptide microarrays |
| bioconductor-pepxmltab |
1.40.0 |
|
|
Artistic-2.0 |
X | X | | X | Parsing pepXML files and filter based on peptide FDR. |
| bioconductor-perfect |
1.14.0 |
|
|
Artistic-2.0 |
| | | X | Permutation filtration for microbiome data |
| bioconductor-periodicdna |
1.16.0 |
|
|
GPL-3 |
| | | X | Set of tools to identify periodic occurrences of k-mers in DNA sequences |
| bioconductor-perturbatr |
1.13.0 |
|
|
GPL-3 |
| | | X | Statistical Analysis of High-Throughput Genetic Perturbation Screens |
| bioconductor-pfam.db |
3.20.0 |
|
|
Artistic-2.0 |
X | X | | X | A set of protein ID mappings for PFAM |
| bioconductor-pfamanalyzer |
1.6.0 |
|
|
MIT |
| | | X | Identification of domain isotypes in pfam data |
| bioconductor-pfp |
1.7.0 |
|
|
GPL-2 |
| | | X | Pathway Fingerprint Framework in R |
| bioconductor-pga |
1.18.0 |
|
|
GPL-2 |
| | | X | An package for identification of novel peptides by customized database... |
| bioconductor-pgca |
1.30.0 |
|
|
GPL |
| | | X | PGCA: An Algorithm to Link Protein Groups Created from MS/MS Data |
| bioconductor-pgsea |
1.61.0 |
|
|
GPL-2 |
X | X | | X | Parametric Gene Set Enrichment Analysis |
| bioconductor-pgxrpi |
1.2.0 |
|
|
Artistic-2.0 |
| | | X | R wrapper for Progenetix |
| bioconductor-phantasus |
1.26.0 |
|
|
MIT |
| | | X | Visual and interactive gene expression analysis |
| bioconductor-phantasuslite |
1.4.0 |
|
|
MIT |
| | | X | Loading and annotation RNA-seq counts matrices |
| bioconductor-pharmacogx |
3.10.0 |
|
|
GPL |
X | X | | X | Analysis of Large-Scale Pharmacogenomic Data |
| bioconductor-phastcons100way.ucsc.hg19 |
3.7.2 |
|
|
Artistic-2.0 |
X | X | | X | UCSC phastCons conservation scores for hg19 |
| bioconductor-phastcons100way.ucsc.hg38 |
3.7.1 |
|
|
Artistic-2.0 |
| | | X | UCSC phastCons conservation scores for hg38 |
| bioconductor-phastcons30way.ucsc.hg38 |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | phastCons30way.UCSC.hg38 AnnotationHub Resource Metadata |
| bioconductor-phastcons35way.ucsc.mm39 |
3.16.0 |
|
|
Artistic-2.0 |
| | | X | UCSC phastCons mm39 conservation scores AnnotationHub Resource Metadata |
| bioconductor-phastcons7way.ucsc.hg38 |
3.7.1 |
|
|
Artistic-2.0 |
| | | X | UCSC phastCons conservation scores for hg38 |
| bioconductor-phemd |
1.18.0 |
|
|
GPL-2 |
| | | X | Phenotypic EMD for comparison of single-cell samples |
| bioconductor-phenodist |
1.27.0 |
|
|
LGPL-2.1 |
X | X | | | PhenoDist is designed for measuring phenotypic distance in image-based... |
| bioconductor-phenogeneranker |
1.14.0 |
|
|
Creative |
| | | X | PhenoGeneRanker: A gene and phenotype prioritization tool |
| bioconductor-phenomis |
1.8.0 |
|
|
CeCILL |
| | | X | Postprocessing and univariate analysis of omics data |
| bioconductor-phenopath |
1.30.0 |
|
|
Apache |
X | X | | | Genomic trajectories with heterogeneous genetic and environmental backgrounds |
| bioconductor-phenotest |
1.54.0 |
|
|
GPL |
| | | X | Tools to test association between gene expression and phenotype in a... |
| bioconductor-phenstat |
2.42.0 |
|
|
file |
X | X | | X | Statistical analysis of phenotypic data |
| bioconductor-philr |
1.32.0 |
|
|
GPL-3 |
X | X | | X | Phylogenetic partitioning based ILR transform for metagenomics data |
| bioconductor-phipdata |
1.14.0 |
|
|
MIT |
| | | X | Container for PhIP-Seq Experiments |
| bioconductor-phosphonormalizer |
1.30.0 |
|
|
GPL |
X | X | | X | Compensates for the bias introduced by median normalization in |
| bioconductor-phosr |
1.16.0 |
|
|
GPL-3 |
| | | X | A set of methods and tools for comprehensive analysis of phosphoproteomics data |
| bioconductor-phylop35way.ucsc.mm39 |
3.16.0 |
|
|
Artistic-2.0 |
| | | X | UCSC phyloP mm39 conservation scores AnnotationHub Resource Metadata |
| bioconductor-phyloprofile |
1.20.0 |
|
|
MIT |
| | | X | PhyloProfile |
| bioconductor-phyloprofiledata |
1.20.0 |
|
|
MIT |
| | | X | Data package for phylogenetic profile analysis using PhyloProfile tool |
| bioconductor-phyloseq |
1.50.0 |
|
|
AGPL-3 |
X | X | | X | Handling and analysis of high-throughput microbiome census data |
| bioconductor-pi |
2.14.0 |
|
|
GPL-3 |
| | | X | Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene and... |
| bioconductor-piano |
2.22.0 |
|
|
GPL |
X | X | | X | Platform for integrative analysis of omics data |
| bioconductor-pickgene |
1.78.0 |
|
|
GPL |
X | X | | X | Adaptive Gene Picking for Microarray Expression Data Analysis |
| bioconductor-pics |
2.50.0 |
|
|
Artistic-2.0 |
X | X | | | Probabilistic inference of ChIP-seq |
| bioconductor-pig.db0 |
3.20.0 |
|
|
Artistic-2.0 |
| | | X | Base Level Annotation databases for pig |
| bioconductor-pigengene |
1.32.0 |
|
|
GPL |
| | | X | Infers biological signatures from gene expression data |
| bioconductor-ping |
2.50.0 |
|
|
Artistic-2.0 |
X | X | | | Probabilistic inference for Nucleosome Positioning with MNase-based or... |
| bioconductor-pint |
1.36.0 |
|
|
BSD_2_clause |
X | X | | X | Pairwise INTegration of functional genomics data |
| bioconductor-pipecomp |
1.12.0 |
|
|
GPL |
| | | X | pipeComp pipeline benchmarking framework |
| bioconductor-pipeframe |
1.22.0 |
|
|
GPL-3 |
| | | X | Pipeline framework for bioinformatics in R |
| bioconductor-pipets |
1.2.0 |
|
|
GPL-3 |
| | | X | Poisson Identification of PEaks from Term-Seq data |
| bioconductor-pirat |
1.0.0 |
|
|
GPL-2 |
| | | X | Precursor or Peptide Imputation under Random Truncation |
| bioconductor-piuma |
1.2.0 |
|
|
GPL-3 |
| | | X | Phenotypes Identification Using Mapper from topological data Analysis |
| bioconductor-pkgdeptools |
1.63.0 |
|
|
GPL-2 |
X | X | | X | Package Dependency Tools |
| bioconductor-planet |
1.14.0 |
|
|
GPL-2 |
| | | X | Placental DNA methylation analysis tools |
| bioconductor-planttfhunter |
1.6.0 |
|
|
GPL-3 |
| | | X | Identification and classification of plant transcription factors |
| bioconductor-plasfia |
1.26.0 |
|
|
LGPL |
| | | X | FIA-HRMS plasma dataset |
| bioconductor-plasmodiumanophelescdf |
2.18.0 |
|
|
LGPL |
| | | X | plasmodiumanophelescdf |
| bioconductor-plasmodiumanophelesprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type plasmodiumanopheles |
| bioconductor-plasmut |
1.4.0 |
|
|
Artistic-2.0 |
| | | X | Stratifying mutations observed in cell-free DNA and white blood cells... |
| bioconductor-platecore |
1.40.1 |
|
|
Artistic-2.0 |
| | | X | Provides basic S4 data structures and routines for analyzing plate... |
| bioconductor-plethy |
1.36.0 |
|
|
GPL-3 |
X | X | | X | R framework for exploration and analysis of respirometry data |
| bioconductor-plgem |
1.78.0 |
|
|
GPL-2 |
X | X | | X | Detect differential expression in microarray and proteomics datasets... |
| bioconductor-plier |
1.76.0 |
|
|
GPL |
X | X | | | Implements the Affymetrix PLIER algorithm |
| bioconductor-plogo2 |
1.14.0 |
|
|
GPL-2 |
| | | X | Plot Gene Ontology and KEGG pathway Annotation and Abundance |
| bioconductor-plotgardener |
1.12.0 |
|
|
MIT |
X | X | | | Coordinate-Based Genomic Visualization Package for R |
| bioconductor-plotgardenerdata |
1.12.0 |
|
|
MIT |
| | | X | Datasets and test data files for the plotgardener package |
| bioconductor-plotgrouper |
1.24.0 |
|
|
GPL-3 |
| | | X | Shiny app GUI wrapper for ggplot with built-in statistical analysis |
| bioconductor-plpe |
1.66.0 |
|
|
GPL |
X | X | | X | Local Pooled Error Test for Differential Expression with Paired... |
| bioconductor-plrs |
1.27.0 |
|
|
GPL |
| | | X | Piecewise Linear Regression Splines (PLRS) for the association between... |
| bioconductor-plsdabatch |
1.2.0 |
|
|
GPL-3 |
| | | X | PLSDA-batch |
| bioconductor-plw |
1.47.0 |
|
|
GPL-2 |
X | X | | | Probe level Locally moderated Weighted t-tests. |
| bioconductor-plyinteractions |
1.4.0 |
|
|
Artistic-2.0 |
| | | X | Extending tidy verbs to genomic interactions |
| bioconductor-plyranges |
1.26.0 |
|
|
Artistic-2.0 |
| | | X | A fluent interface for manipulating GenomicRanges |
| bioconductor-plyxp |
1.0.0 |
|
|
MIT |
| | | X | Data masks for SummarizedExperiment enabling dplyr-like manipulation |
| bioconductor-pmm |
1.38.0 |
|
|
GPL-3 |
X | X | | X | Parallel Mixed Model |
| bioconductor-pmp |
1.18.0 |
|
|
GPL-3 |
| | | X | Peak Matrix Processing and signal batch correction for metabolomics datasets |
| bioconductor-pocrcannotation.db |
3.2.3 |
|
|
Artistic-2.0 |
| | | X | A package containing metadata for POCRC arrays |
| bioconductor-podcall |
1.14.0 |
|
|
GPL-3 |
| | | X | Positive Droplet Calling for DNA Methylation Droplet Digital PCR |
| bioconductor-podkat |
1.38.0 |
|
|
GPL |
X | X | | | Position-Dependent Kernel Association Test |
| bioconductor-pogos |
1.26.0 |
|
|
Artistic-2.0 |
| | | X | PharmacOGenomics Ontology Support |
| bioconductor-polyester |
1.38.0 |
|
|
Artistic-2.0 |
| | | X | Simulate RNA-seq reads |
| bioconductor-polyfit |
1.22.0 |
|
|
GPL |
X | X | | X | Add-on to DESeq to improve p-values and q-values |
| bioconductor-polyphen.hsapiens.dbsnp131 |
1.0.2 |
|
|
Artistic-2.0 |
| | | X | PolyPhen Predictions for Homo sapiens dbSNP build 131 |
| bioconductor-poma |
1.16.0 |
|
|
GPL-3 |
| | | X | Tools for Omics Data Analysis |
| bioconductor-poplarcdf |
2.18.0 |
|
|
LGPL |
| | | X | poplarcdf |
| bioconductor-poplarprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type poplar |
| bioconductor-porcine.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix Porcine Array annotation data (chip porcine) |
| bioconductor-porcinecdf |
2.18.0 |
|
|
LGPL |
| | | X | porcinecdf |
| bioconductor-porcineprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type porcine |
| bioconductor-post |
1.14.0 |
|
|
GPL |
| | | X | Projection onto Orthogonal Space Testing for High Dimensional Data |
| bioconductor-potra |
1.13.0 |
|
|
LGPL |
| | | X | PoTRA: Pathways of Topological Rank Analysis |
| bioconductor-powerexplorer |
1.7.0 |
|
|
Artistic-2.0 |
| | | X | Power Estimation Tool for RNA-Seq and proteomics data |
| bioconductor-powertcr |
1.26.0 |
|
|
Artistic-2.0 |
| | | X | Model-Based Comparative Analysis of the TCR Repertoire |
| bioconductor-powsc |
1.14.0 |
|
|
GPL-2 |
| | | X | Simulation, power evaluation, and sample size recommendation for single... |
| bioconductor-ppcseq |
1.14.0 |
|
|
GPL-3 |
X | X | | | Probabilistic Outlier Identification for RNA Sequencing Generalized... |
| bioconductor-ppidata |
0.32.0 |
|
|
Artistic-2.0 |
X | X | | X | A package that contains the bait to prey directed graphs for... |
| bioconductor-ppinfer |
1.32.0 |
|
|
Artistic-2.0 |
X | X | | X | Inferring functionally related proteins using protein interaction networks |
| bioconductor-ppistats |
1.60.0 |
|
|
Artistic-2.0 |
X | X | | X | Protein-Protein Interaction Statistical Package |
| bioconductor-pqsfinder |
2.22.0 |
|
|
BSD_2_clause |
X | X | | | Identification of potential quadruplex forming sequences |
| bioconductor-prada |
1.63.0 |
|
|
LGPL |
X | X | | | Data analysis for cell-based functional assays |
| bioconductor-pram |
1.22.0 |
|
|
GPL |
| | | X | Pooling RNA-seq datasets for assembling transcript models |
| bioconductor-prebs |
1.46.0 |
|
|
Artistic-2.0 |
X | X | | X | Probe region expression estimation for RNA-seq data for improved... |
| bioconductor-prebsdata |
1.42.0 |
|
|
Artistic-2.0 |
| | | X | Data for 'prebs' package |
| bioconductor-precisetad |
1.16.0 |
|
|
MIT |
| | | X | preciseTAD: A machine learning framework for precise TAD boundary prediction |
| bioconductor-precisetadhub |
1.14.0 |
|
|
MIT |
| | | X | Pre-trained random forest models obtained using preciseTAD |
| bioconductor-precisiontrialdrawer |
1.10.0 |
|
|
GPL-3 |
| | | X | A Tool to Analyze and Design NGS Based Custom Gene Panels |
| bioconductor-preda |
1.52.0 |
|
|
GPL-2 |
X | X | | X | Position Related Data Analysis |
| bioconductor-predasampledata |
0.46.0 |
|
|
Artistic-2.0 |
| | | X | expression and copy number data on clear cell renal carcinoma samples |
| bioconductor-predictionet |
1.40.0 |
|
|
Artistic-2.0 |
X | X | | | Inference for predictive networks designed for (but not limited to) genomic data |
| bioconductor-preprocesscore |
1.68.0 |
|
|
LGPL |
X | X | | | A collection of pre-processing functions |
| bioconductor-primeviewcdf |
2.18.0 |
|
|
LGPL |
| | | X | primeviewcdf |
| bioconductor-primeviewprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type primeview |
| bioconductor-primirtss |
1.24.0 |
|
|
GPL-2 |
| | | X | Prediction of pri-miRNA Transcription Start Site |
| bioconductor-prince |
1.22.0 |
|
|
GPL-3 |
| | | X | Predicting Interactomes from Co-Elution |
| bioconductor-prize |
1.17.0 |
|
|
Artistic-2.0 |
X | X | | X | Prize: an R package for prioritization estimation based on analytic... |
| bioconductor-proactiv |
1.16.0 |
|
|
MIT |
| | | X | Estimate Promoter Activity from RNA-Seq data |
| bioconductor-probamr |
1.40.0 |
|
|
Artistic-2.0 |
X | X | | X | Generating SAM file for PSMs in shotgun proteomics data |
| bioconductor-probatch |
1.13.0 |
|
|
GPL-3 |
| | | X | Tools for Diagnostics and Corrections of Batch Effects in Proteomics |
| bioconductor-process |
1.82.0 |
|
|
Artistic-2.0 |
X | X | | X | Ciphergen SELDI-TOF Processing |
| bioconductor-procoil |
2.34.0 |
|
|
GPL |
X | X | | X | Prediction of Oligomerization of Coiled Coil Proteins |
| bioconductor-proda |
1.20.0 |
|
|
GPL-3 |
| | | X | Differential Abundance Analysis of Label-Free Mass Spectrometry Data |
| bioconductor-prodata |
1.44.0 |
|
|
GPL |
| | | X | SELDI-TOF data of Breast cancer samples |
| bioconductor-profia |
1.23.0 |
|
|
CeCILL |
X | X | | | Preprocessing of FIA-HRMS data |
| bioconductor-profileplyr |
1.22.0 |
|
|
GPL |
| | | X | Visualization and annotation of read signal over genomic ranges with profileplyr |
| bioconductor-profilescoredist |
1.34.0 |
|
|
MIT |
X | X | | | Profile score distributions |
| bioconductor-progeny |
1.28.0 |
|
|
Apache |
| | | X | Pathway RespOnsive GENes for activity inference from gene expression |
| bioconductor-projectr |
1.22.0 |
|
|
GPL |
| | | X | Functions for the projection of weights from PCA, CoGAPS, NMF,... |
| bioconductor-proloc |
1.46.0 |
|
|
GPL-2 |
X | X | | | A unifying bioinformatics framework for spatial proteomics |
| bioconductor-prolocdata |
1.44.0 |
|
|
GPL-2 |
| | | X | Data accompanying the pRoloc package |
| bioconductor-prolocgui |
2.16.0 |
|
|
GPL-2 |
X | X | | X | Interactive visualisation of spatial proteomics data |
| bioconductor-promise |
1.58.0 |
|
|
GPL |
X | X | | X | PRojection Onto the Most Interesting Statistical Evidence |
| bioconductor-prone |
1.0.0 |
|
|
GPL |
| | | X | The PROteomics Normalization Evaluator |
| bioconductor-proper |
1.38.0 |
|
|
GPL |
X | X | | X | PROspective Power Evaluation for RNAseq |
| bioconductor-props |
1.24.0 |
|
|
GPL-2 |
| | | X | PRObabilistic Pathway Score (PROPS) |
| bioconductor-prostar |
1.38.0 |
|
|
Artistic-2.0 |
| | | X | Provides a GUI for DAPAR |
| bioconductor-prostatecancercamcap |
1.34.0 |
|
|
Artistic-2.0 |
| | | X | Prostate Cancer Data |
| bioconductor-prostatecancergrasso |
1.34.0 |
|
|
Artistic-2.0 |
| | | X | Prostate Cancer Data |
| bioconductor-prostatecancerstockholm |
1.34.0 |
|
|
Artistic-2.0 |
| | | X | Prostate Cancer Data |
| bioconductor-prostatecancertaylor |
1.34.0 |
|
|
Artistic-2.0 |
| | | X | Prostate Cancer Data |
| bioconductor-prostatecancervarambally |
1.34.0 |
|
|
Artistic-2.0 |
| | | X | Prostate Cancer Data |
| bioconductor-prot2d |
1.20.0 |
|
|
GPL |
X | X | | X | The purpose of this package is to analyze (i.e. Normalize and select... |
| bioconductor-proteasy |
1.2.0 |
|
|
GPL-3 |
| | | X | Protease Mapping |
| bioconductor-proteinprofiles |
1.46.0 |
|
|
GPL-3 |
| | | X | Protein Profiling |
| bioconductor-proteodisco |
1.12.0 |
|
|
GPL-3 |
| | | X | Generation of customized protein variant databases from genomic... |
| bioconductor-proteomicsannotationhubdata |
1.24.0 |
|
|
Artistic-2.0 |
X | X | | X | Transform public proteomics data resources into Bioconductor Data Structures |
| bioconductor-proteomm |
1.24.0 |
|
|
MIT |
| | | X | Multi-Dataset Model-based Differential Expression Proteomics Analysis Platform |
| bioconductor-proteoqc |
1.21.0 |
|
|
LGPL-2 |
| | | X | An R package for proteomics data quality control |
| bioconductor-protgear |
1.10.0 |
|
|
GPL-3 |
| | | X | Protein Micro Array Data Management and Interactive Visualization |
| bioconductor-protgenerics |
1.38.0 |
|
|
Artistic-2.0 |
X | X | | X | Generic infrastructure for Bioconductor mass spectrometry packages |
| bioconductor-psea |
1.36.0 |
|
|
Artistic-2.0 |
X | X | | X | Population-Specific Expression Analysis. |
| bioconductor-psichomics |
1.32.0 |
|
|
MIT |
X | X | | | Graphical Interface for Alternative Splicing Quantification, Analysis... |
| bioconductor-psicquic |
1.32.0 |
|
|
Apache |
X | X | | X | Proteomics Standard Initiative Common QUery InterfaCe |
| bioconductor-psmatch |
1.10.0 |
|
|
Artistic-2.0 |
| | | X | Handling and Managing Peptide Spectrum Matches |
| bioconductor-psygenet2r |
1.34.0 |
|
|
MIT |
X | X | | X | psygenet2r - An R package for querying PsyGeNET and to perform... |
| bioconductor-ptairdata |
1.14.0 |
|
|
GPL-3 |
| | | X | PTR-TOF-MS volatolomics raw datasets from exhaled air and cell culture headspace |
| bioconductor-ptairms |
1.14.0 |
|
|
GPL-3 |
X | X | | | Pre-processing PTR-TOF-MS Data |
| bioconductor-pth2o2lipids |
1.32.0 |
|
|
MIT |
| | | X | P. tricornutum HPLC-ESI-MS Lipid Data from van Creveld et al. (2015) |
| bioconductor-pubscore |
1.6.0 |
|
|
MIT |
| | | X | Automatic calculation of literature relevance of genes |
| bioconductor-pulsedsilac |
1.8.0 |
|
|
GPL-3 |
| | | X | Analysis of pulsed-SILAC quantitative proteomics data |
| bioconductor-puma |
3.48.0 |
|
|
LGPL |
X | X | | | Propagating Uncertainty in Microarray Analysis(including Affymetrix... |
| bioconductor-pumadata |
2.42.0 |
|
|
LGPL |
| | | X | Various data sets for use with the puma package |
| bioconductor-purecn |
2.12.0 |
|
|
Artistic-2.0 |
X | X | | X | Copy number calling and SNV classification using targeted short read sequencing |
| bioconductor-pvac |
1.54.0 |
|
|
LGPL |
X | X | | X | PCA-based gene filtering for Affymetrix arrays |
| bioconductor-pvca |
1.46.0 |
|
|
LGPL |
X | X | | X | Principal Variance Component Analysis (PVCA) |
| bioconductor-pviz |
1.40.0 |
|
|
Artistic-2.0 |
X | X | | X | Peptide Annotation and Data Visualization using Gviz |
| bioconductor-pwalign |
1.2.0 |
|
|
Artistic-2.0 |
X | X | | | Perform pairwise sequence alignments |
| bioconductor-pwmenrich |
4.42.0 |
|
|
LGPL |
X | X | | X | PWM enrichment analysis |
| bioconductor-pwmenrich.dmelanogaster.background |
4.40.0 |
|
|
GPL-3 |
| | | X | D. melanogaster background for PWMEnrich |
| bioconductor-pwmenrich.hsapiens.background |
4.40.0 |
|
|
GPL-3 |
| | | X | H. sapiens background for PWMEnrich |
| bioconductor-pwmenrich.mmusculus.background |
4.40.0 |
|
|
GPL-3 |
| | | X | M. musculus background for PWMEnrich |
| bioconductor-pwomics |
1.34.0 |
|
|
GPL |
X | X | | X | Pathway-based data integration of omics data |
| bioconductor-pwrewas |
1.14.0 |
|
|
Artistic-2.0 |
| | | X | A user-friendly tool for comprehensive power estimation for epigenome... |
| bioconductor-pwrewas.data |
1.14.0 |
|
|
Artistic-2.0 |
| | | X | pwrEWAS.data: Reference data accompanying pwrEWAS |
| bioconductor-qckitfastq |
1.22.0 |
|
|
Artistic-2.0 |
X | X | | | FASTQ Quality Control |
| bioconductor-qcmetrics |
1.44.0 |
|
|
GPL-2 |
X | X | | X | A Framework for Quality Control |
| bioconductor-qdnaseq |
1.42.0 |
|
|
GPL |
X | X | | X | Quantitative DNA Sequencing for Chromosomal Aberrations |
| bioconductor-qdnaseq.hg19 |
1.36.0 |
|
|
GPL |
| | | X | QDNAseq bin annotation for hg19 |
| bioconductor-qdnaseq.mm10 |
1.36.0 |
|
|
GPL |
X | X | | X | Bin annotation mm10 |
| bioconductor-qfeatures |
1.16.0 |
|
|
Artistic-2.0 |
| | | X | Quantitative features for mass spectrometry data |
| bioconductor-qmtools |
1.10.0 |
|
|
GPL-3 |
| | | X | Quantitative Metabolomics Data Processing Tools |
| bioconductor-qpcrnorm |
1.64.0 |
|
|
LGPL |
X | X | | X | Data-driven normalization strategies for high-throughput qPCR data. |
| bioconductor-qpgraph |
2.40.0 |
|
|
GPL |
X | X | | | Estimation of genetic and molecular regulatory networks from... |
| bioconductor-qplexanalyzer |
1.24.0 |
|
|
GPL-2 |
| | | X | Tools for quantitative proteomics data analysis |
| bioconductor-qplexdata |
1.24.0 |
|
|
GPL-2 |
| | | X | Data accompanying qPLEXanalyzer package |
| bioconductor-qrqc |
1.52.0 |
|
|
GPL |
X | X | | | Quick Read Quality Control |
| bioconductor-qsea |
1.32.0 |
|
|
GPL-2 |
X | X | | | IP-seq data analysis and vizualization |
| bioconductor-qsmooth |
1.22.0 |
|
|
GPL-3 |
| | | X | Smooth quantile normalization |
| bioconductor-qsutils |
1.24.0 |
|
|
GPL-2 |
| | | X | Quasispecies Diversity |
| bioconductor-qsvar |
1.10.0 |
|
|
Artistic-2.0 |
| | | X | Generate Quality Surrogate Variable Analysis for Degradation Correction |
| bioconductor-qtlexperiment |
1.4.0 |
|
|
GPL-3 |
| | | X | S4 classes for QTL summary statistics and metadata |
| bioconductor-qtlizer |
1.20.0 |
|
|
GPL-3 |
| | | X | Comprehensive QTL annotation of GWAS results |
| bioconductor-qualifier |
1.29.1 |
|
|
Artistic-2.0 |
X | X | | X | Quality Control of Gated Flow Cytometry Experiments |
| bioconductor-quantiseqr |
1.14.0 |
|
|
GPL-3 |
| | | X | Quantification of the Tumor Immune contexture from RNA-seq data |
| bioconductor-quantro |
1.40.0 |
|
|
GPL-3 |
X | X | | X | A test for when to use quantile normalization |
| bioconductor-quantsmooth |
1.72.0 |
|
|
GPL-2 |
X | X | | X | Quantile smoothing and genomic visualization of array data |
| bioconductor-quartpac |
1.34.0 |
|
|
GPL-2 |
X | X | | X | Identification of mutational clusters in protein quaternary structures. |
| bioconductor-quasr |
1.46.0 |
|
|
GPL-2 |
X | X | | | Quantify and Annotate Short Reads in R |
| bioconductor-quaternaryprod |
1.40.0 |
|
|
GPL |
X | X | | | Computes the Quaternary Dot Product Scoring Statistic for Signed and... |
| bioconductor-qubic |
1.34.0 |
|
|
CC |
X | X | | | An R package for qualitative biclustering in support of gene... |
| bioconductor-qubicdata |
1.34.0 |
|
|
Unlimited |
| | | X | Data employed in the vignette of the QUBIC package |
| bioconductor-qusage |
2.40.0 |
|
|
GPL |
X | X | | X | qusage: Quantitative Set Analysis for Gene Expression |
| bioconductor-qvalue |
2.38.0 |
|
|
LGPL |
X | X | | X | Q-value estimation for false discovery rate control |
| bioconductor-r10kcod.db |
3.4.0 |
|
|
Artistic-2.0 |
| | | X | Codelink UniSet Rat I Bioarray (~10 000 rat gene targets) annotation... |
| bioconductor-r3cpet |
1.38.0 |
|
|
GPL |
X | X | | | 3CPET: Finding Co-factor Complexes in Chia-PET experiment using a... |
| bioconductor-r3cseq |
1.52.0 |
|
|
GPL-3 |
X | X | | X | Analysis of Chromosome Conformation Capture and Next-generation... |
| bioconductor-r453plus1toolbox |
1.56.0 |
|
|
LGPL-3 |
X | X | | | A package for importing and analyzing data from Roche's Genome... |
| bioconductor-r4rna |
1.34.0 |
|
|
GPL-3 |
X | X | | X | An R package for RNA visualization and analysis |
| bioconductor-radiogx |
2.10.0 |
|
|
GPL-3 |
| | | X | Analysis of Large-Scale Radio-Genomic Data |
| bioconductor-rae230a.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix RAE230A Array annotation data (chip rae230a) |
| bioconductor-rae230acdf |
2.18.0 |
|
|
LGPL |
| | | X | rae230acdf |
| bioconductor-rae230aprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type rae230a |
| bioconductor-rae230b.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix RAE230B Array annotation data (chip rae230b) |
| bioconductor-rae230bcdf |
2.18.0 |
|
|
LGPL |
| | | X | rae230bcdf |
| bioconductor-rae230bprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type rae230b |
| bioconductor-raer |
1.4.0 |
|
|
MIT |
X | X | | | RNA editing tools in R |
| bioconductor-raerdata |
1.4.0 |
|
|
MIT |
| | | X | A collection of datasets for use with raer package |
| bioconductor-raex10stprobeset.db |
8.8.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix raex10 annotation data (chip raex10stprobeset) |
| bioconductor-raex10sttranscriptcluster.db |
8.8.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix raex10 annotation data (chip raex10sttranscriptcluster) |
| bioconductor-raexexonprobesetlocation |
1.15.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type RaEx |
| bioconductor-ragene10stprobeset.db |
8.8.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix ragene10 annotation data (chip ragene10stprobeset) |
| bioconductor-ragene10sttranscriptcluster.db |
8.8.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix ragene10 annotation data (chip ragene10sttranscriptcluster) |
| bioconductor-ragene10stv1cdf |
2.18.0 |
|
|
LGPL |
| | | X | ragene10stv1cdf |
| bioconductor-ragene10stv1probe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type ragene10stv1 |
| bioconductor-ragene11stprobeset.db |
8.8.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix ragene11 annotation data (chip ragene11stprobeset) |
| bioconductor-ragene11sttranscriptcluster.db |
8.8.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix ragene11 annotation data (chip ragene11sttranscriptcluster) |
| bioconductor-ragene20stprobeset.db |
8.8.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix ragene20 annotation data (chip ragene20stprobeset) |
| bioconductor-ragene20sttranscriptcluster.db |
8.8.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix ragene20 annotation data (chip ragene20sttranscriptcluster) |
| bioconductor-ragene21stprobeset.db |
8.8.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix ragene21 annotation data (chip ragene21stprobeset) |
| bioconductor-ragene21sttranscriptcluster.db |
8.8.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix ragene21 annotation data (chip ragene21sttranscriptcluster) |
| bioconductor-raggedexperiment |
1.30.0 |
|
|
Artistic-2.0 |
X | X | | X | Representation of Sparse Experiments and Assays Across Samples |
| bioconductor-raids |
1.4.0 |
|
|
Apache |
| | | X | Accurate Inference of Genetic Ancestry from Cancer Sequences |
| bioconductor-rain |
1.40.0 |
|
|
GPL-2 |
X | X | | X | Rhythmicity Analysis Incorporating Non-parametric Methods |
| bioconductor-rama |
1.72.0 |
|
|
GPL |
X | X | | | Robust Analysis of MicroArrays |
| bioconductor-ramigo |
1.28.0 |
|
|
Artistic-2.0 |
X | X | | | R interface sending requests to AmiGO visualize, retrieving DAG GO... |
| bioconductor-ramr |
1.14.0 |
|
|
Artistic-2.0 |
| | | X | Detection of Rare Aberrantly Methylated Regions in Array and NGS Data |
| bioconductor-ramwas |
1.30.0 |
|
|
LGPL-3 |
X | X | | | Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms |
| bioconductor-randomwalkrestartmh |
1.22.0 |
|
|
GPL |
| | | X | Random walk with restart on multiplex and heterogeneous Networks |
| bioconductor-randpack |
1.52.0 |
|
|
Artistic |
X | X | | X | Randomization routines for Clinical Trials |
| bioconductor-randrotation |
1.18.0 |
|
|
GPL-3 |
| | | X | Random Rotation Methods for High Dimensional Data with Batch Structure |
| bioconductor-rankprod |
3.32.0 |
|
|
file |
X | X | | X | Rank Product method for identifying differentially expressed genes with... |
| bioconductor-raresim |
1.10.0 |
|
|
GPL-3 |
| | | X | Simulation of Rare Variant Genetic Data |
| bioconductor-rarevariantvis |
2.30.0 |
|
|
Artistic-2.0 |
X | X | | X | A suite for analysis of rare genomic variants in whole genome sequencing data |
| bioconductor-rariant |
1.25.0 |
|
|
GPL-3 |
X | X | | X | Identification and Assessment of Single Nucleotide Variants through... |
| bioconductor-rarr |
1.6.0 |
|
|
MIT |
X | X | | | Read Zarr Files in R |
| bioconductor-rat.db0 |
3.20.0 |
|
|
Artistic-2.0 |
| | | X | Base Level Annotation databases for rat |
| bioconductor-rat2302.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix Rat230_2 Array annotation data (chip rat2302) |
| bioconductor-rat2302cdf |
2.18.0 |
|
|
LGPL |
| | | X | rat2302cdf |
| bioconductor-rat2302frmavecs |
0.99.11 |
|
|
GPL |
| | | X | Vectors used by frma for microarrays of type rat2302rnentrezg |
| bioconductor-rat2302probe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type rat2302 |
| bioconductor-ratchrloc |
2.1.6 |
|
|
The |
| | | X | A data package containing annotation data for ratCHRLOC |
| bioconductor-rattoxfxcdf |
2.18.0 |
|
|
LGPL |
| | | X | rattoxfxcdf |
| bioconductor-rattoxfxprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type rattoxfx |
| bioconductor-rattus.norvegicus |
1.3.1 |
|
|
Artistic-2.0 |
| | | X | Annotation package for the Rattus.norvegicus object |
| bioconductor-rawrr |
1.10.2 |
|
|
GPL-3 |
| | | X | Direct Access to Orbitrap Data and Beyond |
| bioconductor-rbcbook1 |
1.74.0 |
|
|
Artistic-2.0 |
X | X | | X | Support for Springer monograph on Bioconductor |
| bioconductor-rbec |
1.14.0 |
|
|
LGPL-3 |
X | X | | | Rbec: a tool for analysis of amplicon sequencing data from synthetic... |
| bioconductor-rbgl |
1.82.0 |
|
|
Artistic-2.0 |
X | X | | | An interface to the BOOST graph library |
| bioconductor-rbioformats |
1.6.0 |
|
|
GPL-3 |
| | | X | R interface to Bio-Formats |
| bioconductor-rbioinf |
1.66.0 |
|
|
Artistic-2.0 |
X | X | | | RBioinf |
| bioconductor-rbiopaxparser |
2.46.0 |
|
|
GPL |
X | X | | X | Parses BioPax files and represents them in R |
| bioconductor-rblast |
1.2.0 |
|
|
GPL-3 |
| | | X | R Interface for the Basic Local Alignment Search Tool |
| bioconductor-rbm |
1.38.0 |
|
|
GPL |
X | X | | X | RBM: a R package for microarray and RNA-Seq data analysis |
| bioconductor-rbowtie |
1.46.0 |
|
|
Artistic-2.0 |
X | X | | | R bowtie wrapper |
| bioconductor-rbowtie2 |
2.8.0 |
|
|
GPL-3.0-or-later |
X | X | | | An R Wrapper for Bowtie2 and AdapterRemoval |
| bioconductor-rbsurv |
2.64.0 |
|
|
GPL |
X | X | | X | Robust likelihood-based survival modeling with microarray data |
| bioconductor-rbwa |
1.10.0 |
|
|
MIT |
X | X | | | R wrapper for BWA-backtrack and BWA-MEM aligners |
| bioconductor-rcade |
1.39.1 |
|
|
GPL-2 |
| | | X | R-based analysis of ChIP-seq And Differential Expression - a tool for... |
| bioconductor-rcas |
1.32.0 |
|
|
Artistic-2.0 |
X | X | | X | RNA Centric Annotation System |
| bioconductor-rcaspar |
1.52.0 |
|
|
GPL |
X | X | | X | A package for survival time prediction based on a piecewise baseline... |
| bioconductor-rcellminer |
2.28.0 |
|
|
LGPL-3 |
| | | X | rcellminer: Molecular Profiles, Drug Response, and Chemical Structures... |
| bioconductor-rcellminerdata |
2.28.0 |
|
|
LGPL-3 |
| | | X | rcellminerData: Molecular Profiles and Drug Response for the NCI-60 Cell Lines |
| bioconductor-rcgh |
1.36.0 |
|
|
Artistic-2.0 |
X | X | | X | Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data |
| bioconductor-rchemcpp |
2.21.1 |
|
|
GPL |
X | X | | | The Rchemcpp package implements the marginalized graph kernel and... |
| bioconductor-rchyoptimyx |
2.28.0 |
|
|
Artistic-2.0 |
X | | | | Optimyzed Cellular Hierarchies for Flow Cytometry |
| bioconductor-rcistarget |
1.26.0 |
|
|
GPL-3 |
| | | X | RcisTarget Identify transcription factor binding motifs enriched on a... |
| bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp |
1.26.0 |
|
|
GPL-3 |
| | | X | RcisTarget motif databases for human (hg19) - Subset of 4.6k motifs |
| bioconductor-rcm |
1.22.0 |
|
|
GPL-2 |
| | | X | Fit row-column association models with the negative binomial... |
| bioconductor-rcollectl |
1.6.0 |
|
|
Artistic-2.0 |
| | | X | Help use collectl with R in Linux, to measure resource consumption in R... |
| bioconductor-rcpi |
1.42.0 |
|
|
Artistic-2.0 |
| | | X | Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery |
| bioconductor-rcsl |
1.14.0 |
|
|
Artistic-2.0 |
X | X | | X | Rank Constrained Similarity Learning for single cell RNA sequencing data |
| bioconductor-rcwl |
1.22.0 |
|
|
GPL-2 |
| | | X | An R interface to the Common Workflow Language |
| bioconductor-rcwlpipelines |
1.22.0 |
|
|
GPL-2 |
| | | X | Bioinformatics pipelines based on Rcwl |
| bioconductor-rcx |
1.10.0 |
|
|
MIT |
| | | X | R package implementing the Cytoscape Exchange (CX) format |
| bioconductor-rcy3 |
2.26.0 |
|
|
MIT |
X | X | | X | Functions to Access and Control Cytoscape |
| bioconductor-rcyjs |
2.28.0 |
|
|
MIT |
| | | X | Display and manipulate graphs in cytoscape.js |
| bioconductor-rcytoscape |
1.27.1 |
|
|
GPL-2 |
X | X | | | Interactvive viewing and exploration of graphs, connecting R to Cytoscape. |
| bioconductor-rdavidwebservice |
1.28.0 |
|
|
GPL |
| | | X | An R Package for retrieving data from DAVID into R objects using Web... |
| bioconductor-rdgidb |
1.28.0 |
|
|
MIT |
X | X | | X | R Wrapper for DGIdb |
| bioconductor-rdisop |
1.66.0 |
|
|
GPL-2 |
X | X | | | Decomposition of Isotopic Patterns |
| bioconductor-rdrtoolbox |
1.56.0 |
|
|
GPL |
| | | X | A package for nonlinear dimension reduction with Isomap and LLE. |
| bioconductor-reactome.db |
1.89.0 |
|
|
CC |
X | X | | X | A set of annotation maps for reactome |
| bioconductor-reactomecontentservice4r |
1.10.0 |
|
|
Apache |
| | | X | Interface for the Reactome Content Service |
| bioconductor-reactomegraph4r |
1.10.0 |
|
|
Apache |
| | | X | Interface for the Reactome Graph Database |
| bioconductor-reactomegsa |
1.20.0 |
|
|
MIT |
| | | X | Client for the Reactome Analysis Service for comparative multi-omics... |
| bioconductor-reactomegsa.data |
1.20.0 |
|
|
Artistic-2.0 |
| | | X | Companion data package for the ReactomeGSA package |
| bioconductor-reactomepa |
1.50.0 |
|
|
GPL-2 |
X | X | | X | Reactome Pathway Analysis |
| bioconductor-readat |
1.11.0 |
|
|
GPL-3 |
| | | X | Functionality to Read and Manipulate SomaLogic ADAT files |
| bioconductor-readqpcr |
1.52.0 |
|
|
LGPL-3 |
X | X | | X | Read qPCR data |
| bioconductor-reb |
1.65.0 |
|
|
GPL-2 |
X | X | | | Regional Expression Biases |
| bioconductor-rebet |
1.24.0 |
|
|
GPL-2 |
X | X | | | The subREgion-based BurdEn Test (REBET) |
| bioconductor-rebook |
1.16.0 |
|
|
GPL-3 |
| | | X | Re-using Content in Bioconductor Books |
| bioconductor-receptloss |
1.18.0 |
|
|
GPL-3 |
| | | X | Unsupervised Identification of Genes with Expression Loss in Subsets of Tumors |
| bioconductor-reconsi |
1.18.0 |
|
|
GPL-2 |
| | | X | Resampling Collapsed Null Distributions for Simultaneous Inference |
| bioconductor-recount |
1.32.0 |
|
|
Artistic-2.0 |
X | X | | X | Explore and download data from the recount project |
| bioconductor-recount3 |
1.16.0 |
|
|
Artistic-2.0 |
| | | X | Explore and download data from the recount3 project |
| bioconductor-recountmethylation |
1.16.0 |
|
|
Artistic-2.0 |
| | | X | Access and analyze public DNA methylation array data compilations |
| bioconductor-recoup |
1.34.0 |
|
|
GPL |
X | X | | X | An R package for the creation of complex genomic profile plots |
| bioconductor-reder |
3.2.0 |
|
|
GPL-3 |
X | X | | X | Interactive visualization and manipulation of nested networks |
| bioconductor-redisparam |
1.8.0 |
|
|
Artistic-2.0 |
| | | X | Provide a 'redis' back-end for BiocParallel |
| bioconductor-redseq |
1.52.0 |
|
|
GPL |
| | | X | Analysis of high-throughput sequencing data processed by restriction... |
| bioconductor-refnet |
1.24.0 |
|
|
Artistic-2.0 |
X | X | | X | A queryable collection of molecular interactions, from many sources |
| bioconductor-refplus |
1.70.0 |
|
|
GPL |
X | X | | X | A function set for the Extrapolation Strategy (RMA+) and Extrapolation... |
| bioconductor-regenrich |
1.16.0 |
|
|
GPL |
| | | X | Gene regulator enrichment analysis |
| bioconductor-regionalpcs |
1.4.0 |
|
|
MIT |
| | | X | Summarizing Regional Methylation with Regional Principal Components Analysis |
| bioconductor-regionalst |
1.0.1 |
|
|
GPL-3 |
| | | X | Investigating regions of interest and performing cross-regional... |
| bioconductor-regioner |
1.38.0 |
|
|
Artistic-2.0 |
X | X | | X | Association analysis of genomic regions based on permutation tests |
| bioconductor-regionereloaded |
1.8.0 |
|
|
Artistic-2.0 |
| | | X | RegioneReloaded: Multiple Association for Genomic Region Sets |
| bioconductor-regionreport |
1.40.0 |
|
|
Artistic-2.0 |
| | | X | Generate HTML or PDF reports for a set of genomic regions or... |
| bioconductor-regparallel |
1.24.0 |
|
|
GPL-3 |
| | | X | Standard regression functions in R enabled for parallel processing over... |
| bioconductor-regsplice |
1.32.0 |
|
|
MIT |
X | X | | X | L1-regularization based methods for detection of differential splicing |
| bioconductor-regutools |
1.18.0 |
|
|
Artistic-2.0 |
| | | X | regutools: an R package for data extraction from RegulonDB |
| bioconductor-remp |
1.30.0 |
|
|
GPL-3 |
| | | X | Repetitive Element Methylation Prediction |
| bioconductor-repitools |
1.52.0 |
|
|
LGPL |
X | X | | | Epigenomic tools |
| bioconductor-reportingtools |
2.46.0 |
|
|
Artistic-2.0 |
X | X | | X | Tools for making reports in various formats |
| bioconductor-repviz |
1.22.0 |
|
|
GPL-3 |
| | | X | Replicate oriented Visualization of a genomic region |
| bioconductor-reqon |
1.48.0 |
|
|
GPL-2 |
| | | X | Recalibrating Quality Of Nucleotides |
| bioconductor-residualmatrix |
1.16.0 |
|
|
GPL-3 |
| | | X | Creating a DelayedMatrix of Regression Residuals |
| bioconductor-resolve |
1.8.0 |
|
|
file |
| | | X | RESOLVE: An R package for the efficient analysis of mutational... |
| bioconductor-restfulse |
1.24.0 |
|
|
Artistic-2.0 |
| | | X | Access matrix-like HDF5 server content or BigQuery content through a... |
| bioconductor-restfulsedata |
1.24.0 |
|
|
Artistic-2.0 |
| | | X | Example metadata for the "restfulSE" R package |
| bioconductor-retrofit |
1.6.0 |
|
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GPL-3 |
X | X | | | RETROFIT: Reference-free deconvolution of cell mixtures in spatial... |
| bioconductor-reusedata |
1.6.0 |
|
|
GPL-3 |
| | | X | Reusable and reproducible Data Management |
| bioconductor-rexposome |
1.28.0 |
|
|
MIT |
| | | X | Exposome exploration and outcome data analysis |
| bioconductor-rfarm |
1.14.0 |
|
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GPL-3 |
| | | X | An R interface to the Rfam database |
| bioconductor-rfastp |
1.16.0 |
|
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GPL-3 |
X | X | | | An Ultra-Fast and All-in-One Fastq Preprocessor (Quality Control,... |
| bioconductor-rforproteomics |
1.44.0 |
|
|
Artistic-2.0 |
| | | X | Companion package to the 'Using R and Bioconductor for proteomics... |
| bioconductor-rfpred |
1.44.0 |
|
|
GPL |
X | X | | | Assign rfPred functional prediction scores to a missense variants list |
| bioconductor-rgadem |
2.54.0 |
|
|
Artistic-2.0 |
X | X | | | de novo motif discovery |
| bioconductor-rgalaxy |
1.37.1 |
|
|
Artistic-2.0 |
X | X | | X | Make an R function available in the Galaxy web platform |
| bioconductor-rgenometracks |
1.12.0 |
|
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GPL-3 |
| | | X | Integerated visualization of epigenomic data |
| bioconductor-rgenometracksdata |
0.99.0 |
|
|
GPL |
| | | X | Demonstration Data from rGenomeTracks Package |
| bioconductor-rgin |
1.14.0 |
|
|
MIT |
X | X | | | gin in R |
| bioconductor-rgmql |
1.22.0 |
|
|
Artistic-2.0 |
| | | X | GenoMetric Query Language for R/Bioconductor |
| bioconductor-rgmqllib |
1.26.0 |
|
|
Artistic-2.0 |
| | | X | RGMQLlib, java libraries to run GMQL scala API |
| bioconductor-rgntx |
1.8.0 |
|
|
Artistic-2.0 |
| | | X | Colocalization analysis of transcriptome elements in the presence of... |
| bioconductor-rgoslin |
1.10.0 |
|
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MIT |
X | X | | | Lipid Shorthand Name Parsing and Normalization |
| bioconductor-rgraph2js |
1.34.0 |
|
|
GPL-2 |
X | X | | X | Convert a Graph into a D3js Script |
| bioconductor-rgraphviz |
2.50.0 |
|
|
EPL |
X | X | | | Provides plotting capabilities for R graph objects |
| bioconductor-rgreat |
2.8.0 |
|
|
MIT |
X | X | | X | GREAT Analysis - Functional Enrichment on Genomic Regions |
| bioconductor-rgsea |
1.40.0 |
|
|
GPL(>=3) |
X | X | | X | Random Gene Set Enrichment Analysis |
| bioconductor-rgsepd |
1.38.0 |
|
|
GPL-3 |
X | X | | X | Gene Set Enrichment / Projection Displays |
| bioconductor-rgu34a.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix RG_U34A Array annotation data (chip rgu34a) |
| bioconductor-rgu34acdf |
2.18.0 |
|
|
LGPL |
| | | X | rgu34acdf |
| bioconductor-rgu34aprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type rgu34a |
| bioconductor-rgu34b.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix RG_U34B Array annotation data (chip rgu34b) |
| bioconductor-rgu34bcdf |
2.18.0 |
|
|
LGPL |
| | | X | rgu34bcdf |
| bioconductor-rgu34bprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type rgu34b |
| bioconductor-rgu34c.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix RG_U34C Array annotation data (chip rgu34c) |
| bioconductor-rgu34ccdf |
2.18.0 |
|
|
LGPL |
| | | X | rgu34ccdf |
| bioconductor-rgu34cprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type rgu34c |
| bioconductor-rguatlas4k.db |
3.2.3 |
|
|
Artistic-2.0 |
| | | X | Clontech BD Atlas Long Oligos Rat 4K annotation data (chip rguatlas4k) |
| bioconductor-rgug4105a.db |
3.2.3 |
|
|
Artistic-2.0 |
| | | X | Agilent annotation data (chip rgug4105a) |
| bioconductor-rgug4130a.db |
3.2.3 |
|
|
Artistic-2.0 |
| | | X | Agilent Rat annotation data (chip rgug4130a) |
| bioconductor-rgug4131a.db |
3.2.3 |
|
|
Artistic-2.0 |
| | | X | Agilent "Rat Genome, Whole" annotation data (chip rgug4131a) |
| bioconductor-rhdf5 |
2.50.0 |
|
|
Artistic-2.0 |
X | X | | | R Interface to HDF5 |
| bioconductor-rhdf5client |
1.28.0 |
|
|
Artistic-2.0 |
X | X | | | Access HDF5 content from HDF Scalable Data Service |
| bioconductor-rhdf5filters |
1.18.0 |
|
|
BSD_2_clause |
X | X | | | HDF5 Compression Filters |
| bioconductor-rhdf5lib |
1.28.0 |
|
|
Artistic-2.0 |
X | X | | | hdf5 library as an R package |
| bioconductor-rhesus.db0 |
3.20.0 |
|
|
Artistic-2.0 |
| | | X | Base Level Annotation databases for rhesus |
| bioconductor-rhesuscdf |
2.18.0 |
|
|
LGPL |
| | | X | rhesuscdf |
| bioconductor-rhesusprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type rhesus |
| bioconductor-rheumaticconditionwollbold |
1.44.0 |
|
|
Artistic-2.0 |
| | | X | Normalized gene expression dataset published by Wollbold et al. [2009]... |
| bioconductor-rhinotyper |
1.0.0 |
|
|
MIT |
| | | X | Rhinovirus genotyping |
| bioconductor-rhisat2 |
1.22.0 |
|
|
GPL-3 |
X | X | | | R Wrapper for HISAT2 Aligner |
| bioconductor-rhtslib |
3.2.0 |
|
|
LGPL |
X | X | | | HTSlib high-throughput sequencing library as an R package |
| bioconductor-rhvdm |
1.49.0 |
|
|
GPL-2 |
| | | X | A R implementation of HVDM (Genome Biol 2006, V7(3) R25) |
| bioconductor-ri16cod.db |
3.4.0 |
|
|
Artistic-2.0 |
| | | X | Codelink Rat Inflammation 16 Bioarray annotation data (chip ri16cod) |
| bioconductor-ribocrypt |
1.12.0 |
|
|
MIT |
| | | X | Interactive visualization in genomics |
| bioconductor-ribodipa |
1.14.0 |
|
|
LGPL |
X | X | | | Differential pattern analysis for Ribo-seq data |
| bioconductor-riboprofiling |
1.36.0 |
|
|
GPL-3 |
X | X | | X | Ribosome Profiling Data Analysis: from BAM to Data Representation and... |
| bioconductor-ribor |
1.18.0 |
|
|
GPL-3 |
| | | X | An R Interface for Ribo Files |
| bioconductor-riboseqr |
1.40.0 |
|
|
GPL-3 |
X | X | | X | Analysis of sequencing data from ribosome profiling experiments |
| bioconductor-ribosomaldatabaseproject11.5mgdb |
1.00.0 |
|
|
Artistic-2.0 |
| | | X | Ribosomal Database Project 16S rRNA release 11.5 Annotation Data |
| bioconductor-ribosomeprofilingqc |
1.18.0 |
|
|
GPL |
| | | X | Ribosome Profiling Quality Control |
| bioconductor-ricecdf |
2.18.0 |
|
|
LGPL |
| | | X | ricecdf |
| bioconductor-riceprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type rice |
| bioconductor-rifi |
1.10.0 |
|
|
GPL-3 |
| | | X | 'rifi' analyses data from rifampicin time series created by... |
| bioconductor-rificomparative |
1.6.0 |
|
|
GPL-3 |
| | | X | 'rifiComparative' compares the output of rifi from two... |
| bioconductor-rimmport |
1.34.0 |
|
|
GPL-3 |
X | X | | X | RImmPort: Enabling Ready-for-analysis Immunology Research Data |
| bioconductor-ringo |
1.66.0 |
|
|
Artistic-2.0 |
X | X | | | R Investigation of ChIP-chip Oligoarrays |
| bioconductor-ripat |
1.10.0 |
|
|
Artistic-2.0 |
| | | X | Retroviral Integration Pattern Analysis Tool (RIPAT) |
| bioconductor-ripseeker |
1.26.0 |
|
|
GPL-2 |
X | X | | X | RIPSeeker: a statistical package for identifying protein-associated... |
| bioconductor-ripseekerdata |
1.22.0 |
|
|
GPL-2 |
| | | X | test data for RIPSeeker |
| bioconductor-risa |
1.44.0 |
|
|
LGPL |
X | X | | | Converting experimental metadata from ISA-tab into Bioconductor data structures |
| bioconductor-ritan |
1.26.0 |
|
|
file |
| | | X | Rapid Integration of Term Annotation and Network resources |
| bioconductor-ritandata |
1.30.0 |
|
|
file |
| | | X | This package contains reference annotation and network data sets |
| bioconductor-river |
1.30.0 |
|
|
GPL |
| | | X | R package for RIVER (RNA-Informed Variant Effect on Regulation) |
| bioconductor-rjmcmcnucleosomes |
1.30.0 |
|
|
Artistic-2.0 |
X | X | | | Bayesian hierarchical model for genome-wide nucleosome positioning with... |
| bioconductor-rlassocox |
1.14.0 |
|
|
Artistic-2.0 |
| | | X | A reweighted Lasso-Cox by integrating gene interaction information |
| bioconductor-rlhub |
1.6.0 |
|
|
MIT |
| | | X | An ExperimentHub package for accessing processed RLSuite data sets |
| bioconductor-rlmm |
1.68.0 |
|
|
LGPL |
X | X | | X | A Genotype Calling Algorithm for Affymetrix SNP Arrays |
| bioconductor-rlseq |
1.6.0 |
|
|
MIT |
| | | X | RLSeq: An analysis package for R-loop mapping data |
| bioconductor-rmagpie |
1.62.0 |
|
|
GPL |
| | | X | MicroArray Gene-expression-based Program In Error rate estimation |
| bioconductor-rmassbank |
3.16.0 |
|
|
Artistic-2.0 |
X | X | | | Workflow to process tandem MS files and build MassBank records |
| bioconductor-rmassbankdata |
1.44.0 |
|
|
Artistic-2.0 |
| | | X | Test dataset for RMassBank |
| bioconductor-rmat |
3.33.0 |
|
|
Artistic-2.0 |
X | X | | | This package is an R version of the package MAT and contains functions... |
| bioconductor-rmelting |
1.22.0 |
|
|
GPL-2 |
| | | X | R Interface to MELTING 5 |
| bioconductor-rmir |
1.49.0 |
|
|
Artistic-2.0 |
X | X | | X | Package to work with miRNAs and miRNA targets with R |
| bioconductor-rmir.hs.mirna |
1.0.7 |
|
|
The |
X | X | | X | Various databases of microRNA Targets |
| bioconductor-rmir.hsa |
1.0.5 |
|
|
The |
| | | X | Various databases of microRNA Targets |
| bioconductor-rmmquant |
1.24.0 |
|
|
GPL-3 |
X | X | | | RNA-Seq multi-mapping Reads Quantification Tool |
| bioconductor-rmspc |
1.8.0 |
|
|
GPL-3 |
| | | X | Multiple Sample Peak Calling |
| bioconductor-rnaagecalc |
1.18.0 |
|
|
GPL-2 |
| | | X | A multi-tissue transcriptional age calculator |
| bioconductor-rnadecay |
1.26.0 |
|
|
GPL-2 |
X | X | | | Maximum Likelihood Decay Modeling of RNA Degradation Data |
| bioconductor-rnaeditr |
1.16.0 |
|
|
GPL-3 |
| | | X | Statistical analysis of RNA editing sites and hyper-editing regions |
| bioconductor-rnagilentdesign028282.db |
3.2.3 |
|
|
Artistic-2.0 |
| | | X | Agilent Chips that use Agilent design number 028282 annotation data... |
| bioconductor-rnainteract |
1.50.0 |
|
|
Artistic-2.0 |
X | X | | X | Estimate Pairwise Interactions from multidimensional features |
| bioconductor-rnainteractmapk |
1.40.0 |
|
|
Artistic-2.0 |
| | | X | Mapping of Signalling Networks through Synthetic Genetic Interaction... |
| bioconductor-rnaither |
2.36.0 |
|
|
Artistic-2.0 |
X | X | | X | Statistical analysis of high-throughput RNAi screens |
| bioconductor-rnamodr |
1.20.0 |
|
|
Artistic-2.0 |
| | | X | Detection of post-transcriptional modifications in high throughput... |
| bioconductor-rnamodr.alkanilineseq |
1.20.0 |
|
|
Artistic-2.0 |
| | | X | Detection of m7G, m3C and D modification by AlkAnilineSeq |
| bioconductor-rnamodr.data |
1.16.0 |
|
|
Artistic-2.0 |
| | | X | Example data for the RNAmodR package |
| bioconductor-rnamodr.ml |
1.20.0 |
|
|
Artistic-2.0 |
| | | X | Detecting patterns of post-transcriptional modifications using machine learning |
| bioconductor-rnamodr.ribomethseq |
1.20.0 |
|
|
Artistic-2.0 |
| | | X | Detection of 2'-O methylations by RiboMethSeq |
| bioconductor-rnaprobr |
1.22.0 |
|
|
GPL |
X | X | | X | An R package for analysis of massive parallel sequencing based RNA... |
| bioconductor-rnasense |
1.20.0 |
|
|
GPL-3 |
| | | X | Analysis of Time-Resolved RNA-Seq Data |
| bioconductor-rnaseqcomp |
1.36.0 |
|
|
GPL-3 |
X | X | | X | Benchmarks for RNA-seq Quantification Pipelines |
| bioconductor-rnaseqcovarimpute |
1.4.0 |
|
|
GPL-3 |
| | | X | Impute Covariate Data in RNA Sequencing Studies |
| bioconductor-rnaseqdata.hnrnpc.bam.chr14 |
0.44.0 |
|
|
LGPL |
| | | X | Aligned reads from RNAseq experiment: Transcription profiling by high... |
| bioconductor-rnaseqmap |
2.46.0 |
|
|
GPL-2 |
X | X | | | rnaSeq secondary analyses |
| bioconductor-rnaseqpower |
1.46.0 |
|
|
LGPL |
X | X | | X | Sample size for RNAseq studies |
| bioconductor-rnaseqr |
1.15.1 |
|
|
Artistic-2.0 |
| | | X | RNASeqR: an R package for automated two-group RNA-Seq analysis workflow |
| bioconductor-rnaseqrdata |
1.16.0 |
|
|
Artistic-2.0 |
| | | X | RNASeqRData: sample data for RNASeqR software package demonstration |
| bioconductor-rnaseqsamplesize |
2.16.0 |
|
|
GPL |
X | X | | | RnaSeqSampleSize |
| bioconductor-rnaseqsamplesizedata |
1.38.0 |
|
|
GPL |
X | X | | X | RnaSeqSampleSizeData |
| bioconductor-rnbeads |
2.24.0 |
|
|
GPL-3 |
X | X | | X | RnBeads |
| bioconductor-rnbeads.hg19 |
1.38.0 |
|
|
GPL-3 |
X | X | | X | RnBeads.hg19 |
| bioconductor-rnbeads.hg38 |
1.38.0 |
|
|
GPL-3 |
| | | X | RnBeads.hg38 |
| bioconductor-rnbeads.mm10 |
2.14.0 |
|
|
GPL-3 |
X | X | | X | RnBeads.mm10 |
| bioconductor-rnbeads.mm9 |
1.38.0 |
|
|
GPL-3 |
X | X | | X | RnBeads.mm9 |
| bioconductor-rnbeads.rn5 |
1.38.0 |
|
|
GPL-3 |
X | X | | X | RnBeads.rn5 |
| bioconductor-rnits |
1.40.0 |
|
|
GPL-3 |
X | X | | X | R Normalization and Inference of Time Series data |
| bioconductor-rnu34.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix RN_U34 Array annotation data (chip rnu34) |
| bioconductor-rnu34cdf |
2.18.0 |
|
|
LGPL |
| | | X | rnu34cdf |
| bioconductor-rnu34probe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type rnu34 |
| bioconductor-roar |
1.42.0 |
|
|
GPL-3 |
X | X | | X | Identify differential APA usage from RNA-seq alignments |
| bioconductor-roastgsa |
1.4.0 |
|
|
GPL-3 |
| | | X | Rotation based gene set analysis |
| bioconductor-roberts2005annotation.db |
3.2.3 |
|
|
Artistic-2.0 |
| | | X | Roberts2005Annotation Annotation Data (Roberts2005Annotation) |
| bioconductor-roc |
1.82.0 |
|
|
Artistic-2.0 |
X | X | | | utilities for ROC, with microarray focus |
| bioconductor-rocpai |
1.14.0 |
|
|
GPL-3 |
| | | X | Receiver Operating Characteristic Partial Area Indexes for evaluating... |
| bioconductor-rolde |
1.10.0 |
|
|
GPL-3 |
| | | X | RolDE: Robust longitudinal Differential Expression |
| bioconductor-roleswitch |
1.25.0 |
|
|
GPL-2 |
X | X | | X | Infer miRNA-mRNA interactions using paired expression data from a single sample |
| bioconductor-rols |
3.2.0 |
|
|
GPL-2 |
X | X | | X | An R interface to the Ontology Lookup Service |
| bioconductor-rontotools |
2.34.0 |
|
|
CC |
X | X | | X | R Onto-Tools suite |
| bioconductor-ropls |
1.38.0 |
|
|
CeCILL |
X | X | | X | PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature... |
| bioconductor-roseq |
1.18.0 |
|
|
GPL-3 |
| | | X | Modeling expression ranks for noise-tolerant differential expression... |
| bioconductor-rots |
1.34.0 |
|
|
GPL |
X | X | | | Reproducibility-Optimized Test Statistic |
| bioconductor-rpa |
1.62.0 |
|
|
BSD_2_clause |
X | X | | X | RPA: Robust Probabilistic Averaging for probe-level analysis |
| bioconductor-rprimer |
1.10.0 |
|
|
GPL-3 |
| | | X | Design Degenerate Oligos from a Multiple DNA Sequence Alignment |
| bioconductor-rprotobuflib |
2.18.0 |
|
|
BSD_3_clause |
X | X | | | C++ headers and static libraries of Protocol buffers |
| bioconductor-rpsixml |
2.36.0 |
|
|
LGPL-3 |
X | X | | X | R interface to PSI-MI 2.5 files |
| bioconductor-rpx |
2.14.0 |
|
|
GPL-2 |
X | X | | X | R Interface to the ProteomeXchange Repository |
| bioconductor-rqc |
1.40.0 |
|
|
GPL |
X | X | | | Quality Control Tool for High-Throughput Sequencing Data |
| bioconductor-rqt |
1.32.0 |
|
|
GPL |
| | | X | rqt: utilities for gene-level meta-analysis |
| bioconductor-rqubic |
1.52.0 |
|
|
GPL-2 |
X | X | | | Qualitative biclustering algorithm for expression data analysis in R |
| bioconductor-rrbsdata |
1.26.0 |
|
|
LGPL-3 |
| | | X | An RRBS data set with 12 samples and 10,000 simulated DMRs |
| bioconductor-rrdp |
1.40.0 |
|
|
GPL-2 |
X | X | | X | Interface to the RDP Classifier |
| bioconductor-rrdpdata |
1.26.0 |
|
|
GPL-2 |
| | | X | Databases for the Default RDP Classifier |
| bioconductor-rrho |
1.46.0 |
|
|
GPL-2 |
X | X | | X | Inference on agreement between ordered lists |
| bioconductor-rrvgo |
1.18.0 |
|
|
GPL-3 |
| | | X | Reduce + Visualize GO |
| bioconductor-rsamtools |
2.22.0 |
|
|
Artistic-2.0 |
X | X | | | Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import |
| bioconductor-rsbml |
2.60.0 |
|
|
Artistic-2.0 |
X | X | | | R support for SBML, using libsbml |
| bioconductor-rscudo |
1.22.0 |
|
|
GPL-3 |
| | | X | Signature-based Clustering for Diagnostic Purposes |
| bioconductor-rsemmed |
1.16.0 |
|
|
Artistic-2.0 |
| | | X | An interface to the Semantic MEDLINE database |
| bioconductor-rseqan |
1.26.0 |
|
|
BSD_3_clause |
X | X | | X | R SeqAn |
| bioconductor-rsffreader |
0.31.0 |
|
|
Artistic-2.0 |
X | X | | | rSFFreader reads sequence, qualities and clip point values from sff... |
| bioconductor-rsubread |
2.20.0 |
|
|
GPL |
X | X | | | Mapping, quantification and variant analysis of sequencing data |
| bioconductor-rsvsim |
1.46.0 |
|
|
LGPL-3 |
X | X | | X | RSVSim: an R/Bioconductor package for the simulation of structural variations |
| bioconductor-rsweep |
1.18.0 |
|
|
GPL |
| | | X | Spaced Words Projection (SWeeP) |
| bioconductor-rta10probeset.db |
8.8.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix rta10 annotation data (chip rta10probeset) |
| bioconductor-rta10transcriptcluster.db |
8.8.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix rta10 annotation data (chip rta10transcriptcluster) |
| bioconductor-rtandem |
1.27.0 |
|
|
Artistic-1.0 |
X | X | | | Interfaces the tandem protein identification algorithm in R |
| bioconductor-rtca |
1.58.0 |
|
|
LGPL-3 |
X | X | | X | Open-source toolkit to analyse data from xCELLigence System (RTCA) |
| bioconductor-rtcga |
1.36.0 |
|
|
GPL-2 |
X | X | | X | The Cancer Genome Atlas Data Integration |
| bioconductor-rtcga.clinical |
20151101.36.0 |
|
|
GPL-2 |
| | | X | Clinical datasets from The Cancer Genome Atlas Project |
| bioconductor-rtcga.cnv |
1.34.0 |
|
|
GPL-2 |
| | | X | CNV (Copy-number variation) datasets from The Cancer Genome Atlas Project |
| bioconductor-rtcga.methylation |
1.34.0 |
|
|
GPL-2 |
| | | X | Methylation datasets from The Cancer Genome Atlas Project |
| bioconductor-rtcga.mirnaseq |
1.34.0 |
|
|
GPL-2 |
| | | X | miRNASeq datasets from The Cancer Genome Atlas Project |
| bioconductor-rtcga.mrna |
1.34.0 |
|
|
GPL-2 |
X | X | | X | mRNA datasets from The Cancer Genome Atlas Project |
| bioconductor-rtcga.mutations |
20151101.36.0 |
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|
GPL-2 |
| | | X | Mutations datasets from The Cancer Genome Atlas Project |
| bioconductor-rtcga.pancan12 |
1.34.0 |
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|
GPL-2 |
| | | X | PanCan 12 from Genome Cancer Browser |
| bioconductor-rtcga.rnaseq |
20151101.36.0 |
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|
GPL-2 |
| | | X | Rna-seq datasets from The Cancer Genome Atlas Project |
| bioconductor-rtcga.rppa |
1.34.0 |
|
|
GPL-2 |
| | | X | RPPA datasets from The Cancer Genome Atlas Project |
| bioconductor-rtcgatoolbox |
2.36.0 |
|
|
GPL-2 |
X | X | | X | A new tool for exporting TCGA Firehose data |
| bioconductor-rtn |
2.30.0 |
|
|
Artistic-2.0 |
| | | X | RTN: Reconstruction of Transcriptional regulatory Networks and analysis... |
| bioconductor-rtnduals |
1.30.0 |
|
|
Artistic-2.0 |
| | | X | Analysis of co-regulation and inference of 'dual regulons' |
| bioconductor-rtnsurvival |
1.30.0 |
|
|
Artistic-2.0 |
| | | X | Survival analysis using transcriptional networks inferred by the RTN package |
| bioconductor-rtopper |
1.52.0 |
|
|
GPL |
X | X | | X | This package is designed to perform Gene Set Analysis across multiple... |
| bioconductor-rtpca |
1.16.0 |
|
|
GPL-3 |
| | | X | Thermal proximity co-aggregation with R |
| bioconductor-rtracklayer |
1.66.0 |
|
|
Artistic-2.0 |
X | X | | | R interface to genome annotation files and the UCSC genome browser |
| bioconductor-rtreemix |
1.68.0 |
|
|
LGPL |
X | X | | | Rtreemix: Mutagenetic trees mixture models. |
| bioconductor-rtrm |
1.44.0 |
|
|
GPL-3 |
X | X | | X | Identification of Transcriptional Regulatory Modules from... |
| bioconductor-rtrmui |
1.44.0 |
|
|
GPL-3 |
X | X | | X | A shiny user interface for rTRM |
| bioconductor-rtu34.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix RT_U34 Array annotation data (chip rtu34) |
| bioconductor-rtu34cdf |
2.18.0 |
|
|
LGPL |
| | | X | rtu34cdf |
| bioconductor-rtu34probe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type rtu34 |
| bioconductor-runibic |
1.28.0 |
|
|
MIT |
X | X | | | runibic: row-based biclustering algorithm for analysis of gene... |
| bioconductor-ruvcorr |
1.38.0 |
|
|
GPL-2 |
| | | X | Removal of unwanted variation for gene-gene correlations and related analysis |
| bioconductor-ruvnormalize |
1.40.0 |
|
|
GPL-3 |
X | X | | X | RUV for normalization of expression array data |
| bioconductor-ruvnormalizedata |
1.26.0 |
|
|
GPL-3 |
X | X | | X | Gender data for the RUVnormalize package |
| bioconductor-ruvseq |
1.40.0 |
|
|
Artistic-2.0 |
X | X | | X | Remove Unwanted Variation from RNA-Seq Data |
| bioconductor-rvisdiff |
1.4.0 |
|
|
GPL-2 |
| | | X | Interactive Graphs for Differential Expression |
| bioconductor-rvs |
1.28.0 |
|
|
GPL-2 |
| | | X | Computes estimates of the probability of related individuals sharing a... |
| bioconductor-rwgcod.db |
3.4.0 |
|
|
Artistic-2.0 |
| | | X | Codelink Rat Whole Genome Bioarray (~34 000 rat gene targets)... |
| bioconductor-rwikipathways |
1.26.0 |
|
|
MIT |
| | | X | rWikiPathways - R client library for the WikiPathways API |
| bioconductor-s4arrays |
1.6.0 |
|
|
Artistic-2.0 |
X | X | | | Foundation of array-like containers in Bioconductor |
| bioconductor-s4vectors |
0.44.0 |
|
|
Artistic-2.0 |
X | X | | | Foundation of vector-like and list-like containers in Bioconductor |
| bioconductor-safe |
3.46.0 |
|
|
GPL |
X | X | | X | Significance Analysis of Function and Expression |
| bioconductor-sagenhaft |
1.76.0 |
|
|
GPL |
X | X | | X | Collection of functions for reading and comparing SAGE libraries |
| bioconductor-sagx |
1.64.0 |
|
|
GPL-3 |
X | X | | | Statistical Analysis of the GeneChip |
| bioconductor-saigegds |
2.6.0 |
|
|
GPL-3 |
X | X | | | Scalable Implementation of Generalized mixed models using GDS files in... |
| bioconductor-samexplorer |
1.13.0 |
|
|
GPL-3 |
| | | X | samExploreR package high-performance read summarisation to count... |
| bioconductor-sampleclassifier |
1.30.0 |
|
|
Artistic-2.0 |
| | | X | Sample Classifier |
| bioconductor-sampleclassifierdata |
1.30.0 |
|
|
Artistic-2.0 |
| | | X | Pre-processed data for use with the sampleClassifier package |
| bioconductor-samspectral |
1.60.0 |
|
|
GPL |
X | X | | | Identifies cell population in flow cytometry data |
| bioconductor-sangeranalyser |
1.16.0 |
|
|
GPL-2 |
| | | X | sangeranalyseR: a suite of functions for the analysis of Sanger... |
| bioconductor-sangerseqr |
1.42.0 |
|
|
GPL-2 |
X | X | | X | Tools for Sanger Sequencing Data in R |
| bioconductor-santa |
2.42.0 |
|
|
GPL |
X | X | | | Spatial Analysis of Network Associations |
| bioconductor-sapfinder |
1.26.0 |
|
|
GPL-2 |
X | X | | | A package for variant peptides detection and visualization in shotgun... |
| bioconductor-sarc |
1.4.0 |
|
|
GPL-3 |
| | | X | Statistical Analysis of Regions with CNVs |
| bioconductor-sarks |
1.18.0 |
|
|
BSD_3_clause |
| | | X | Suffix Array Kernel Smoothing for discovery of correlative sequence... |
| bioconductor-saser |
1.2.0 |
|
|
Artistic-2.0 |
| | | X | Scalable Aberrant Splicing and Expression Retrieval |
| bioconductor-saturn |
1.14.0 |
|
|
Artistic-2.0 |
| | | X | Scalable Analysis of Differential Transcript Usage for Bulk and... |
| bioconductor-saureuscdf |
2.18.0 |
|
|
LGPL |
| | | X | saureuscdf |
| bioconductor-saureusprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type saureus |
| bioconductor-savr |
1.37.0 |
|
|
AGPL-3 |
X | X | | X | Parse and analyze Illumina SAV files |
| bioconductor-sbgnview |
1.20.0 |
|
|
AGPL-3 |
| | | X | "SBGNview: Data Analysis, Integration and Visualization on SBGN... |
| bioconductor-sbgnview.data |
1.20.0 |
|
|
AGPL-3 |
| | | X | Supporting datasets for SBGNview package |
| bioconductor-sbmlr |
2.2.0 |
|
|
GPL-2 |
| | | X | SBML-R Interface and Analysis Tools |
| bioconductor-sc3 |
1.34.0 |
|
|
GPL-3 |
X | X | | | Single-Cell Consensus Clustering |
| bioconductor-sc3-scripts |
0.0.3 |
|
dev |
GPL-3 |
| | | X | A set of wrappers for individual components of the SC3 package.... |
| bioconductor-scale4c |
1.28.0 |
|
|
LGPL-3 |
| | | X | Scale4C: an R/Bioconductor package for scale-space transformation of 4C-seq data |
| bioconductor-scaledmatrix |
1.14.0 |
|
|
GPL-3 |
| | | X | Creating a DelayedMatrix of Scaled and Centered Values |
| bioconductor-scalign |
1.11.0 |
|
|
GPL-3 |
| | | X | An alignment and integration method for single cell genomics |
| bioconductor-scan.upc |
2.48.0 |
|
|
MIT |
X | X | | X | Single-channel array normalization (SCAN) and Universal exPression Codes (UPC) |
| bioconductor-scanmir |
1.12.0 |
|
|
GPL-3 |
| | | X | scanMiR |
| bioconductor-scanmirapp |
1.12.0 |
|
|
GPL-3 |
| | | X | scanMiR shiny application |
| bioconductor-scanmirdata |
1.12.0 |
|
|
GPL-3 |
| | | X | miRNA Affinity models for the scanMiR package |
| bioconductor-scannotatr |
1.12.0 |
|
|
MIT |
| | | X | Pretrained learning models for cell type prediction on single cell... |
| bioconductor-scannotatr.models |
0.99.10 |
|
|
MIT |
| | | X | Pretrained models for scAnnotatR package |
| bioconductor-scanvis |
1.20.0 |
|
|
file |
| | | X | SCANVIS - a tool for SCoring, ANnotating and VISualizing splice junctions |
| bioconductor-scarray |
1.14.0 |
|
|
GPL-3 |
X | X | | X | Large-scale single-cell omics data manipulation with GDS files |
| bioconductor-scarray.sat |
1.6.0 |
|
|
GPL-3 |
| | | X | Large-scale single-cell RNA-seq data analysis using GDS files and Seurat |
| bioconductor-scatac.explorer |
1.12.1 |
|
|
Artistic-2.0 |
| | | X | A Collection of Single-cell ATAC Sequencing Datasets and Corresponding Metadata |
| bioconductor-scate |
1.10.0 |
|
|
MIT |
| | | X | SCATE: Single-cell ATAC-seq Signal Extraction and Enhancement |
| bioconductor-scatedata |
1.10.0 |
|
|
MIT |
| | | X | Data for SCATE (Single-cell ATAC-seq Signal Extraction and Enhancement) |
| bioconductor-scater |
1.34.0 |
|
|
GPL-3 |
X | X | | X | Single-Cell Analysis Toolkit for Gene Expression Data in R |
| bioconductor-scatterhatch |
1.12.0 |
|
|
MIT |
| | | X | Creates hatched patterns for scatterplots |
| bioconductor-scbfa |
1.20.0 |
|
|
GPL-3 |
| | | X | A dimensionality reduction tool using gene detection pattern to... |
| bioconductor-scbn |
1.24.0 |
|
|
GPL-2 |
| | | X | A statistical normalization method and differential expression analysis... |
| bioconductor-scbubbletree |
1.8.0 |
|
|
GPL-3 |
| | | X | Quantitative visual exploration of scRNA-seq data |
| bioconductor-sccb2 |
1.16.0 |
|
|
GPL-3 |
| | | X | CB2 improves power of cell detection in droplet-based single-cell RNA... |
| bioconductor-scclassifr |
1.2.0 |
|
|
MIT |
| | | X | Pretrained learning models for cell type prediction on single cell... |
| bioconductor-scclassify |
1.18.0 |
|
|
GPL-3 |
| | | X | scClassify: single-cell Hierarchical Classification |
| bioconductor-sccomp |
1.4.0 |
|
|
GPL-3 |
X | X | | | Robust Outlier-aware Estimation of Composition and Heterogeneity for... |
| bioconductor-scdataviz |
1.16.0 |
|
|
GPL-3 |
| | | X | scDataviz: single cell dataviz and downstream analyses |
| bioconductor-scdblfinder |
1.16.0 |
|
|
GPL-3 |
| | | X | scDblFinder |
| bioconductor-scdd |
1.30.0 |
|
|
GPL-2 |
| | | X | Mixture modeling of single-cell RNA-seq data to identify genes with... |
| bioconductor-scddboost |
1.4.0 |
|
|
GPL |
X | X | | | A compositional model to assess expression changes from single-cell rna-seq data |
| bioconductor-scde |
2.34.0 |
|
|
GPL-2 |
X | X | | | Single Cell Differential Expression |
| bioconductor-scdesign3 |
1.4.0 |
|
|
MIT |
| | | X | A unified framework of realistic in silico data generation and... |
| bioconductor-scdiagnostics |
1.0.0 |
|
|
Artistic-2.0 |
| | | X | Cell type annotation diagnostics |
| bioconductor-scdotplot |
1.0.0 |
|
|
Artistic-2.0 |
| | | X | Cluster a Single-cell RNA-seq Dot Plot |
| bioconductor-scds |
1.18.0 |
|
|
MIT |
| | | X | In-Silico Annotation of Doublets for Single Cell RNA Sequencing Data |
| bioconductor-scfa |
1.16.0 |
|
|
LGPL |
| | | X | SCFA: Subtyping via Consensus Factor Analysis |
| bioconductor-scfeaturefilter |
1.26.0 |
|
|
MIT |
| | | X | A correlation-based method for quality filtering of single-cell RNAseq data |
| bioconductor-scfeatures |
1.6.0 |
|
|
GPL-3 |
| | | X | scFeatures: Multi-view representations of single-cell and spatial data... |
| bioconductor-scfind |
1.9.0 |
|
|
GPL-3 |
X | X | | | A search tool for single cell RNA-seq data by gene lists |
| bioconductor-scgps |
1.20.0 |
|
|
GPL-3 |
X | X | | | A complete analysis of single cell subpopulations, from identifying... |
| bioconductor-schex |
1.20.0 |
|
|
GPL-3 |
| | | X | Hexbin plots for single cell omics data |
| bioconductor-schot |
1.18.0 |
|
|
GPL-3 |
| | | X | single-cell higher order testing |
| bioconductor-scider |
1.4.0 |
|
|
GPL-3 |
| | | X | Spatial cell-type inter-correlation by density in R |
| bioconductor-scifer |
1.8.0 |
|
|
MIT |
| | | X | Scifer: Single-Cell Immunoglobulin Filtering of Sanger Sequences |
| bioconductor-scisi |
1.65.0 |
|
|
LGPL |
X | X | | X | In Silico Interactome |
| bioconductor-sclcbam |
1.38.0 |
|
|
GPL-2 |
| | | X | Sequence data from chromosome 4 of a small-cell lung tumor |
| bioconductor-scmageck |
1.9.1 |
|
|
BSD_2_clause |
| | | X | Identify genes associated with multiple expression phenotypes in... |
| bioconductor-scmap |
1.28.0 |
|
|
GPL-3 |
X | X | | | A tool for unsupervised projection of single cell RNA-seq data |
| bioconductor-scmerge |
1.22.0 |
|
|
GPL-3 |
X | X | | X | scMerge: Merging multiple batches of scRNA-seq data |
| bioconductor-scmet |
1.8.0 |
|
|
GPL-3 |
X | X | | | Bayesian modelling of cell-to-cell DNA methylation heterogeneity |
| bioconductor-scmeth |
1.26.0 |
|
|
GPL-2 |
| | | X | Functions to conduct quality control analysis in methylation data |
| bioconductor-scmitomut |
1.2.0 |
|
|
Artistic-2.0 |
X | X | | | Single-cell Mitochondrial Mutation Analysis Tool |
| bioconductor-scmultiome |
1.6.0 |
|
|
CC |
| | | X | Collection of Public Single-Cell Multiome (scATAC + scRNAseq) Datasets |
| bioconductor-scmultisim |
1.2.0 |
|
|
Artistic-2.0 |
| | | X | Simulation of Multi-Modality Single Cell Data Guided By Gene Regulatory... |
| bioconductor-scnorm |
1.28.0 |
|
|
GPL |
X | X | | X | Normalization of single cell RNA-seq data |
| bioconductor-scone |
1.30.0 |
|
|
Artistic-2.0 |
| | | X | Single Cell Overview of Normalized Expression data |
| bioconductor-sconify |
1.26.0 |
|
|
Artistic-2.0 |
| | | X | A toolkit for performing KNN-based statistics for flow and mass cytometry data |
| bioconductor-scope |
1.18.0 |
|
|
GPL-2 |
| | | X | A normalization and copy number estimation method for single-cell DNA sequencing |
| bioconductor-scoreinvhap |
1.28.0 |
|
|
file |
| | | X | Get inversion status in predefined regions |
| bioconductor-scoup |
1.0.0 |
|
|
GPL |
| | | X | Simulate Codons with Darwinian Selection Modelled as an OU Process |
| bioconductor-scp |
1.16.0 |
|
|
Artistic-2.0 |
| | | X | Mass Spectrometry-Based Single-Cell Proteomics Data Analysis |
| bioconductor-scpca |
1.20.0 |
|
|
MIT |
| | | X | Sparse Contrastive Principal Component Analysis |
| bioconductor-scpdata |
1.13.0 |
|
|
GPL-2 |
| | | X | Single-Cell Proteomics Data Package |
| bioconductor-scpipe |
2.6.0 |
|
|
GPL |
X | X | | | Pipeline for single cell multi-omic data pre-processing |
| bioconductor-scran |
1.34.0 |
|
|
GPL-3 |
X | X | | | Methods for Single-Cell RNA-Seq Data Analysis |
| bioconductor-scrapper |
1.0.0 |
|
|
MIT |
X | | | | Bindings to C++ Libraries for Single-Cell Analysis |
| bioconductor-screclassify |
1.12.0 |
|
|
GPL-3 |
| | | X | scReClassify: post hoc cell type classification of single-cell RNA-seq data |
| bioconductor-screcover |
1.22.0 |
|
|
GPL |
| | | X | scRecover for imputation of single-cell RNA-seq data |
| bioconductor-screencounter |
1.6.0 |
|
|
MIT |
X | X | | | Counting Reads in High-Throughput Sequencing Screens |
| bioconductor-screenr |
1.8.0 |
|
|
MIT |
| | | X | Package to Perform High Throughput Biological Screening |
| bioconductor-screpertoire |
2.2.0 |
|
|
MIT |
X | | | X | A toolkit for single-cell immune receptor profiling |
| bioconductor-scrnaseq |
2.20.0 |
|
|
CC0 |
X | X | | X | Collection of Public Single-Cell RNA-Seq Datasets |
| bioconductor-scrnaseqapp |
1.6.0 |
|
|
GPL-3 |
| | | X | A single-cell RNAseq Shiny app-package |
| bioconductor-scruff |
1.24.0 |
|
|
MIT |
| | | X | Single Cell RNA-Seq UMI Filtering Facilitator (scruff) |
| bioconductor-scry |
1.18.0 |
|
|
Artistic-2.0 |
| | | X | Small-Count Analysis Methods for High-Dimensional Data |
| bioconductor-scshapes |
1.12.0 |
|
|
GPL-3 |
| | | X | A Statistical Framework for Modeling and Identifying Differential... |
| bioconductor-scsr |
1.23.0 |
|
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GPL-2 |
| | | X | SiRNA correction for seed mediated off-target effect |
| bioconductor-sctensor |
2.16.0 |
|
|
Artistic-2.0 |
| | | X | Detection of cell-cell interaction from single-cell RNA-seq dataset by... |
| bioconductor-sctgif |
1.20.0 |
|
|
Artistic-2.0 |
X | X | | | Cell type annotation for unannotated single-cell RNA-Seq data |
| bioconductor-scthi |
1.18.0 |
|
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GPL-2 |
| | | X | Indentification of significantly activated ligand-receptor interactions... |
| bioconductor-scthi.data |
1.18.0 |
|
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GPL-2 |
| | | X | The package contains examples of single cell data used in vignettes and... |
| bioconductor-sctreeviz |
1.12.0 |
|
|
Artistic-2.0 |
| | | X | R/Bioconductor package to interactively explore and visualize single... |
| bioconductor-scuttle |
1.16.0 |
|
|
GPL-3 |
X | X | | | Single-Cell RNA-Seq Analysis Utilities |
| bioconductor-scvir |
1.6.0 |
|
|
Artistic-2.0 |
| | | X | experimental inferface from R to scvi-tools |
| bioconductor-sdams |
1.26.0 |
|
|
GPL |
| | | X | Differential Abundant/Expression Analysis for Metabolomics, Proteomics... |
| bioconductor-seahtrue |
1.0.0 |
|
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Artistic-2.0 |
| | | X | Seahtrue revives XF data for structured data analysis |
| bioconductor-sechm |
1.14.0 |
|
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GPL-3 |
| | | X | sechm: Complex Heatmaps from a SummarizedExperiment |
| bioconductor-segmenter |
1.12.0 |
|
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GPL-3 |
| | | X | Perform Chromatin Segmentation Analysis in R by Calling ChromHMM |
| bioconductor-segmentseq |
2.40.0 |
|
|
GPL-3 |
X | X | | X | Methods for identifying small RNA loci from high-throughput sequencing data |
| bioconductor-selectksigs |
1.18.0 |
|
|
GPL-3 |
X | X | | | Selecting the number of mutational signatures using a perplexity-based... |
| bioconductor-selex |
1.38.0 |
|
|
GPL |
| | | X | Functions for analyzing SELEX-seq data |
| bioconductor-semdist |
1.40.0 |
|
|
GPL |
X | X | | X | Information Accretion-based Function Predictor Evaluation |
| bioconductor-semisup |
1.30.0 |
|
|
GPL-3 |
X | X | | X | Semi-Supervised Mixture Model |
| bioconductor-sepa |
1.13.0 |
|
|
GPL(>=2) |
X | X | | X | Given single-cell RNA-seq data and true experiment time of cells or... |
| bioconductor-sepira |
1.20.0 |
|
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GPL-3 |
| | | X | Systems EPigenomics Inference of Regulatory Activity |
| bioconductor-seq.hotspot |
1.6.0 |
|
|
Artistic-2.0 |
| | | X | Targeted sequencing panel design based on mutation hotspots |
| bioconductor-seq2pathway |
1.34.0 |
|
|
GPL-2 |
X | X | | X | a novel tool for functional gene-set (or termed as pathway) analysis of... |
| bioconductor-seq2pathway.data |
1.38.0 |
|
|
GPL |
X | X | | X | data set for R package seq2pathway |
| bioconductor-seqarchr |
1.6.0 |
|
|
GPL-3 |
| | | X | Identify Different Architectures of Sequence Elements |
| bioconductor-seqarchrplus |
1.2.0 |
|
|
GPL-3 |
| | | X | Downstream analyses of promoter sequence architectures and HTML report... |
| bioconductor-seqarray |
1.46.0 |
|
|
GPL-3 |
X | X | | | Data Management of Large-Scale Whole-Genome Sequence Variant Calls |
| bioconductor-seqbias |
1.50.0 |
|
|
LGPL-3 |
X | X | | | Estimation of per-position bias in high-throughput sequencing data |
| bioconductor-seqc |
1.40.0 |
|
|
GPL-3 |
| | | X | RNA-seq data generated from SEQC (MAQC-III) study |
| bioconductor-seqcat |
1.28.0 |
|
|
MIT |
| | | X | High Throughput Sequencing Cell Authentication Toolkit |
| bioconductor-seqcna |
1.48.0 |
|
|
GPL-3 |
X | X | | | Copy number analysis of high-throughput sequencing cancer data |
| bioconductor-seqcna.annot |
1.38.0 |
|
|
GPL-3 |
| | | X | Annotation for the copy number analysis of deep sequencing cancer data... |
| bioconductor-seqcombo |
1.28.0 |
|
|
Artistic-2.0 |
| | | X | Visualization Tool for Genetic Reassortment |
| bioconductor-seqgate |
1.16.0 |
|
|
GPL |
| | | X | Filtering of Lowly Expressed Features |
| bioconductor-seqgsea |
1.46.0 |
|
|
GPL |
X | X | | X | Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating... |
| bioconductor-seqlogo |
1.72.0 |
|
|
LGPL |
X | X | | X | Sequence logos for DNA sequence alignments |
| bioconductor-seqpattern |
1.38.0 |
|
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GPL-3 |
X | X | | X | Visualising oligonucleotide patterns and motif occurrences across a set... |
| bioconductor-seqplots |
1.27.0 |
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|
GPL-3 |
| | | X | An interactive tool for visualizing NGS signals and sequence motif... |
| bioconductor-seqsetvis |
1.26.0 |
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|
MIT |
| | | X | Set Based Visualizations for Next-Gen Sequencing Data |
| bioconductor-seqsqc |
1.28.0 |
|
|
GPL-3 |
| | | X | A bioconductor package for sample quality check with next generation... |
| bioconductor-seqtools |
1.40.0 |
|
|
Artistic-2.0 |
X | X | | | Analysis of nucleotide, sequence and quality content on fastq files |
| bioconductor-seqvartools |
1.44.0 |
|
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GPL-3 |
| | | X | Tools for variant data |
| bioconductor-serumstimulation |
1.42.0 |
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|
GPL |
| | | X | serumStimulation is a data package which is used by examples in package... |
| bioconductor-sesame |
1.24.0 |
|
|
MIT |
| | | X | SEnsible Step-wise Analysis of DNA MEthylation BeadChips |
| bioconductor-sesamedata |
1.24.0 |
|
|
Artistic-2.0 |
| | | X | Supporting Data for SeSAMe Package |
| bioconductor-setools |
1.20.0 |
|
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GPL |
| | | X | SEtools: tools for working with SummarizedExperiment |
| bioconductor-sevenbridges |
1.36.0 |
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|
Apache |
| | | X | Seven Bridges Platform API Client and Common Workflow Language Tool Builder in R |
| bioconductor-sevenc |
1.26.0 |
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GPL-3 |
| | | X | Computational Chromosome Conformation Capture by Correlation of... |
| bioconductor-seventygenedata |
1.42.0 |
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|
Artistic-2.0 |
| | | X | ExpressionSets from the van't Veer and Van de Vijver breast cancer studies |
| bioconductor-sfedata |
1.4.0 |
|
|
Artistic-2.0 |
| | | X | Example SpatialFeatureExperiment datasets |
| bioconductor-sgcp |
1.6.0 |
|
|
GPL-3 |
| | | X | SGCP: A semi-supervised pipeline for gene clustering using... |
| bioconductor-sgseq |
1.40.0 |
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|
Artistic-2.0 |
X | X | | X | Splice event prediction and quantification from RNA-seq data |
| bioconductor-sharedobject |
1.20.0 |
|
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GPL-3 |
X | X | | | Sharing R objects across multiple R processes without memory duplication |
| bioconductor-shdz.db |
3.2.3 |
|
|
Artistic-2.0 |
| | | X | SHDZ http://genome-www5.stanford.edu/ Annotation Data (SHDZ) |
| bioconductor-shiny.gosling |
1.2.0 |
|
|
LGPL-3 |
| | | X | A Grammar-based Toolkit for Scalable and Interactive Genomics Data... |
| bioconductor-shinyepico |
1.14.0 |
|
|
AGPL-3 |
| | | X | ShinyÉPICo |
| bioconductor-shinymethyl |
1.42.0 |
|
|
Artistic-2.0 |
X | X | | X | Interactive visualization for Illumina methylation arrays |
| bioconductor-shinymethyldata |
1.26.0 |
|
|
Artistic-2.0 |
| | | X | Example dataset of input data for shinyMethyl |
| bioconductor-shinytandem |
1.26.0 |
|
|
GPL-3 |
| | | X | Provides a GUI for rTANDEM |
| bioconductor-shortread |
1.64.0 |
|
|
Artistic-2.0 |
X | X | | | FASTQ input and manipulation |
| bioconductor-siamcat |
2.10.0 |
|
|
GPL-3 |
| | | X | Statistical Inference of Associations between Microbial Communities And... |
| bioconductor-sictools |
1.36.0 |
|
|
GPL |
X | X | | | Find SNV/Indel differences between two bam files with near relationship |
| bioconductor-sift.hsapiens.dbsnp132 |
1.0.2 |
|
|
Artistic-2.0 |
| | | X | SIFT Predictions for Homo sapiens dbSNP build 132 |
| bioconductor-sift.hsapiens.dbsnp137 |
1.0.0 |
|
|
Artistic-2.0 |
| | | X | PROVEAN/SIFT Predictions for Homo sapiens dbSNP build 137 |
| bioconductor-sigar |
1.35.0 |
|
|
GPL |
X | X | | X | Statistics for Integrative Genomics Analyses in R |
| bioconductor-sigcheck |
2.38.0 |
|
|
Artistic-2.0 |
| | | X | Check a gene signature's prognostic performance against random... |
| bioconductor-sigfeature |
1.24.0 |
|
|
GPL |
| | | X | sigFeature: Significant feature selection using SVM-RFE & t-statistic |
| bioconductor-sigfuge |
1.44.0 |
|
|
GPL-3 |
X | X | | X | SigFuge |
| bioconductor-siggenes |
1.80.0 |
|
|
LGPL |
X | X | | X | Multiple Testing using SAM and Efron's Empirical Bayes Approaches |
| bioconductor-sights |
1.32.0 |
|
|
GPL-3 |
X | X | | X | Statistics and dIagnostic Graphs for HTS |
| bioconductor-signaturesearch |
1.20.0 |
|
|
Artistic-2.0 |
X | X | | | Environment for Gene Expression Searching Combined with Functional... |
| bioconductor-signaturesearchdata |
1.20.0 |
|
|
Artistic-2.0 |
| | | X | Datasets for signatureSearch package |
| bioconductor-signer |
2.8.0 |
|
|
GPL-3 |
X | X | | | Empirical Bayesian approach to mutational signature discovery |
| bioconductor-signet |
1.7.0 |
|
|
GPL-2 |
| | | X | signet: Selection Inference in Gene NETworks |
| bioconductor-signifinder |
1.4.0 |
|
|
AGPL-3 |
| | | X | Implementations of transcriptional cancer signatures |
| bioconductor-sigpathway |
1.66.0 |
|
|
GPL-2 |
X | X | | | Pathway Analysis |
| bioconductor-sigspack |
1.20.0 |
|
|
GPL-3 |
| | | X | Mutational Signature Estimation for Single Samples |
| bioconductor-sigsquared |
1.38.0 |
|
|
GPL |
| | | X | Gene signature generation for functionally validated signaling pathways |
| bioconductor-silva128.1mgdb |
1.00.0 |
|
|
Artistic-2.0 |
| | | X | SILVA SSR rRNA release 128.1 Annotation Data |
| bioconductor-sim |
1.76.0 |
|
|
GPL |
X | X | | | Integrated Analysis on two human genomic datasets |
| bioconductor-simat |
1.38.0 |
|
|
GPL-2 |
X | X | | | GC-SIM-MS data processing and alaysis tool |
| bioconductor-simbenchdata |
1.14.0 |
|
|
GPL-3 |
| | | X | SimBenchData: a collection of 35 single-cell RNA-seq data covering a... |
| bioconductor-simbindprofiles |
1.40.0 |
|
|
GPL-3 |
X | X | | X | Similar Binding Profiles |
| bioconductor-simbu |
1.8.0 |
|
|
GPL-3 |
| | | X | Simulate Bulk RNA-seq Datasets from Single-Cell Datasets |
| bioconductor-simd |
1.24.0 |
|
|
GPL-3 |
X | X | | | Statistical Inferences with MeDIP-seq Data (SIMD) to infer the... |
| bioconductor-simffpe |
1.18.0 |
|
|
LGPL-3 |
| | | X | NGS Read Simulator for FFPE Tissue |
| bioconductor-similarpeak |
1.38.0 |
|
|
Artistic-2.0 |
X | X | | X | Metrics to estimate a level of similarity between two ChIP-Seq profiles |
| bioconductor-simlr |
1.32.0 |
|
|
file |
X | X | | | Single-cell Interpretation via Multi-kernel LeaRning (SIMLR) |
| bioconductor-simona |
1.4.0 |
|
|
MIT |
X | X | | | Semantic Similarity on Bio-Ontologies |
| bioconductor-simpic |
1.2.0 |
|
|
GPL-3 |
| | | X | simPIC: flexible simulation of paired-insertion counts for single-cell... |
| bioconductor-simpintlists |
1.42.0 |
|
|
GPL |
X | X | | X | The package contains BioGRID interactions for various organisms in a... |
| bioconductor-simpleaffy |
2.66.0 |
|
|
GPL |
X | X | | | Very simple high level analysis of Affymetrix data |
| bioconductor-simpleseg |
1.8.0 |
|
|
GPL-3 |
| | | X | A package to perform simple cell segmentation |
| bioconductor-simplifyenrichment |
2.0.0 |
|
|
MIT |
| | | X | Simplify Functional Enrichment Results |
| bioconductor-simulatorz |
1.24.0 |
|
|
Artistic-2.0 |
X | X | | | Simulator for Collections of Independent Genomic Data Sets |
| bioconductor-sincell |
1.38.0 |
|
|
GPL |
X | X | | | R package for the statistical assessment of cell state hierarchies from... |
| bioconductor-single |
1.6.0 |
|
|
MIT |
| | | X | Accurate consensus sequence from nanopore reads of a gene library |
| bioconductor-single.mtec.transcriptomes |
1.34.0 |
|
|
LGPL |
| | | X | Single Cell Transcriptome Data and Analysis of Mouse mTEC cells |
| bioconductor-singlecellalleleexperiment |
1.2.0 |
|
|
MIT |
| | | X | S4 Class for Single Cell Data with Allele and Functional Levels for Immune Genes |
| bioconductor-singlecellexperiment |
1.28.0 |
|
|
GPL-3 |
X | X | | X | S4 Classes for Single Cell Data |
| bioconductor-singlecellexperiment-scripts |
0.0.3 |
|
dev |
GPL-3 |
| | | X | A set of wrappers for operations associated with the... |
| bioconductor-singlecellmultimodal |
1.18.0 |
|
|
Artistic-2.0 |
| | | X | Integrating Multi-modal Single Cell Experiment datasets |
| bioconductor-singlecellsignalr |
1.18.0 |
|
|
GPL-3 |
| | | X | Cell Signalling Using Single Cell RNAseq Data Analysis |
| bioconductor-singlecelltk |
2.12.0 |
|
|
MIT |
| | | X | Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data |
| bioconductor-singlemoleculefootprinting |
2.0.0 |
|
|
GPL-3 |
| | | X | Analysis tools for Single Molecule Footprinting (SMF) data |
| bioconductor-singlemoleculefootprintingdata |
1.14.0 |
|
|
GPL-3 |
| | | X | Data supporting the SingleMoleculeFootprinting pkg |
| bioconductor-singler |
2.8.0 |
|
|
GPL-3 |
X | X | | | Reference-Based Single-Cell RNA-Seq Annotation |
| bioconductor-singscore |
1.26.0 |
|
|
GPL-3 |
| | | X | Rank-based single-sample gene set scoring method |
| bioconductor-sipsic |
1.6.0 |
|
|
file |
| | | X | Calculate Pathway Scores for Each Cell in scRNA-Seq Data |
| bioconductor-sispa |
1.30.0 |
|
|
GPL-2 |
X | X | | X | SISPA: Method for Sample Integrated Set Profile Analysis |
| bioconductor-sitadela |
1.14.0 |
|
|
Artistic-2.0 |
| | | X | An R package for the easy provision of simple but complete... |
| bioconductor-sitepath |
1.22.0 |
|
|
MIT |
X | X | | | Phylogeny-based sequence clustering with site polymorphism |
| bioconductor-sizepower |
1.76.0 |
|
|
LGPL |
X | X | | X | Sample Size and Power Calculation in Micorarray Studies |
| bioconductor-sketchr |
1.2.0 |
|
|
MIT |
| | | X | An R interface for python subsampling/sketching algorithms |
| bioconductor-skewr |
1.38.0 |
|
|
GPL-2 |
| | | X | Visualize Intensities Produced by Illumina's Human Methylation 450k BeadChip |
| bioconductor-slalom |
1.28.0 |
|
|
GPL-2 |
X | X | | | Factorial Latent Variable Modeling of Single-Cell RNA-Seq Data |
| bioconductor-slgi |
1.54.0 |
|
|
Artistic-2.0 |
X | X | | X | Synthetic Lethal Genetic Interaction |
| bioconductor-slingshot |
2.14.0 |
|
|
Artistic-2.0 |
| | | X | Tools for ordering single-cell sequencing |
| bioconductor-slinky |
1.12.0 |
|
|
MIT |
| | | X | Putting the fun in LINCS L1000 data analysis |
| bioconductor-slqpcr |
1.72.0 |
|
|
GPL |
X | X | | X | Functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH |
| bioconductor-smad |
1.22.0 |
|
|
MIT |
X | X | | | Statistical Modelling of AP-MS Data (SMAD) |
| bioconductor-smap |
1.66.0 |
|
|
GPL-2 |
X | X | | | A Segmental Maximum A Posteriori Approach to Array-CGH Copy Number Profiling |
| bioconductor-smartid |
1.2.0 |
|
|
MIT |
| | | X | Scoring and Marker Selection Method Based on Modified TF-IDF |
| bioconductor-smite |
1.34.0 |
|
|
GPL |
X | X | | X | Significance-based Modules Integrating the Transcriptome and Epigenome |
| bioconductor-smokingmouse |
1.4.0 |
|
|
Artistic-2.0 |
| | | X | Provides access to smokingMouse project data |
| bioconductor-smoothclust |
1.2.0 |
|
|
MIT |
| | | X | smoothclust |
| bioconductor-snadata |
1.52.0 |
|
|
LGPL |
| | | X | Social Networks Analysis Data Examples |
| bioconductor-snagee |
1.46.0 |
|
|
Artistic-2.0 |
X | X | | X | Signal-to-Noise applied to Gene Expression Experiments |
| bioconductor-snageedata |
1.42.0 |
|
|
Artistic-2.0 |
X | X | | X | SNAGEE data |
| bioconductor-snapcgh |
1.72.0 |
|
|
GPL |
X | X | | | Segmentation, normalisation and processing of aCGH data |
| bioconductor-snapcount |
1.18.0 |
|
|
MIT |
| | | X | R/Bioconductor Package for interfacing with Snaptron for rapid querying... |
| bioconductor-snifter |
1.16.0 |
|
|
GPL-3 |
| | | X | R wrapper for the python openTSNE library |
| bioconductor-snm |
1.54.0 |
|
|
LGPL |
X | X | | X | Supervised Normalization of Microarrays |
| bioconductor-snpchip |
2.32.0 |
|
|
LGPL |
X | X | | X | Visualizations for copy number alterations |
| bioconductor-snpediar |
1.32.0 |
|
|
GPL-2 |
X | X | | X | Query data from SNPedia |
| bioconductor-snphood |
1.36.0 |
|
|
LGPL |
X | X | | X | SNPhood: Investigate, quantify and visualise the epigenomic... |
| bioconductor-snphooddata |
1.36.0 |
|
|
LGPL |
| | | X | Additional and more complex example data for the SNPhood package |
| bioconductor-snplocs.hsapiens.dbsnp.20101109 |
0.99.7 |
|
|
Artistic-2.0 |
| | | X | SNP locations for Homo sapiens (dbSNP Build 132) |
| bioconductor-snplocs.hsapiens.dbsnp.20120608 |
0.99.11 |
|
|
Artistic-2.0 |
| | | X | SNP locations for Homo sapiens (dbSNP Build 137) |
| bioconductor-snplocs.hsapiens.dbsnp141.grch38 |
0.99.11 |
|
|
Artistic-2.0 |
| | | X | SNP locations for Homo sapiens (dbSNP Build 141) |
| bioconductor-snplocs.hsapiens.dbsnp142.grch37 |
0.99.5 |
|
|
Artistic-2.0 |
| | | X | SNP locations for Homo sapiens (dbSNP Build 142) |
| bioconductor-snplocs.hsapiens.dbsnp144.grch37 |
0.99.20 |
|
|
Artistic-2.0 |
| | | X | SNP locations for Homo sapiens (dbSNP Build 144) |
| bioconductor-snplocs.hsapiens.dbsnp144.grch38 |
0.99.20 |
|
|
Artistic-2.0 |
X | X | | X | SNP locations for Homo sapiens (dbSNP Build 144) |
| bioconductor-snplocs.hsapiens.dbsnp149.grch38 |
0.99.20 |
|
|
Artistic-2.0 |
| | | X | SNP locations for Homo sapiens (dbSNP Build 149) |
| bioconductor-snplocs.hsapiens.dbsnp150.grch38 |
0.99.20 |
|
|
Artistic-2.0 |
| | | X | SNP locations for Homo sapiens (dbSNP Build 150) |
| bioconductor-snplocs.hsapiens.dbsnp151.grch38 |
0.99.20 |
|
|
Artistic-2.0 |
| | | X | SNP locations for Homo sapiens (dbSNP Build 151) |
| bioconductor-snprelate |
1.40.0 |
|
|
GPL-3 |
X | X | | | Parallel Computing Toolset for Relatedness and Principal Component... |
| bioconductor-snpstats |
1.56.0 |
|
|
GPL-3 |
X | X | | | SnpMatrix and XSnpMatrix classes and methods |
| bioconductor-soggi |
1.38.0 |
|
|
GPL |
X | X | | X | Visualise ChIP-seq, MNase-seq and motif occurrence as aggregate plots... |
| bioconductor-sojourner |
1.11.0 |
|
|
Artistic-2.0 |
X | X | | | Statistical analysis of single molecule trajectories |
| bioconductor-somascan.db |
0.99.10 |
|
|
MIT |
| | | X | Somalogic SomaScan Annotation Data |
| bioconductor-somaticadata |
1.44.0 |
|
|
Artistic-2.0 |
| | | X | An example cancer whole genome sequencing data for the SomatiCA package |
| bioconductor-somaticcanceralterations |
1.42.0 |
|
|
GPL-3 |
| | | X | Somatic Cancer Alterations |
| bioconductor-somaticsignatures |
2.42.0 |
|
|
MIT |
X | X | | X | Somatic Signatures |
| bioconductor-somnibus |
1.10.0 |
|
|
MIT |
| | | X | Smooth modeling of bisulfite sequencing |
| bioconductor-soybeancdf |
2.18.0 |
|
|
LGPL |
| | | X | soybeancdf |
| bioconductor-soybeanprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type soybean |
| bioconductor-spacemarkers |
1.2.1 |
|
|
MIT |
| | | X | Spatial Interaction Markers |
| bioconductor-spacepac |
1.40.0 |
|
|
GPL-2 |
X | X | | X | Identification of Mutational Clusters in 3D Protein Space via Simulation. |
| bioconductor-spaniel |
1.20.0 |
|
|
MIT |
| | | X | Spatial Transcriptomics Analysis |
| bioconductor-spanorm |
1.0.0 |
|
|
GPL |
| | | X | Spatially-aware normalisation for spatial transcriptomics data |
| bioconductor-sparrow |
1.12.0 |
|
|
MIT |
| | | X | Take command of set enrichment analyses through a unified interface |
| bioconductor-sparsearray |
1.6.0 |
|
|
Artistic-2.0 |
X | X | | | High-performance sparse data representation and manipulation in R |
| bioconductor-sparsedossa |
1.24.0 |
|
|
MIT |
| | | X | Sparse Data Observations for Simulating Synthetic Abundance |
| bioconductor-sparsematrixstats |
1.18.0 |
|
|
MIT |
X | X | | | Summary Statistics for Rows and Columns of Sparse Matrices |
| bioconductor-sparsenetgls |
1.24.0 |
|
|
GPL-3 |
| | | X | Using Gaussian graphical structue learning estimation in generalized... |
| bioconductor-sparsesignatures |
2.16.0 |
|
|
file |
| | | X | SparseSignatures |
| bioconductor-spasim |
1.8.0 |
|
|
Artistic-2.0 |
| | | X | Spatial point data simulator for tissue images |
| bioconductor-spatialcpie |
1.22.0 |
|
|
MIT |
| | | X | Cluster analysis of Spatial Transcriptomics data |
| bioconductor-spatialdatasets |
1.4.0 |
|
|
GPL-3 |
| | | X | Collection of spatial omics datasets |
| bioconductor-spatialde |
1.12.0 |
|
|
MIT |
| | | X | R wrapper for SpatialDE |
| bioconductor-spatialdecon |
1.16.0 |
|
|
MIT |
| | | X | Deconvolution of mixed cells from spatial and/or bulk gene expression data |
| bioconductor-spatialdmelxsim |
1.12.0 |
|
|
GPL-3 |
| | | X | Spatial allelic expression counts for fly cross embryo |
| bioconductor-spatialexperiment |
1.16.0 |
|
|
GPL-3 |
| | | X | S4 Class for Spatially Resolved -omics Data |
| bioconductor-spatialfeatureexperiment |
1.8.0 |
|
|
Artistic-2.0 |
| | | X | Integrating SpatialExperiment with Simple Features in sf |
| bioconductor-spatialheatmap |
2.12.0 |
|
|
Artistic-2.0 |
| | | X | spatialHeatmap |
| bioconductor-spatiallibd |
1.18.0 |
|
|
Artistic-2.0 |
| | | X | spatialLIBD: an R/Bioconductor package to visualize spatially-resolved... |
| bioconductor-spatialomicsoverlay |
1.6.0 |
|
|
MIT |
| | | X | Spatial Overlay for Omic Data from Nanostring GeoMx Data |
| bioconductor-spatialsimgp |
1.0.0 |
|
|
MIT |
| | | X | Simulate Spatial Transcriptomics Data with the Mean-variance Relationship |
| bioconductor-spatzie |
1.12.0 |
|
|
GPL-3 |
| | | X | Identification of enriched motif pairs from chromatin interaction data |
| bioconductor-speckle |
1.6.0 |
|
|
GPL-3 |
| | | X | Statistical methods for analysing single cell RNA-seq data |
| bioconductor-specl |
1.40.0 |
|
|
GPL-3 |
X | X | | X | specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics |
| bioconductor-specond |
1.60.0 |
|
|
LGPL |
X | X | | X | Condition specific detection from expression data |
| bioconductor-spectra |
1.16.0 |
|
|
Artistic-2.0 |
| | | X | Spectra Infrastructure for Mass Spectrometry Data |
| bioconductor-spectraltad |
1.22.0 |
|
|
MIT |
| | | X | SpectralTAD: Hierarchical TAD detection using spectral clustering |
| bioconductor-spectraql |
1.0.0 |
|
|
Artistic-2.0 |
| | | X | MassQL support for Spectra |
| bioconductor-spem |
1.46.0 |
|
|
GPL-2 |
X | X | | X | S-system parameter estimation method |
| bioconductor-spia |
2.58.0 |
|
|
file |
X | X | | X | Signaling Pathway Impact Analysis (SPIA) using combined evidence of... |
| bioconductor-spiat |
1.8.0 |
|
|
Artistic-2.0 |
| | | X | Spatial Image Analysis of Tissues |
| bioconductor-spicyr |
1.18.0 |
|
|
GPL |
| | | X | Spatial analysis of in situ cytometry data |
| bioconductor-spidermir |
1.32.0 |
|
|
GPL |
X | X | | X | SpidermiR: An R/Bioconductor package for integrative network analysis... |
| bioconductor-spikein |
1.48.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Spike-In Experiment Data |
| bioconductor-spikeinsubset |
1.46.0 |
|
|
LGPL |
| | | X | Part of Affymetrix's Spike-In Experiment Data |
| bioconductor-spikeli |
2.66.0 |
|
|
GPL-2 |
X | X | | X | Affymetrix Spike-in Langmuir Isotherm Data Analysis Tool |
| bioconductor-spiky |
1.12.0 |
|
|
GPL-2 |
| | | X | Spike-in calibration for cell-free MeDIP |
| bioconductor-spillr |
1.2.0 |
|
|
LGPL-3 |
| | | X | Spillover Compensation in Mass Cytometry Data |
| bioconductor-spktools |
1.62.0 |
|
|
GPL |
X | X | | X | Methods for Spike-in Arrays |
| bioconductor-splatter |
1.30.0 |
|
|
GPL-3 |
X | X | | X | Simple Simulation of Single-cell RNA Sequencing Data |
| bioconductor-splicegear |
1.58.0 |
|
|
LGPL |
X | X | | X | splicegear |
| bioconductor-splicer |
1.22.0 |
|
|
GPL |
X | X | | | An R package for classification of alternative splicing and prediction... |
| bioconductor-splicesites |
1.31.0 |
|
|
GPL-2 |
X | X | | | Performs splice centered analysis on RNA-seq data. |
| bioconductor-splicewiz |
1.8.0 |
|
|
MIT |
X | X | | | interactive analysis and visualization of alternative splicing in R |
| bioconductor-splicingfactory |
1.14.0 |
|
|
GPL-3 |
| | | X | Splicing Diversity Analysis for Transcriptome Data |
| bioconductor-splicinggraphs |
1.46.0 |
|
|
Artistic-2.0 |
X | X | | X | Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them |
| bioconductor-splinetimer |
1.34.0 |
|
|
GPL-3 |
X | X | | X | Time-course differential gene expression data analysis using spline... |
| bioconductor-splinter |
1.28.0 |
|
|
GPL-2 |
X | X | | X | Splice Interpreter of Transcripts |
| bioconductor-splots |
1.72.0 |
|
|
LGPL |
X | X | | X | Visualization of high-throughput assays in microtitre plate or slide format |
| bioconductor-sponge |
1.28.0 |
|
|
GPL |
| | | X | Sparse Partial Correlations On Gene Expression |
| bioconductor-spoon |
1.2.0 |
|
|
MIT |
| | | X | Address the Mean-variance Relationship in Spatial Transcriptomics Data |
| bioconductor-spotclean |
1.8.0 |
|
|
GPL-3 |
| | | X | SpotClean adjusts for spot swapping in spatial transcriptomics data |
| bioconductor-spotlight |
1.10.0 |
|
|
GPL-3 |
| | | X | `SPOTlight`: Spatial Transcriptomics Deconvolution |
| bioconductor-spotsegmentation |
1.61.0 |
|
|
GPL |
X | X | | X | Microarray Spot Segmentation and Gridding for Blocks of Microarray Spots |
| bioconductor-spqn |
1.18.0 |
|
|
Artistic-2.0 |
| | | X | Spatial quantile normalization |
| bioconductor-spqndata |
1.18.0 |
|
|
Artistic-2.0 |
| | | X | Data for the spqn package |
| bioconductor-spsimseq |
1.16.0 |
|
|
GPL-2 |
| | | X | Semi-parametric simulation tool for bulk and single-cell RNA sequencing data |
| bioconductor-sqldataframe |
1.20.0 |
|
|
LGPL |
| | | X | Representation of SQL tables in DataFrame metaphor |
| bioconductor-squadd |
1.52.0 |
|
|
GPL |
X | X | | X | Add-on of the SQUAD Software |
| bioconductor-sracipe |
1.22.0 |
|
|
MIT |
X | X | | | Systems biology tool to simulate gene regulatory circuits |
| bioconductor-sradb |
1.64.0 |
|
|
Artistic-2.0 |
X | X | | X | A compilation of metadata from NCBI SRA and tools |
| bioconductor-srap |
1.27.0 |
|
|
GPL-3 |
X | X | | X | Simplified RNA-Seq Analysis Pipeline |
| bioconductor-srgnet |
1.16.0 |
|
|
GPL-2 |
| | | X | SRGnet: An R package for studying synergistic response to gene... |
| bioconductor-srnadiff |
1.22.0 |
|
|
GPL-3 |
X | X | | | Finding differentially expressed unannotated genomic regions from RNA-seq data |
| bioconductor-sscore |
1.72.0 |
|
|
GPL |
X | X | | X | S-Score Algorithm for Affymetrix Oligonucleotide Microarrays |
| bioconductor-sscu |
2.36.0 |
|
|
GPL |
X | X | | X | Strength of Selected Codon Usage |
| bioconductor-sseq |
1.44.0 |
|
|
GPL |
X | X | | X | Shrinkage estimation of dispersion in Negative Binomial models for... |
| bioconductor-ssize |
1.80.0 |
|
|
LGPL |
X | X | | X | Estimate Microarray Sample Size |
| bioconductor-ssnappy |
1.10.0 |
|
|
GPL-3 |
X | X | | X | Single Sample directioNAl Pathway Perturbation analYsis |
| bioconductor-sspa |
2.30.0 |
|
|
GPL |
X | X | | | General Sample Size and Power Analysis for Microarray and... |
| bioconductor-sspaths |
1.20.0 |
|
|
MIT |
| | | X | ssPATHS: Single Sample PATHway Score |
| bioconductor-ssrch |
1.22.0 |
|
|
Artistic-2.0 |
| | | X | a simple search engine |
| bioconductor-ssviz |
1.40.0 |
|
|
GPL-2 |
X | X | | X | A small RNA-seq visualizer and analysis toolkit |
| bioconductor-stabmap |
1.0.0 |
|
|
GPL-2 |
| | | X | Stabilised mosaic single cell data integration using unshared features |
| bioconductor-stager |
1.28.0 |
|
|
GNU |
| | | X | stageR: stage-wise analysis of high throughput gene expression data in R |
| bioconductor-stan |
2.26.0 |
|
|
GPL |
X | X | | | The Genomic STate ANnotation Package |
| bioconductor-standr |
1.10.0 |
|
|
MIT |
| | | X | Spatial transcriptome analyses of Nanostring's DSP data in R |
| bioconductor-starank |
1.44.0 |
|
|
GPL |
X | X | | X | Stability Ranking |
| bioconductor-starbiotrek |
1.28.0 |
|
|
GPL |
X | X | | X | StarBioTrek |
| bioconductor-starr |
1.43.0 |
|
|
Artistic-2.0 |
X | X | | | Simple tiling array analysis of Affymetrix ChIP-chip data |
| bioconductor-stategra |
1.42.0 |
|
|
GPL-2 |
X | X | | X | Classes and methods for multi-omics data integration |
| bioconductor-statial |
1.8.0 |
|
|
GPL-3 |
| | | X | A package to identify changes in cell state relative to spatial associations |
| bioconductor-stattarget |
1.36.0 |
|
|
LGPL |
| | | X | Statistical Analysis of Molecular Profiles |
| bioconductor-stdeconvolve |
1.2.0 |
|
|
GPL-3 |
| | | X | Reference-free Cell-Type Deconvolution of Multi-Cellular Spatially... |
| bioconductor-stemhypoxia |
1.42.0 |
|
|
GPL |
X | X | | X | Differentiation of Human Embryonic Stem Cells under Hypoxia gene... |
| bioconductor-stepnorm |
1.78.0 |
|
|
LGPL |
X | X | | X | Stepwise normalization functions for cDNA microarrays |
| bioconductor-stexampledata |
1.14.0 |
|
|
MIT |
| | | X | Collection of spatial transcriptomics datasets in SpatialExperiment... |
| bioconductor-stjoincount |
1.8.0 |
|
|
MIT |
| | | X | stJoincount - Join count statistic for quantifying spatial correlation... |
| bioconductor-stjudem |
1.42.0 |
|
|
LGPL |
| | | X | Microarray Data from Yeoh et al. in MACAT format |
| bioconductor-strandcheckr |
1.24.0 |
|
|
GPL |
| | | X | Calculate strandness information of a bam file |
| bioconductor-streamer |
1.52.0 |
|
|
Artistic-2.0 |
X | X | | | Enabling stream processing of large files |
| bioconductor-stringdb |
2.18.0 |
|
|
GPL-2 |
X | X | | X | STRINGdb - Protein-Protein Interaction Networks and Functional... |
| bioconductor-stroma4 |
1.24.0 |
|
|
GPL-3 |
| | | X | Assign Properties to TNBC Patients |
| bioconductor-struct |
1.18.0 |
|
|
GPL-3 |
| | | X | Statistics in R Using Class-based Templates |
| bioconductor-structstrings |
1.22.0 |
|
|
Artistic-2.0 |
X | X | | | Implementation of the dot bracket annotations with Biostrings |
| bioconductor-structtoolbox |
1.18.0 |
|
|
GPL-3 |
| | | X | Data processing & analysis tools for Metabolomics and other omics |
| bioconductor-structuralvariantannotation |
1.22.0 |
|
|
GPL-3 |
| | | X | Variant annotations for structural variants |
| bioconductor-subcellbarcode |
1.22.0 |
|
|
GPL-2 |
| | | X | SubCellBarCode: Integrated workflow for robust mapping and visualizing... |
| bioconductor-subseq |
1.36.0 |
|
|
MIT |
X | X | | X | Subsampling of high-throughput sequencing count data |
| bioconductor-sugarcanecdf |
2.18.0 |
|
|
LGPL |
| | | X | sugarcanecdf |
| bioconductor-sugarcaneprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type sugarcane |
| bioconductor-suitor |
1.8.0 |
|
|
GPL-2 |
X | X | | | Selecting the number of mutational signatures through cross-validation |
| bioconductor-summarizedbenchmark |
2.20.0 |
|
|
GPL |
| | | X | Classes and methods for performing benchmark comparisons |
| bioconductor-summarizedexperiment |
1.36.0 |
|
|
Artistic-2.0 |
X | X | | X | A container (S4 class) for matrix-like assays |
| bioconductor-summix |
2.8.0 |
|
|
MIT |
| | | X | Summix: A method to estimate and adjust for population structure in... |
| bioconductor-supersigs |
1.14.0 |
|
|
GPL-3 |
| | | X | Supervised mutational signatures |
| bioconductor-suprahex |
1.40.0 |
|
|
GPL-2 |
X | X | | X | supraHex: a supra-hexagonal map for analysing tabular omics data |
| bioconductor-surfaltr |
1.12.0 |
|
|
MIT |
| | | X | Rapid Comparison of Surface Protein Isoform Membrane Topologies Through surfaltr |
| bioconductor-survclust |
1.0.0 |
|
|
MIT |
X | X | | | Identification Of Clinically Relevant Genomic Subtypes Using Outcome... |
| bioconductor-survcomp |
1.56.0 |
|
|
Artistic-2.0 |
X | X | | | Performance Assessment and Comparison for Survival Analysis |
| bioconductor-survtype |
1.22.0 |
|
|
Artistic-2.0 |
| | | X | Subtype Identification with Survival Data |
| bioconductor-sushi |
1.31.0 |
|
|
GPL |
X | X | | X | Tools for visualizing genomics data |
| bioconductor-sva |
3.54.0 |
|
|
Artistic-2.0 |
X | X | | | Surrogate Variable Analysis |
| bioconductor-svanumt |
1.12.0 |
|
|
GPL-3 |
| | | X | NUMT detection from structural variant calls |
| bioconductor-svaplsseq |
1.13.0 |
|
|
GPL-3 |
X | X | | X | SVAPLSseq-An R package to estimate the hidden factors of unwanted... |
| bioconductor-svaretro |
1.12.0 |
|
|
GPL-3 |
| | | X | Retrotransposed transcript detection from structural variants |
| bioconductor-svm2crm |
1.16.0 |
|
|
GPL-3 |
| | | X | Detection of cis-regulatory elements using svm implemented in LiblineaR. |
| bioconductor-svm2crmdata |
1.38.0 |
|
|
LGPL |
| | | X | An example dataset for use with the SVM2CRM package |
| bioconductor-svmdo |
1.6.0 |
|
|
GPL-3 |
| | | X | Identification of Tumor-Discriminating mRNA Signatures via Support... |
| bioconductor-swath2stats |
1.36.0 |
|
|
GPL-3 |
X | X | | X | Transform and Filter SWATH Data for Statistical Packages |
| bioconductor-swathxtend |
2.28.0 |
|
|
GPL-2 |
X | X | | X | SWATH extended library generation and statistical data analysis |
| bioconductor-swfdr |
1.32.0 |
|
|
GPL |
| | | X | Estimation of the science-wise false discovery rate and the false... |
| bioconductor-swimr |
1.29.0 |
|
|
LGPL-2 |
X | X | | X | SwimR: A Suite of Analytical Tools for Quantification of C. elegans... |
| bioconductor-switchbox |
1.42.0 |
|
|
GPL-2 |
X | X | | | Utilities to train and validate classifiers based on pair switching... |
| bioconductor-switchde |
1.32.0 |
|
|
GPL |
X | X | | X | Switch-like differential expression across single-cell trajectories |
| bioconductor-synapsis |
1.12.0 |
|
|
MIT |
| | | X | An R package to automate the analysis of double-strand break repair... |
| bioconductor-synapter |
2.30.0 |
|
|
GPL-2 |
X | X | | X | Label-free data analysis pipeline for optimal identification and quantitation |
| bioconductor-synapterdata |
1.44.0 |
|
|
GPL-2 |
| | | X | Data accompanying the synapter package |
| bioconductor-synaptome.data |
0.99.6 |
|
|
Artistic-2.0 |
| | | X | AnnotationData for Synaptome.DB package |
| bioconductor-synaptome.db |
0.99.16 |
|
|
Artistic-2.0 |
| | | X | Synamptosome Proteome Database |
| bioconductor-synergyfinder |
3.14.0 |
|
|
Mozilla |
X | X | | X | Calculate and Visualize Synergy Scores for Drug Combinations |
| bioconductor-synextend |
1.18.0 |
|
|
GPL-3 |
X | X | | X | Tools for Working With Synteny Objects |
| bioconductor-synlet |
2.6.0 |
|
|
GPL-3 |
X | X | | X | Hits Selection for Synthetic Lethal RNAi Screen Data |
| bioconductor-synmut |
1.22.0 |
|
|
GPL-2 |
| | | X | SynMut: Designing Synonymously Mutated Sequences with Different Genomic... |
| bioconductor-syntenet |
1.8.0 |
|
|
GPL-3 |
X | X | | | Inference And Analysis Of Synteny Networks |
| bioconductor-systempiper |
2.12.0 |
|
|
Artistic-2.0 |
X | X | | X | systemPipeR: Workflow Environment for Data Analysis and Report Generation |
| bioconductor-systempiperdata |
2.10.0 |
|
|
Artistic-2.0 |
| | | X | systemPipeRdata: Workflow templates and sample data |
| bioconductor-systempipeshiny |
1.16.0 |
|
|
GPL |
| | | X | systemPipeShiny: An Interactive Framework for Workflow Management and... |
| bioconductor-systempipetools |
1.14.0 |
|
|
Artistic-2.0 |
| | | X | Tools for data visualization |
| bioconductor-tabulamurisdata |
1.24.0 |
|
|
MIT |
| | | X | 10x And SmartSeq2 Data From The Tabula Muris Consortium |
| bioconductor-tabulamurissenisdata |
1.12.0 |
|
|
MIT |
| | | X | Bulk and single-cell RNA-seq data from the Tabula Muris Senis project |
| bioconductor-tadar |
1.4.0 |
|
|
GPL-3 |
| | | X | Transcriptome Analysis of Differential Allelic Representation |
| bioconductor-tadcompare |
1.16.0 |
|
|
MIT |
| | | X | TADCompare: Identification and characterization of differential TADs |
| bioconductor-tanggle |
1.12.0 |
|
|
Artistic-2.0 |
| | | X | Visualization of Phylogenetic Networks |
| bioconductor-tapseq |
1.18.0 |
|
|
MIT |
| | | X | Targeted scRNA-seq primer design for TAP-seq |
| bioconductor-target |
1.20.0 |
|
|
GPL-3 |
| | | X | Predict Combined Function of Transcription Factors |
| bioconductor-targetdecoy |
1.12.0 |
|
|
Artistic-2.0 |
| | | X | Diagnostic Plots to Evaluate the Target Decoy Approach |
| bioconductor-targetscan.hs.eg.db |
0.6.1 |
|
|
file |
X | X | | X | TargetScan miRNA target predictions for human |
| bioconductor-targetscan.mm.eg.db |
0.6.1 |
|
|
file |
| | | X | TargetScan miRNA target predictions for mouse |
| bioconductor-targetscore |
1.44.0 |
|
|
GPL-2 |
X | X | | X | TargetScore: Infer microRNA targets using microRNA-overexpression data... |
| bioconductor-targetscoredata |
1.42.0 |
|
|
GPL-2 |
| | | X | TargetScoreData |
| bioconductor-targetsearch |
2.8.0 |
|
|
GPL |
X | X | | | A package for the analysis of GC-MS metabolite profiling data |
| bioconductor-targetsearchdata |
1.44.0 |
|
|
GPL |
| | | X | Example GC-MS data for TargetSearch Package |
| bioconductor-tarseqqc |
1.27.0 |
|
|
GPL |
X | X | | X | TARgeted SEQuencing Experiment Quality Control |
| bioconductor-tartare |
1.20.0 |
|
|
GPL-3 |
| | | X | Raw ground spectra recorded on Thermo Fisher Scientific mass spectrometers |
| bioconductor-tbsignatureprofiler |
1.14.0 |
|
|
MIT |
| | | X | Profile RNA-Seq Data Using TB Pathway Signatures |
| bioconductor-tbx20bamsubset |
1.42.0 |
|
|
LGPL |
| | | X | Subset of BAM files from the "TBX20" experiment |
| bioconductor-tcc |
1.46.0 |
|
|
GPL-2 |
X | X | | X | TCC: Differential expression analysis for tag count data with robust... |
| bioconductor-tcgabiolinks |
2.34.0 |
|
|
GPL |
X | X | | X | TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data |
| bioconductor-tcgabiolinksgui |
1.23.0 |
|
|
GPL |
| | | X | "TCGAbiolinksGUI: A Graphical User Interface to analyze cancer... |
| bioconductor-tcgabiolinksgui.data |
1.26.0 |
|
|
GPL-3 |
| | | X | Data for the TCGAbiolinksGUI package |
| bioconductor-tcgacrcmirna |
1.26.0 |
|
|
GPL-2 |
| | | X | TCGA CRC 450 miRNA dataset |
| bioconductor-tcgacrcmrna |
1.26.0 |
|
|
GPL-2 |
| | | X | TCGA CRC 450 mRNA dataset |
| bioconductor-tcgamethylation450k |
1.42.0 |
|
|
GPL-2 |
| | | X | The Cancer Genome Atlas Illumina 450k methylation example data |
| bioconductor-tcgautils |
1.26.0 |
|
|
Artistic-2.0 |
| | | X | TCGA utility functions for data management |
| bioconductor-tcgawgbsdata.hg19 |
1.12.0 |
|
|
GPL-2 |
| | | X | Data |
| bioconductor-tcgaworkflowdata |
1.30.0 |
|
|
GPL-3 |
| | | X | Data for TCGA Workflow |
| bioconductor-tcseq |
1.30.0 |
|
|
GPL |
| | | X | Time course sequencing data analysis |
| bioconductor-tdaracne |
1.47.0 |
|
|
GPL-2 |
X | X | | X | Network reverse engineering from time course data. |
| bioconductor-tdbasedufe |
1.6.0 |
|
|
GPL-3 |
| | | X | Tensor Decomposition Based Unsupervised Feature Extraction |
| bioconductor-tdbasedufeadv |
1.6.0 |
|
|
GPL-3 |
| | | X | Advanced package of tensor decomposition based unsupervised feature extraction |
| bioconductor-tekrabber |
1.10.0 |
|
|
LGPL |
X | X | | | An R package estimates the correlations of orthologs and transposable... |
| bioconductor-tenxbraindata |
1.26.0 |
|
|
CC |
| | | X | Data from the 10X 1.3 Million Brain Cell Study |
| bioconductor-tenxbusdata |
1.20.0 |
|
|
BSD_2_clause |
| | | X | Single cell dataset from 10x in BUS format |
| bioconductor-tenxio |
1.8.0 |
|
|
Artistic-2.0 |
| | | X | Import methods for 10X Genomics files |
| bioconductor-tenxpbmcdata |
1.24.0 |
|
|
CC |
| | | X | PBMC data from 10X Genomics |
| bioconductor-tenxplore |
1.28.0 |
|
|
Artistic-2.0 |
| | | X | ontological exploration of scRNA-seq of 1.3 million mouse neurons from... |
| bioconductor-tenxvisiumdata |
1.14.0 |
|
|
MIT |
| | | X | Visium spatial gene expression data by 10X Genomics |
| bioconductor-teqc |
4.28.0 |
|
|
GPL |
X | X | | X | Quality control for target capture experiments |
| bioconductor-ternarynet |
1.50.0 |
|
|
GPL |
X | X | | | Ternary Network Estimation |
| bioconductor-terratcgadata |
1.10.0 |
|
|
Artistic-2.0 |
| | | X | OpenAccess TCGA Data on Terra as MultiAssayExperiment |
| bioconductor-test1cdf |
2.18.0 |
|
|
LGPL |
| | | X | test1cdf |
| bioconductor-test2cdf |
2.18.0 |
|
|
LGPL |
| | | X | test2cdf |
| bioconductor-test3cdf |
2.18.0 |
|
|
LGPL |
| | | X | test3cdf |
| bioconductor-test3probe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type test3 |
| bioconductor-tfarm |
1.28.0 |
|
|
Artistic-2.0 |
| | | X | Transcription Factors Association Rules Miner |
| bioconductor-tfbstools |
1.44.0 |
|
|
GPL-2 |
X | X | | | Software Package for Transcription Factor Binding Site (TFBS) Analysis |
| bioconductor-tfea.chip |
1.26.0 |
|
|
Artistic-2.0 |
| | | X | Analyze Transcription Factor Enrichment |
| bioconductor-tfhaz |
1.28.0 |
|
|
Artistic-2.0 |
| | | X | Transcription Factor High Accumulation Zones |
| bioconductor-tfutils |
1.26.0 |
|
|
Artistic-2.0 |
| | | X | TFutils |
| bioconductor-tidybulk |
1.18.0 |
|
|
GPL-3 |
| | | X | Brings transcriptomics to the tidyverse |
| bioconductor-tidycoverage |
1.2.0 |
|
|
MIT |
| | | X | Extract and aggregate genomic coverage over features of interest |
| bioconductor-tidyflowcore |
1.0.0 |
|
|
MIT |
| | | X | tidyFlowCore: Bringing flowCore to the tidyverse |
| bioconductor-tidyomics |
1.2.0 |
|
|
MIT |
| | | X | Easily install and load the tidyomics ecosystem |
| bioconductor-tidysbml |
1.0.0 |
|
|
CC |
| | | X | Extract SBML's data into dataframes |
| bioconductor-tidysinglecellexperiment |
1.16.0 |
|
|
GPL-3 |
| | | X | Brings SingleCellExperiment to the Tidyverse |
| bioconductor-tidyspatialexperiment |
1.2.0 |
|
|
GPL |
| | | X | SpatialExperiment with tidy principles |
| bioconductor-tidysummarizedexperiment |
1.16.0 |
|
|
GPL-3 |
| | | X | Brings SummarizedExperiment to the Tidyverse |
| bioconductor-tidytof |
1.0.0 |
|
|
MIT |
X | X | | | Analyze High-dimensional Cytometry Data Using Tidy Data Principles |
| bioconductor-tigre |
1.60.0 |
|
|
AGPL-3 |
X | X | | | Transcription factor Inference through Gaussian process Reconstruction... |
| bioconductor-tiledbarray |
1.16.0 |
|
|
MIT |
X | X | | X | Using TileDB as a DelayedArray Backend |
| bioconductor-tilingarray |
1.84.0 |
|
|
Artistic-2.0 |
X | X | | | Transcript mapping with high-density oligonucleotide tiling arrays |
| bioconductor-timecourse |
1.78.0 |
|
|
LGPL |
X | X | | X | Statistical Analysis for Developmental Microarray Time Course Data |
| bioconductor-timecoursedata |
1.16.0 |
|
|
BSD |
| | | X | A data package for timecourse RNA-seq and microarray gene expression data sets |
| bioconductor-timeomics |
1.18.0 |
|
|
GPL-3 |
| | | X | Time-Course Multi-Omics data integration |
| bioconductor-timerquant |
1.36.0 |
|
|
Artistic-2.0 |
| | | X | Timer Quantification |
| bioconductor-timescape |
1.30.0 |
|
|
GPL-3 |
| | | X | Patient Clonal Timescapes |
| bioconductor-timeseriesexperiment |
1.12.0 |
|
|
MIT |
| | | X | Analysis for short time-series data |
| bioconductor-timirgen |
1.11.0 |
|
|
GPL-3 |
| | | X | Time sensitive microRNA-mRNA integration, analysis and network generation tool |
| bioconductor-tin |
1.38.0 |
|
|
Artistic-2.0 |
X | X | | X | Transcriptome instability analysis |
| bioconductor-tinesath1cdf |
1.44.0 |
|
|
Artistic-2.0 |
| | | X | tinesath1cdf |
| bioconductor-tinesath1probe |
1.44.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type tinesath1 |
| bioconductor-tissueenrich |
1.26.0 |
|
|
MIT |
X | | | X | Tissue-specific gene enrichment analysis |
| bioconductor-tissuetreg |
1.26.0 |
|
|
GPL |
| | | X | TWGBS and RNA-seq data from tissue T regulatory cells from mice |
| bioconductor-titancna |
1.44.0 |
|
|
GPL-3 |
X | X | | | Subclonal copy number and LOH prediction from whole genome sequencing of tumours |
| bioconductor-tkwidgets |
1.84.0 |
|
|
Artistic-2.0 |
| | | X | R based tk widgets |
| bioconductor-tloh |
1.14.0 |
|
|
MIT |
| | | X | Assessment of evidence for LOH in spatial transcriptomics pre-processed... |
| bioconductor-tmexplorer |
1.16.0 |
|
|
Artistic-2.0 |
| | | X | A Collection of Tumour Microenvironment Single-cell RNA Sequencing... |
| bioconductor-tmixclust |
1.28.0 |
|
|
GPL |
| | | X | Time Series Clustering of Gene Expression with Gaussian Mixed-Effects... |
| bioconductor-tmsig |
1.0.0 |
|
|
GPL |
| | | X | Tools for Molecular Signatures |
| bioconductor-tnbc.cms |
1.18.0 |
|
|
GPL-3 |
| | | X | TNBC.CMS: Prediction of TNBC Consensus Molecular Subtypes |
| bioconductor-tnt |
1.28.0 |
|
|
AGPL-3 |
| | | X | Interactive Visualization for Genomic Features |
| bioconductor-toast |
1.20.0 |
|
|
GPL-2 |
| | | X | Tools for the analysis of heterogeneous tissues |
| bioconductor-tofsims |
1.22.0 |
|
|
GPL-3 |
X | X | | | Import, process and analysis of Time-of-Flight Secondary Ion Mass... |
| bioconductor-tofsimsdata |
1.34.0 |
|
|
GPL-3 |
| | | X | Import, process and analysis of ToF-SIMS imaging data |
| bioconductor-tomatocdf |
2.18.0 |
|
|
LGPL |
| | | X | tomatocdf |
| bioconductor-tomatoprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type tomato |
| bioconductor-tomoda |
1.16.0 |
|
|
MIT |
| | | X | Tomo-seq data analysis |
| bioconductor-tomoseqr |
1.10.0 |
|
|
MIT |
| | | X | R Package for Analyzing Tomo-seq Data |
| bioconductor-top |
1.6.0 |
|
|
GPL-3 |
| | | X | TOP Constructs Transferable Model Across Gene Expression Platforms |
| bioconductor-topaseq |
1.24.0 |
|
|
AGPL-3 |
X | X | | | Topology-based pathway analysis of RNA-seq data |
| bioconductor-topconfects |
1.22.0 |
|
|
LGPL-2.1 |
| | | X | Top Confident Effect Sizes |
| bioconductor-topdownr |
1.28.0 |
|
|
GPL |
| | | X | Investigation of Fragmentation Conditions in Top-Down Proteomics |
| bioconductor-topdownrdata |
1.28.0 |
|
|
GPL |
| | | X | Example Files for the topdownr R Package |
| bioconductor-topgo |
2.58.0 |
|
|
LGPL |
X | X | | X | Enrichment Analysis for Gene Ontology |
| bioconductor-toxicogx |
2.10.0 |
|
|
MIT |
| | | X | Analysis of Large-Scale Toxico-Genomic Data |
| bioconductor-tpp |
3.34.0 |
|
|
Artistic-2.0 |
| | | X | Analyze thermal proteome profiling (TPP) experiments |
| bioconductor-tpp2d |
1.22.0 |
|
|
GPL-3 |
| | | X | Detection of ligand-protein interactions from 2D thermal profiles (DLPTP) |
| bioconductor-tpsvg |
1.2.0 |
|
|
MIT |
| | | X | Thin plate models to detect spatially variable genes |
| bioconductor-tracktables |
1.40.0 |
|
|
GPL |
X | X | | X | Build IGV tracks and HTML reports |
| bioconductor-trackviewer |
1.42.0 |
|
|
GPL |
X | X | | X | A R/Bioconductor package with web interface for drawing elegant... |
| bioconductor-tradeseq |
1.20.0 |
|
|
MIT |
| | | X | trajectory-based differential expression analysis for sequencing data |
| bioconductor-trajectorygeometry |
1.14.0 |
|
|
MIT |
| | | X | This Package Discovers Directionality in Time and Pseudo-times Series... |
| bioconductor-trajectoryutils |
1.14.0 |
|
|
GPL-3 |
| | | X | Single-Cell Trajectory Analysis Utilities |
| bioconductor-transcriptogramer |
1.28.0 |
|
|
GPL |
| | | X | Transcriptional analysis based on transcriptograms |
| bioconductor-transcriptr |
1.34.0 |
|
|
GPL-3 |
X | X | | X | An Integrative Tool for ChIP- And RNA-Seq Based Primary Transcripts... |
| bioconductor-transformgampoi |
1.12.0 |
|
|
GPL-3 |
X | X | | X | Variance Stabilizing Transformation for Gamma-Poisson Models |
| bioconductor-transite |
1.24.0 |
|
|
MIT |
X | X | | | RNA-binding protein motif analysis |
| bioconductor-translatome |
1.44.0 |
|
|
GPL-3 |
X | X | | X | Comparison between multiple levels of gene expression |
| bioconductor-transmogr |
1.2.0 |
|
|
GPL-3 |
| | | X | Modify a set of reference sequences using a set of variants |
| bioconductor-transomics2cytoscape |
1.16.0 |
|
|
Artistic-2.0 |
| | | X | A tool set for 3D Trans-Omic network visualization with Cytoscape |
| bioconductor-transview |
1.46.0 |
|
|
GPL-3 |
X | X | | | Read density map construction and accession. Visualization of ChIPSeq... |
| bioconductor-trare |
1.5.0 |
|
|
MIT |
| | | X | Transcriptional Rewiring |
| bioconductor-traser |
1.36.0 |
|
|
GPL |
X | X | | X | GWAS trait-associated SNP enrichment analyses in genomic intervals |
| bioconductor-traviz |
1.6.0 |
|
|
MIT |
| | | X | Trajectory functions for visualization and interpretation. |
| bioconductor-treeandleaf |
1.18.0 |
|
|
Artistic-2.0 |
| | | X | Displaying binary trees with focus on dendrogram leaves |
| bioconductor-treeclimbr |
1.2.0 |
|
|
Artistic-2.0 |
| | | X | An algorithm to find optimal signal levels in a tree |
| bioconductor-treeio |
1.30.0 |
|
|
Artistic-2.0 |
X | X | | X | Base Classes and Functions for Phylogenetic Tree Input and Output |
| bioconductor-treekor |
1.14.0 |
|
|
GPL-3 |
| | | X | Cytometry Cluster Hierarchy and Cellular-to-phenotype Associations |
| bioconductor-treesummarizedexperiment |
2.14.0 |
|
|
GPL |
| | | X | TreeSummarizedExperiment: a S4 Class for Data with Tree Structures |
| bioconductor-treg |
1.10.0 |
|
|
Artistic-2.0 |
| | | X | Tools for finding Total RNA Expression Genes in single nucleus RNA-seq data |
| bioconductor-trena |
1.20.0 |
|
|
GPL-3 |
| | | X | Fit transcriptional regulatory networks using gene expression, priors,... |
| bioconductor-trendy |
1.28.0 |
|
|
GPL-3 |
| | | X | Breakpoint analysis of time-course expression data |
| bioconductor-tress |
1.12.0 |
|
|
GPL-3 |
| | | X | Toolbox for mRNA epigenetics sequencing analysis |
| bioconductor-tricycle |
1.14.0 |
|
|
GPL-3 |
| | | X | tricycle: Transferable Representation and Inference of cell cycle |
| bioconductor-triform |
1.29.0 |
|
|
GPL-2 |
X | X | | X | Triform finds enriched regions (peaks) in transcription factor... |
| bioconductor-trigger |
1.52.0 |
|
|
GPL-3 |
X | X | | | Transcriptional Regulatory Inference from Genetics of Gene ExpRession |
| bioconductor-trio |
3.44.0 |
|
|
LGPL-2 |
X | X | | X | Testing of SNPs and SNP Interactions in Case-Parent Trio Studies |
| bioconductor-triplex |
1.46.0 |
|
|
BSD_2_clause |
X | X | | | Search and visualize intramolecular triplex-forming sequences in DNA |
| bioconductor-tripr |
1.12.0 |
|
|
MIT |
| | | X | T-cell Receptor/Immunoglobulin Profiler (TRIP) |
| bioconductor-trna |
1.24.0 |
|
|
GPL-3 |
| | | X | Analyzing tRNA sequences and structures |
| bioconductor-trnadbimport |
1.24.0 |
|
|
GPL-3 |
| | | X | Importing from tRNAdb and mitotRNAdb as GRanges objects |
| bioconductor-trnascanimport |
1.26.0 |
|
|
GPL-3 |
| | | X | Importing a tRNAscan-SE result file as GRanges object |
| bioconductor-tronco |
2.38.0 |
|
|
GPL-3 |
| | | X | TRONCO, an R package for TRanslational ONCOlogy |
| bioconductor-tsar |
1.4.0 |
|
|
AGPL-3 |
| | | X | Thermal Shift Analysis in R |
| bioconductor-tscan |
1.44.0 |
|
|
GPL(>=2) |
X | X | | X | Tools for Single-Cell Analysis |
| bioconductor-tscr |
1.11.0 |
|
|
Artistic-2.0 |
X | | | | A time series clustering package combining slope and Frechet distances |
| bioconductor-tspair |
1.52.0 |
|
|
GPL-2 |
X | X | | | Top Scoring Pairs for Microarray Classification |
| bioconductor-tsrchitect |
1.20.0 |
|
|
GPL-3 |
| | | X | Promoter identification from large-scale TSS profiling data |
| bioconductor-tssi |
1.29.0 |
|
|
GPL-3 |
X | X | | | Identify and normalize transcription start sites in high-throughput... |
| bioconductor-ttgsea |
1.14.0 |
|
|
Artistic-2.0 |
| | | X | Tokenizing Text of Gene Set Enrichment Analysis |
| bioconductor-ttmap |
1.28.0 |
|
|
GPL-2 |
| | | X | Two-Tier Mapper: a clustering tool based on topological data analysis |
| bioconductor-tuberculosis |
1.12.0 |
|
|
Artistic-2.0 |
| | | X | Tuberculosis Gene Expression Data for Machine Learning |
| bioconductor-tumourmethdata |
1.3.0 |
|
|
Artistic-2.0 |
| | | X | A Collection of DNA Methylation Datasets for Human Tumour Samples and... |
| bioconductor-turbonorm |
1.54.0 |
|
|
LGPL |
X | X | | | A fast scatterplot smoother suitable for microarray normalization |
| bioconductor-tvtb |
1.32.0 |
|
|
Artistic-2.0 |
X | X | | X | TVTB: The VCF Tool Box |
| bioconductor-tweedeseq |
1.52.0 |
|
|
GPL |
X | X | | | RNA-seq data analysis using the Poisson-Tweedie family of distributions |
| bioconductor-tweedeseqcountdata |
1.38.0 |
|
|
GPL |
| | | X | RNA-seq count data employed in the vignette of the tweeDEseq package |
| bioconductor-twilight |
1.82.0 |
|
|
GPL |
X | X | | | Estimation of local false discovery rate |
| bioconductor-twoddpcr |
1.30.0 |
|
|
GPL-3 |
| | | X | Classify 2-d Droplet Digital PCR (ddPCR) data and quantify the number... |
| bioconductor-txcutr |
1.12.0 |
|
|
GPL-3 |
| | | X | Transcriptome CUTteR |
| bioconductor-txdb.athaliana.biomart.plantsmart22 |
3.0.1 |
|
|
Artistic-2.0 |
| | | X | Annotation package for TxDb object(s) |
| bioconductor-txdb.athaliana.biomart.plantsmart25 |
3.1.3 |
|
|
Artistic-2.0 |
| | | X | Annotation package for TxDb object(s) |
| bioconductor-txdb.athaliana.biomart.plantsmart28 |
3.2.2 |
|
|
Artistic-2.0 |
| | | X | Annotation package for TxDb object(s) |
| bioconductor-txdb.athaliana.biomart.plantsmart51 |
0.99.0 |
|
|
Artistic-2.0 |
| | | X | Annotation package for TxDb object(s) |
| bioconductor-txdb.btaurus.ucsc.bostau8.refgene |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Annotation package for TxDb object(s) |
| bioconductor-txdb.btaurus.ucsc.bostau9.refgene |
3.10.0 |
|
|
Artistic-2.0 |
| | | X | Annotation package for TxDb object(s) |
| bioconductor-txdb.celegans.ucsc.ce11.ensgene |
3.15.0 |
|
|
Artistic-2.0 |
| | | X | Annotation package for TxDb object(s) |
| bioconductor-txdb.celegans.ucsc.ce11.refgene |
3.4.6 |
|
|
Artistic-2.0 |
X | X | | X | Annotation package for TxDb object(s) |
| bioconductor-txdb.celegans.ucsc.ce6.ensgene |
3.2.2 |
|
|
Artistic-2.0 |
X | X | | X | Annotation package for TxDb object(s) |
| bioconductor-txdb.cfamiliaris.ucsc.canfam3.refgene |
3.11.0 |
|
|
Artistic-2.0 |
| | | X | Annotation package for TxDb object(s) |
| bioconductor-txdb.cfamiliaris.ucsc.canfam4.refgene |
3.14.0 |
|
|
Artistic-2.0 |
| | | X | Annotation package for TxDb object(s) |
| bioconductor-txdb.cfamiliaris.ucsc.canfam5.refgene |
3.14.0 |
|
|
Artistic-2.0 |
| | | X | Annotation package for TxDb object(s) |
| bioconductor-txdb.cfamiliaris.ucsc.canfam6.refgene |
3.17.0 |
|
|
Artistic-2.0 |
| | | X | Annotation package for TxDb object(s) |
| bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene |
3.2.2 |
|
|
Artistic-2.0 |
X | X | | X | Annotation package for TxDb object(s) |
| bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene |
3.12.0 |
|
|
Artistic-2.0 |
X | X | | X | Annotation package for TxDb object(s) |
| bioconductor-txdb.drerio.ucsc.danrer10.refgene |
3.4.6 |
|
|
Artistic-2.0 |
X | X | | X | Annotation package for TxDb object(s) |
| bioconductor-txdb.drerio.ucsc.danrer11.refgene |
3.4.6 |
|
|
Artistic-2.0 |
| | | X | Annotation package for TxDb object(s) |
| bioconductor-txdb.ggallus.ucsc.galgal4.refgene |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Annotation package for TxDb object(s) |
| bioconductor-txdb.ggallus.ucsc.galgal5.refgene |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Annotation package for TxDb object(s) |
| bioconductor-txdb.ggallus.ucsc.galgal6.refgene |
3.10.0 |
|
|
Artistic-2.0 |
| | | X | Annotation package for TxDb object(s) |
| bioconductor-txdb.hsapiens.biomart.igis |
2.3.2 |
|
|
Artistic-2.0 |
| | | X | Annotation package for TxDb object(s) |
| bioconductor-txdb.hsapiens.ucsc.hg18.knowngene |
3.2.2 |
|
|
Artistic-2.0 |
X | X | | X | Annotation package for TxDb object(s) |
| bioconductor-txdb.hsapiens.ucsc.hg19.knowngene |
3.2.2 |
|
|
Artistic-2.0 |
X | X | | X | Annotation package for TxDb object(s) |
| bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts |
3.2.2 |
|
|
Artistic-2.0 |
X | X | | X | Annotation package for TxDb object(s) |
| bioconductor-txdb.hsapiens.ucsc.hg38.knowngene |
3.20.0 |
|
|
Artistic-2.0 |
X | X | | X | Annotation package for TxDb object(s) |
| bioconductor-txdb.hsapiens.ucsc.hg38.refgene |
3.19.0 |
|
|
Artistic-2.0 |
| | | X | Annotation package for TxDb object(s) |
| bioconductor-txdb.mmulatta.ucsc.rhemac10.refgene |
3.14.0 |
|
|
Artistic-2.0 |
| | | X | Annotation package for TxDb object(s) |
| bioconductor-txdb.mmulatta.ucsc.rhemac3.refgene |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Annotation package for TxDb object(s) |
| bioconductor-txdb.mmulatta.ucsc.rhemac8.refgene |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Annotation package for TxDb object(s) |
| bioconductor-txdb.mmusculus.ucsc.mm10.ensgene |
3.4.0 |
|
|
Artistic-2.0 |
X | X | | X | Annotation package for TxDb object(s) |
| bioconductor-txdb.mmusculus.ucsc.mm10.knowngene |
3.10.0 |
|
|
Artistic-2.0 |
X | X | | X | Annotation package for TxDb object(s) |
| bioconductor-txdb.mmusculus.ucsc.mm39.knowngene |
3.20.0 |
|
|
Artistic-2.0 |
| | | X | Annotation package for TxDb object(s) |
| bioconductor-txdb.mmusculus.ucsc.mm39.refgene |
3.19.0 |
|
|
Artistic-2.0 |
| | | X | Annotation package for TxDb object(s) |
| bioconductor-txdb.mmusculus.ucsc.mm9.knowngene |
3.2.2 |
|
|
Artistic-2.0 |
X | X | | X | Annotation package for TxDb object(s) |
| bioconductor-txdb.ptroglodytes.ucsc.pantro4.refgene |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Annotation package for TxDb object(s) |
| bioconductor-txdb.ptroglodytes.ucsc.pantro5.refgene |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Annotation package for TxDb object(s) |
| bioconductor-txdb.ptroglodytes.ucsc.pantro6.refgene |
3.10.0 |
|
|
Artistic-2.0 |
| | | X | Annotation package for TxDb object(s) |
| bioconductor-txdb.rnorvegicus.biomart.igis |
2.3.2 |
|
|
Artistic-2.0 |
| | | X | Annotation package for TxDb object(s) |
| bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene |
3.2.2 |
|
|
Artistic-2.0 |
X | X | | X | Annotation package for TxDb object(s) |
| bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene |
3.12.0 |
|
|
Artistic-2.0 |
X | X | | X | Annotation package for TxDb object(s) |
| bioconductor-txdb.rnorvegicus.ucsc.rn6.ncbirefseq |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Annotation package for TxDb object(s) |
| bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene |
3.4.6 |
|
|
Artistic-2.0 |
X | X | | X | Annotation package for TxDb object(s) |
| bioconductor-txdb.rnorvegicus.ucsc.rn7.refgene |
3.15.0 |
|
|
Artistic-2.0 |
| | | X | Annotation package for TxDb object(s) |
| bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene |
3.2.2 |
|
|
Artistic-2.0 |
X | X | | X | Annotation package for TxDb object(s) |
| bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene |
3.2.2 |
|
|
Artistic-2.0 |
X | X | | X | Annotation package for TxDb object(s) |
| bioconductor-txdb.sscrofa.ucsc.susscr11.refgene |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Annotation package for TxDb object(s) |
| bioconductor-txdb.sscrofa.ucsc.susscr3.refgene |
3.12.0 |
|
|
Artistic-2.0 |
| | | X | Annotation package for TxDb object(s) |
| bioconductor-txdbmaker |
1.2.0 |
|
|
Artistic-2.0 |
| | | X | Tools for making TxDb objects from genomic annotations |
| bioconductor-tximeta |
1.24.0 |
|
|
GPL-2 |
| | | X | Transcript Quantification Import with Automatic Metadata |
| bioconductor-tximport |
1.34.0 |
|
|
LGPL |
X | X | | X | Import and summarize transcript-level estimates for transcript- and... |
| bioconductor-tximportdata |
1.34.0 |
|
|
GPL |
| | | X | tximportData |
| bioconductor-txreginfra |
1.10.0 |
|
|
Artistic-2.0 |
| | | X | Metadata management for multiomic specification of transcriptional... |
| bioconductor-typeinfo |
1.68.0 |
|
|
BSD_2_clause |
| | | X | Optional Type Specification Prototype |
| bioconductor-u133aaofav2cdf |
2.18.0 |
|
|
LGPL |
| | | X | u133aaofav2cdf |
| bioconductor-u133x3p.db |
3.2.3 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Human X3P Array annotation data (chip u133x3p) |
| bioconductor-u133x3pcdf |
2.18.0 |
|
|
LGPL |
| | | X | u133x3pcdf |
| bioconductor-u133x3pprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type u133x3p |
| bioconductor-ucell |
2.10.1 |
|
|
GPL-3 |
| | | X | Rank-based signature enrichment analysis for single-cell data |
| bioconductor-ucsc.utils |
1.2.0 |
|
|
Artistic-2.0 |
X | X | | X | Low-level utilities to retrieve data from the UCSC Genome Browser |
| bioconductor-ucscrepeatmasker |
3.15.2 |
|
|
Artistic-2.0 |
| | | X | UCSC RepeatMasker AnnotationHub resource metadata |
| bioconductor-ularcirc |
1.24.0 |
|
|
file |
| | | X | Shiny app for canonical and back splicing analysis (i.e. circular and... |
| bioconductor-umi4cats |
1.12.0 |
|
|
Artistic-2.0 |
| | | X | UMI4Cats: Processing, analysis and visualization of UMI-4C chromatin... |
| bioconductor-uncoverapplib |
1.12.0 |
|
|
MIT |
| | | X | Interactive graphical application for clinical assessment of sequence... |
| bioconductor-undo |
1.48.0 |
|
|
GPL-2 |
X | X | | X | Unsupervised Deconvolution of Tumor-Stromal Mixed Expressions |
| bioconductor-unifiedwmwqpcr |
1.42.0 |
|
|
GPL |
X | X | | X | Unified Wilcoxon-Mann Whitney Test for testing differential expression... |
| bioconductor-uniprot.ws |
2.46.0 |
|
|
Artistic-2.0 |
X | X | | X | R Interface to UniProt Web Services |
| bioconductor-uniprotkeywords |
0.99.7 |
|
|
MIT |
| | | X | Keywords from UniProt Database |
| bioconductor-uniquorn |
2.26.0 |
|
|
Artistic-2.0 |
X | X | | X | Identification of cancer cell lines based on their weighted mutational/... |
| bioconductor-universalmotif |
1.24.0 |
|
|
GPL-3 |
X | X | | | Import, Modify, and Export Motifs with R |
| bioconductor-updateobject |
1.10.0 |
|
|
Artistic-2.0 |
| | | X | Find/fix old serialized S4 instances |
| bioconductor-usort |
1.32.0 |
|
|
Artistic-2.0 |
| | | X | uSORT: A self-refining ordering pipeline for gene selection |
| bioconductor-vaexprs |
1.12.0 |
|
|
Artistic-2.0 |
| | | X | Generating Samples of Gene Expression Data with Variational Autoencoders |
| bioconductor-vanillaice |
1.68.0 |
|
|
LGPL-2 |
X | X | | | A Hidden Markov Model for high throughput genotyping arrays |
| bioconductor-varcon |
1.14.0 |
|
|
GPL-3 |
| | | X | VarCon: an R package for retrieving neighboring nucleotides of an SNV |
| bioconductor-variancepartition |
1.36.2 |
|
|
GPL-2 |
X | X | | X | Quantify and interpret drivers of variation in multilevel gene... |
| bioconductor-variantannotation |
1.52.0 |
|
|
Artistic-2.0 |
X | X | | | Annotation of Genetic Variants |
| bioconductor-variantexperiment |
1.20.0 |
|
|
GPL-3 |
| | | X | A RangedSummarizedExperiment Container for VCF/GDS Data with GDS Backend |
| bioconductor-variantfiltering |
1.42.0 |
|
|
Artistic-2.0 |
X | X | | | Filtering of coding and non-coding genetic variants |
| bioconductor-varianttools |
1.48.0 |
|
|
Artistic-2.0 |
X | X | | X | Tools for Exploratory Analysis of Variant Calls |
| bioconductor-varianttoolsdata |
1.30.0 |
|
|
Artistic-2.0 |
| | | X | Data for the VariantTools tutorial |
| bioconductor-vasp |
1.18.0 |
|
|
GPL |
| | | X | Quantification and Visualization of Variations of Splicing in Population |
| bioconductor-vbmp |
1.74.0 |
|
|
GPL |
X | X | | X | Variational Bayesian Multinomial Probit Regression |
| bioconductor-vcfarray |
1.22.0 |
|
|
GPL-3 |
| | | X | Representing on-disk / remote VCF files as array-like objects |
| bioconductor-vdjdive |
1.8.0 |
|
|
Artistic-2.0 |
X | X | | X | Analysis Tools for 10X V(D)J Data |
| bioconductor-vectrapolarisdata |
1.10.0 |
|
|
Artistic-2.0 |
| | | X | Vectra Polaris and Vectra 3 multiplex single-cell imaging data |
| bioconductor-vega |
1.35.0 |
|
|
GPL-2 |
X | X | | | An R package for copy number data segmentation |
| bioconductor-vegamc |
3.44.0 |
|
|
GPL-2 |
X | X | | | VegaMC: A Package Implementing a Variational Piecewise Smooth Model for... |
| bioconductor-velociraptor |
1.16.0 |
|
|
MIT |
| | | X | Toolkit for Single-Cell Velocity |
| bioconductor-veloviz |
1.12.0 |
|
|
GPL-3 |
X | X | | | VeloViz: RNA-velocity informed 2D embeddings for visualizing cell state... |
| bioconductor-venndetail |
1.22.0 |
|
|
GPL-2 |
| | | X | A package for visualization and extract details |
| bioconductor-verso |
1.16.0 |
|
|
file |
| | | X | Viral Evolution ReconStructiOn (VERSO) |
| bioconductor-vidger |
1.26.0 |
|
|
GPL-3 |
| | | X | Create rapid visualizations of RNAseq data in R |
| bioconductor-viper |
1.40.0 |
|
|
file |
X | X | | X | Virtual Inference of Protein-activity by Enriched Regulon analysis |
| bioconductor-viseago |
1.16.0 |
|
|
GPL-3 |
| | | X | ViSEAGO: a Bioconductor package for clustering biological functions... |
| bioconductor-visiumio |
1.2.0 |
|
|
Artistic-2.0 |
| | | X | Import Visium data from the 10X Space Ranger pipeline |
| bioconductor-visse |
1.14.0 |
|
|
GPL-3 |
| | | X | Visualising Set Enrichment Analysis Results |
| bioconductor-vitisviniferacdf |
2.18.0 |
|
|
LGPL |
| | | X | vitisviniferacdf |
| bioconductor-vitisviniferaprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type vitisvinifera |
| bioconductor-voyager |
1.8.1 |
|
|
Artistic-2.0 |
| | | X | From geospatial to spatial omics |
| bioconductor-vplotr |
1.16.0 |
|
|
GPL |
| | | X | Set of tools to make V-plots and compute footprint profiles |
| bioconductor-vsclust |
1.8.0 |
|
|
GPL-2 |
X | X | | | Feature-based variance-sensitive quantitative clustering |
| bioconductor-vsn |
3.74.0 |
|
|
Artistic-2.0 |
X | X | | | Variance stabilization and calibration for microarray data |
| bioconductor-vtpnet |
0.46.0 |
|
|
Artistic-2.0 |
| | | X | variant-transcription factor-phenotype networks |
| bioconductor-vulcan |
1.28.0 |
|
|
LGPL-3 |
| | | X | VirtUaL ChIP-Seq data Analysis using Networks |
| bioconductor-vulcandata |
1.28.0 |
|
|
LGPL-3 |
| | | X | VirtUaL ChIP-Seq data Analysis using Networks, dummy dataset |
| bioconductor-waddr |
1.20.0 |
|
|
MIT |
X | X | | | Statistical tests for detecting differential distributions based on the... |
| bioconductor-watermelon |
2.12.0 |
|
|
GPL-3 |
X | X | | X | Illumina DNA methylation array normalization and metrics |
| bioconductor-wavcluster |
2.40.0 |
|
|
GPL-2 |
X | X | | X | Sensitive and highly resolved identification of RNA-protein interaction... |
| bioconductor-wavetiling |
1.28.0 |
|
|
GPL |
X | X | | | Wavelet-Based Models for Tiling Array Transcriptome Analysis |
| bioconductor-wavetilingdata |
1.26.0 |
|
|
GPL |
| | | X | waveTiling Example Data |
| bioconductor-weaver |
1.72.0 |
|
|
GPL-2 |
X | X | | X | Tools and extensions for processing Sweave documents |
| bioconductor-webbioc |
1.78.0 |
|
|
GPL |
X | X | | X | Bioconductor Web Interface |
| bioconductor-weberdivechalcdata |
1.8.0 |
|
|
MIT |
| | | X | Spatially-resolved transcriptomics and single-nucleus RNA-sequencing... |
| bioconductor-weitrix |
1.18.0 |
|
|
LGPL-2.1 |
| | | X | Tools for matrices with precision weights, test and explore weighted or... |
| bioconductor-wes.1kg.wugsc |
1.38.0 |
|
|
GPL-2 |
| | | X | Whole Exome Sequencing (WES) of chromosome 22 401st to 500th exon from... |
| bioconductor-wgsmapp |
1.18.0 |
|
|
GPL-2 |
| | | X | Mappability tracks of Whole-genome Sequencing from the ENCODE Project |
| bioconductor-wheatcdf |
2.18.0 |
|
|
LGPL |
| | | X | wheatcdf |
| bioconductor-wheatprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type wheat |
| bioconductor-widgettools |
1.84.0 |
|
|
LGPL |
| | | X | Creates an interactive tcltk widget |
| bioconductor-wiggleplotr |
1.30.0 |
|
|
Apache |
X | X | | X | Make read coverage plots from BigWig files |
| bioconductor-worm.db0 |
3.20.0 |
|
|
Artistic-2.0 |
| | | X | Base Level Annotation databases for worm |
| bioconductor-wpm |
1.16.0 |
|
|
Artistic-2.0 |
| | | X | Well Plate Maker |
| bioconductor-wppi |
1.10.0 |
|
|
MIT |
| | | X | Weighting protein-protein interactions |
| bioconductor-wrench |
1.24.0 |
|
|
Artistic-2.0 |
| | | X | Wrench normalization for sparse count data |
| bioconductor-xbseq |
1.22.0 |
|
|
GPL |
X | X | | X | Test for differential expression for RNA-seq data |
| bioconductor-xcir |
1.7.0 |
|
|
GPL-2 |
| | | X | XCI-inference |
| bioconductor-xcms |
4.4.0 |
|
|
GPL |
X | X | | | LC-MS and GC-MS Data Analysis |
| bioconductor-xcore |
1.10.0 |
|
|
GPL-2 |
| | | X | xcore expression regulators inference |
| bioconductor-xcoredata |
1.10.0 |
|
|
GPL-2 |
| | | X | data package for xcore |
| bioconductor-xde |
2.52.0 |
|
|
LGPL-2 |
X | X | | | XDE: a Bayesian hierarchical model for cross-study analysis of... |
| bioconductor-xenlite |
1.0.0 |
|
|
Artistic-2.0 |
| | | X | Simple classes and methods for managing Xenium datasets |
| bioconductor-xenopus.db0 |
3.20.0 |
|
|
Artistic-2.0 |
| | | X | Base Level Annotation databases for xenopus |
| bioconductor-xenopuslaeviscdf |
2.18.0 |
|
|
LGPL |
| | | X | xenopuslaeviscdf |
| bioconductor-xenopuslaevisprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type xenopuslaevis |
| bioconductor-xeva |
1.22.0 |
|
|
GPL-3 |
| | | X | Analysis of patient-derived xenograft (PDX) data |
| bioconductor-xhybcasneuf |
1.44.0 |
|
|
Artistic-2.0 |
| | | X | EBI/PSB cross-hybridisation study package |
| bioconductor-xina |
1.24.0 |
|
|
GPL-3 |
| | | X | Multiplexes Isobaric Mass Tagged-based Kinetics Data for Network Analysis |
| bioconductor-xlaevis.db |
3.2.3 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Xenopus laevis annotation data (chip xlaevis) |
| bioconductor-xlaevis2cdf |
2.18.0 |
|
|
LGPL |
| | | X | xlaevis2cdf |
| bioconductor-xlaevis2probe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type xlaevis2 |
| bioconductor-xmapbridge |
1.64.0 |
|
|
LGPL-3 |
X | X | | X | Export plotting files to the xmapBridge for visualisation in X:Map |
| bioconductor-xnastring |
1.14.0 |
|
|
GPL-2 |
X | X | | | Efficient Manipulation of Modified Oligonucleotide Sequences |
| bioconductor-xtrasnplocs.hsapiens.dbsnp141.grch38 |
0.99.12 |
|
|
Artistic-2.0 |
| | | X | Extra SNP locations for Homo sapiens (dbSNP Build 141) |
| bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37 |
0.99.12 |
|
|
Artistic-2.0 |
| | | X | Extra SNP locations for Homo sapiens (dbSNP Build 144) |
| bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38 |
0.99.12 |
|
|
Artistic-2.0 |
| | | X | Extra SNP locations for Homo sapiens (dbSNP Build 144) |
| bioconductor-xtropicaliscdf |
2.18.0 |
|
|
LGPL |
| | | X | xtropicaliscdf |
| bioconductor-xtropicalisprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type xtropicalis |
| bioconductor-xvector |
0.46.0 |
|
|
Artistic-2.0 |
X | X | | | Foundation of external vector representation and manipulation in Bioconductor |
| bioconductor-yamss |
1.32.0 |
|
|
Artistic-2.0 |
X | X | | X | Tools for high-throughput metabolomics |
| bioconductor-yapsa |
1.28.0 |
|
|
GPL-3 |
X | X | | X | Yet Another Package for Signature Analysis |
| bioconductor-yaqcaffy |
1.50.0 |
|
|
Artistic-2.0 |
X | X | | X | Affymetrix expression data quality control and reproducibility analysis |
| bioconductor-yarn |
1.32.0 |
|
|
Artistic-2.0 |
X | X | | X | YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization |
| bioconductor-ye6100subacdf |
2.18.0 |
|
|
LGPL |
| | | X | ye6100subacdf |
| bioconductor-ye6100subbcdf |
2.18.0 |
|
|
LGPL |
| | | X | ye6100subbcdf |
| bioconductor-ye6100subccdf |
2.18.0 |
|
|
LGPL |
| | | X | ye6100subccdf |
| bioconductor-ye6100subdcdf |
2.18.0 |
|
|
LGPL |
| | | X | ye6100subdcdf |
| bioconductor-yeast.db0 |
3.20.0 |
|
|
Artistic-2.0 |
| | | X | Base Level Annotation databases for yeast |
| bioconductor-yeast2.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix Yeast_2 Array annotation data (chip yeast2) |
| bioconductor-yeast2cdf |
2.18.0 |
|
|
LGPL |
| | | X | yeast2cdf |
| bioconductor-yeast2probe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type yeast2 |
| bioconductor-yeastcc |
1.46.0 |
|
|
Artistic-2.0 |
X | X | | X | Spellman et al. (1998) and Pramila/Breeden (2006) yeast cell cycle... |
| bioconductor-yeastexpdata |
0.52.0 |
|
|
GPL |
X | X | | X | Yeast Experimental Data |
| bioconductor-yeastgsdata |
0.44.0 |
|
|
Artistic-2.0 |
| | | X | Yeast Gold Standard Data |
| bioconductor-yeastnagalakshmi |
1.42.0 |
|
|
Artistic-2.0 |
| | | X | Yeast genome RNA sequencing data based on Nagalakshmi et. al. |
| bioconductor-yeastrnaseq |
0.44.0 |
|
|
GPL |
| | | X | Yeast RNA-Seq Experimental Data from Lee et al. 2008 |
| bioconductor-ygs98.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix YG_S98 Array annotation data (chip ygs98) |
| bioconductor-ygs98cdf |
2.18.0 |
|
|
LGPL |
| | | X | ygs98cdf |
| bioconductor-ygs98frmavecs |
1.3.0 |
|
|
GPL |
| | | X | Vectors used by frma for microarrays of type ygs98 |
| bioconductor-ygs98probe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type ygs98 |
| bioconductor-yri1kgv |
0.32.0 |
|
|
Artistic-2.0 |
| | | X | expression + genotype on 79 unrelated YRI individuals |
| bioconductor-yrimulti |
0.18.0 |
|
|
Artistic-2.0 |
| | | X | support for expression, methylation, DHS, VCF for YRI |
| bioconductor-zebrafish.db |
3.13.0 |
|
|
Artistic-2.0 |
| | | X | Affymetrix Affymetrix Zebrafish Array annotation data (chip zebrafish) |
| bioconductor-zebrafish.db0 |
3.20.0 |
|
|
Artistic-2.0 |
| | | X | Base Level Annotation databases for zebrafish |
| bioconductor-zebrafishcdf |
2.18.0 |
|
|
LGPL |
| | | X | zebrafishcdf |
| bioconductor-zebrafishprobe |
2.18.0 |
|
|
LGPL |
| | | X | Probe sequence data for microarrays of type zebrafish |
| bioconductor-zebrafishrnaseq |
1.26.0 |
|
|
GPL |
| | | X | Zebrafish RNA-Seq Experimental Data from Ferreira et al. (2014) |
| bioconductor-zellkonverter |
1.16.0 |
|
|
MIT |
| | | X | Conversion Between scRNA-seq Objects |
| bioconductor-zenith |
1.8.0 |
|
|
Artistic-2.0 |
| | | X | Gene set analysis following differential expression using linear... |
| bioconductor-zfpkm |
1.28.0 |
|
|
GPL-3 |
X | X | | X | A suite of functions to facilitate zFPKM transformations |
| bioconductor-zinbwave |
1.28.0 |
|
|
Artistic-2.0 |
X | | | X | Zero-Inflated Negative Binomial Model for RNA-Seq Data |
| bioconductor-zitools |
1.0.0 |
|
|
BSD_3_clause |
| | | X | Analysis of zero-inflated count data |
| bioconductor-zlibbioc |
1.52.0 |
|
|
Artistic-2.0 |
X | X | | | An R packaged zlib-1.2.5 |
| bioconductor-zygositypredictor |
1.6.0 |
|
|
GPL-2 |
| | | X | Package for prediction of zygosity for variants/genes in NGS data |
| bioconvert |
1.1.1 |
doc |
dev |
GPL-3.0 |
X | X | | X | Convert between bioinformatics formats |
| biodiff |
0.2.2 |
|
|
GPLv3+ |
X | X | | | exact comparison of biological sequences |
| biodigest |
0.2.16 |
|
|
GPL-3.0-or-later |
| | | X | In silico Validation of Disease and Gene sets, Clusterings or... |
| bioepic |
0.1.6 |
|
|
GNU |
X | X | | | Chip-Seq broad peak/domain finder. |
| bioexcel_seqqc |
0.6 |
|
|
Apache |
| | | X | Sequence Quality Control pipeline/modules |
| biofluff |
3.0.4 |
|
|
MIT |
X | X | | X | Exploratory analysis and visualization of high-throughput sequencing data |
| bioformats |
0.1.15 |
|
|
MIT |
X | X | | X | A collection of Python classes to handle bioinformatics data. |
| bioframe |
0.7.2 |
doc |
|
MIT |
| | | X | Pandas utilities for tab-delimited and other genomic files |
| biogridpy |
0.1.1 |
|
|
MIT |
X | X | | X | Python client for the BioGRID REST API webservice |
| bioinfokit |
2.1.3 |
doc |
|
MIT |
| | | X | The bioinfokit toolkit aimed to provide various easy-to-use... |
| biokit |
0.5.0 |
|
|
BSD |
X | X | | X | Set of visualisation and analysis tools for biological data sets |
| biolib |
0.1.9 |
|
|
GPL3 |
X | X | | X | Package for common tasks in bioinformatics. |
| biolite |
1.2.0 |
|
|
GPLv3 |
X | X | | | A lightweight bioinformatics framework with automated tracking of... |
| biolite-tools |
0.4.0 |
|
|
GPLv3 |
X | X | | | C++ tools for biolite, a lightweight bioinformatics framework with... |
| biom-format |
2.1.7 |
|
|
BSD |
X | X | | | Biological Observation Matrix (BIOM) format |
| biomaj |
3.0.19 |
|
|
GNU |
X | X | | | Automates the update cycle and the supervision of the locally mirrored... |
| bionetcomp |
1.1 |
|
|
GNU |
| | | X | BioNetComp: A Python package for biological network comparison from... |
| bionumpy |
1.0.13 |
doc |
dev |
MIT |
| | | X | Library for working with biological sequence data as numpy arrays. |
| biopet |
0.9.0 |
|
|
https://github. |
X | X | | X | Biopet (Bio Pipeline Execution Toolkit) is the main pipeline... |
| biopet-bamstats |
1.0.1 |
|
|
MIT |
| | | X | BamStats is a package that contains tools to generate stats from a BAM... |
| biopet-basecounter |
0.1 |
|
|
MIT |
| | | X | BaseCounter counts the bases from genes and transcripts and outputs... |
| biopet-extractadaptersfastqc |
0.2 |
|
|
MIT |
X | X | | X | ExtractAdaptersFastqc reads which adapter sequences where found from a... |
| biopet-fastqsplitter |
0.1 |
|
|
MIT |
| | | X | This tool divides a fastq file into smaller fastq files, based on the... |
| biopet-sampleconfig |
0.3 |
|
|
MIT |
X | X | | X | #### Tools - ExtractTsv This mean can extract samples, libraries and... |
| biopet-scatterregions |
0.2 |
|
|
MIT |
| | | X | This tool breaks a reference or bed file into smaller scatter regions... |
| biopet-seattleseqkit |
0.2 |
|
|
MIT |
| | | X | #### Tool - Filter This tool can filter a seattle seq file. |
| biopet-seqstat |
1.0.1 |
|
|
MIT |
X | X | | X | SeqStat is a package that contains tools to generate stats from a FastQ... |
| biopet-validateannotation |
0.1 |
|
|
MIT |
| | | X | ValidateAnnotationvalidates whether an annotation file is correct. |
| biopet-validatefastq |
0.1.1 |
|
|
MIT |
X | X | | X | This tool validates a FASTQ file. |
| biopet-validatevcf |
0.1 |
|
|
MIT |
| | | X | ValidateVcf validates a VCF file against a reference genomes. |
| biopet-vcffilter |
0.2 |
|
|
MIT |
| | | X | This tool enables a user to filter VCF files. |
| biopet-vcfstats |
1.2 |
|
|
MIT |
X | X | | X | Vcfstats is a tool that can generate metrics from a vcf file. |
| biophi |
1.0.10 |
doc |
dev |
MIT |
| | | X | BioPhi open-source antibody design platform. |
| bioprov |
0.1.23 |
doc |
dev |
MIT |
| | | X | BioProv - Provenance capture for bioinformatics workflows |
| biopython |
1.70 |
|
|
Biopython |
X | X | | | Freely available tools for computational molecular biology. |
| biopython.convert |
1.3.3 |
doc |
dev |
MIT |
| | | X | Interconvert various file formats supported by BioPython |
| bioservices |
1.7.11 |
|
|
GPLv3 |
X | X | | X | Access to Biological Web Services from Python |
| biosniff |
1.0.0 |
doc |
|
BSD |
| | | X | A Sniffer for Biological formats |
| biotdg |
0.1.0 |
doc |
dev |
MIT |
| | | X | Bioinformatics Test Data Generator |
| biothings_client |
0.2.6 |
|
|
BSD |
| | | X | Python Client for BioThings API services. |
| biotradis |
1.4.5 |
|
|
GPL-3.0-only |
X | | | X | A set of tools to analyse the output from TraDIS analyses |
| biotransformer |
3.0.20230403 |
|
|
GPL3 |
| | | X | Predicts small molecule metabolism. |
| bioutils |
0.6.1 |
doc |
dev |
Apache-2.0 |
| | | X | miscellaneous simple bioinformatics utilities and lookup tables |
| biowdl-input-converter |
0.3.0 |
doc |
dev |
MIT |
| | | X | Converting various input formats into WDL structs for BioWDL pipelines. |
| biox |
1.2.0 |
|
dev |
GPL-3.0-only |
| | | X | Biological Sequence Compression and Analysis Tool |
| bird_tool_utils_python |
0.4.1 |
|
|
GPL-3.0-or-later |
| | | X | Python utilities used as part of the bird suite of bioinformatic tools. |
| bis-snp |
1.0.1 |
|
|
MIT |
X | X | | X | Bisulfite-seq/NOMe-seq SNPs & cytosine methylation caller |
| bis-snp-utils |
0.0.1 |
|
|
MIT |
X | X | | X | bis-snp-utils are support tools for Bis-SNP |
| biscot |
2.3.3 |
|
|
LGPL-2.1 |
| | | X | Bionano SCaffolding Correction Tool |
| biscuit |
1.6.0.20241216 |
doc |
dev |
MIT |
X | X | | | A utility for analyzing sodium bisulfite conversion-based DNA... |
| biskit |
2.5.1 |
doc |
dev |
GNU |
X | X | | X | A Python platform for structural bioinformatics |
| bismark |
0.24.2 |
|
|
GNU |
X | X | | X | Bismark is a program to map bisulfite treated sequencing reads to a... |
| bitmapperbs |
1.0.2.3 |
|
|
Apache |
X | | | | BitMapperBS: a fast and accurate read aligner for whole-genome... |
| bitstring |
3.1.5 |
|
|
MIT |
X | X | | | Simple construction, analysis and modification of binary data. |
| blacksheep-outliers |
0.0.8 |
doc |
dev |
MIT |
| | | X | A package for differential extreme values analysis |
| blasr |
5.3.5 |
|
|
BSD-3-Clause-Clear |
X | X | | | BLASR - The PacBio long read aligner |
| blasr_libcpp |
5.3.4 |
|
|
BSD-3-Clause-Clear |
X | X | | | blasr_libcpp is a support library used by blasr and other PacBio tools |
| blast |
2.16.0 |
|
|
NCBI-PD |
X | X | | | BLAST+ is a new suite of BLAST tools that utilizes the NCBI C++ Toolkit. |
| blast-legacy |
2.2.26 |
|
|
Public |
X | X | | | The Basic Local Alignment Search Tool (BLAST) finds regions of local... |
| blast2galaxy |
1.0.0 |
doc |
dev |
MIT |
| | | X | A Python package with a CLI and API to perform BLAST queries against... |
| blastalign |
1.4 |
|
|
GNU |
X | | | | BlastAlign uses NCBI Blast to align nucleotide sequences that have... |
| blastbesties |
1.1.2 |
|
|
MIT |
X | X | | X | Rapid discovery of reciprocal best blast pairs from BLAST output files. |
| blastmining |
1.2.0 |
doc |
dev |
GNU |
| | | X | blastMining: Mining NCBI BLAST outputs |
| blat |
36 |
|
|
Free |
X | X | | | BLAT is a bioinformatics software tool which performs rapid mRNA/DNA... |
| blaze2 |
2.5.1 |
doc |
dev |
GPL-3.0-or-later |
| | | X | Barcode identification from (Nanopore) Long reads for AnalyZing... |
| bleach |
1.4.2 |
|
|
Apache |
X | X | | | An easy whitelist-based HTML-sanitizing tool. |
| blend-bio |
1.0.0 |
|
|
MIT |
X | X | | | BLEND is a Fast, Memory-Efficient, and Accurate Mechanism to Find Fuzzy... |
| bleties |
0.1.11 |
|
|
MIT |
| | | X | BleTIES: Basic Long-read Enabled Toolkit for Interspersed DNA... |
| blksheep |
0.0.7 |
doc |
dev |
MIT |
| | | X | A package for differential extreme values analysis |
| blobtools |
1.1.1 |
|
|
GPLv3 |
X | | | X | Modular command-line solution for visualisation, quality control and... |
| blockbuster |
0.0.1.1 |
|
|
The |
X | X | | | Blockbuster detects blocks of overlapping reads using a... |
| blockclust |
1.1.1 |
|
|
GPL-2.0-or-later |
X | | | | Efficient clustering and classification of non-coding RNAs from short... |
| bloocoo |
1.0.7 |
|
|
aGPL |
X | X | | | Bloocoo is a k-mer spectrum-based read error corrector, designed to... |
| bloomfiltertrie |
0.8.7 |
|
|
MIT |
X | X | | | An alignment-free, reference-free and incremental data structure for... |
| blosum |
2.0.3 |
doc |
dev |
GPL-3.0-or-later |
| | | X | A small module for easy access to BLOSUM matrices without dependencies. |
| bmfilter |
3.101 |
|
|
Public |
X | X | | | bmfilter is part of BMTagger aka Best Match Tagger, for removing human... |
| bmge |
1.12 |
doc |
|
GPL2 |
| | | X | BMGE (Block Mapping and Gathering with Entropy) is a program that... |
| bmtagger |
3.101 |
|
|
Public |
X | X | | | BMTagger aka Best Match Tagger is for removing human reads from... |
| bmtool |
3.101 |
|
|
Public |
X | X | | | bmtool is part of BMTagger aka Best Match Tagger, for removing human... |
| bohra |
2.3.7 |
doc |
|
GPL-3.0-or-later |
| | | X | Pipeline for analysing Illumina data for microbiological public health. |
| bold-identification |
0.0.27 |
|
|
GNU |
| | | X | A tool for taxonomic assignment for given sequences using the BOLD... |
| bolt |
0.3.0 |
|
|
MIT |
X | X | | | A variant caller for short-read sequencing data |
| bolt-lmm |
2.3.4 |
|
|
GPL-3+ |
X | X | | | Efficient large cohorts genome-wide Bayesian mixed-model association testing |
| boltons |
16.4.1 |
|
|
|
X | X | | | None |
| boms |
1.1.0 |
|
|
MIT |
X | | | | Cell Segmentation for Spatial Transcriptomics Data using BOMS |
| booster |
0.1.2 |
|
|
GPL-2.0 |
X | X | | | BOOSTER is a new way of computing bootstrap supports in large phylogenies. |
| boquila |
0.6.1 |
|
|
MIT |
| | | X | NGS read simulator to eliminate read nucleotide bias in sequence analysis. |
| borf |
1.2 |
|
|
MIT |
| | | X | ORF predictions from .fa files |
| botocore |
1.3.6 |
|
|
Apache |
X | X | | | None |
| boutroslabplottinggeneral |
5.3.4 |
|
|
GPL-2extra |
X | X | | | None |
| bowtie |
1.3.1 |
|
|
Artistic-2.0-only |
X | X | | | An ultrafast memory-efficient short read aligner |
| bowtie2 |
2.5.4 |
doc |
dev |
GPL-3.0-only |
X | X | | | A fast and sensitive gapped read aligner. |
| bpipe |
0.9.13 |
|
|
BSD-3-Clause |
X | X | | X | Bpipe - a tool for running and managing bioinformatics pipelines |
| bpp-core |
2.4.1 |
|
|
CeCILL |
X | X | | | Bio++ is a set of C++ libraries for Bioinformatics. |
| bpp-phyl |
2.4.1 |
|
|
CeCILL |
X | X | | | Bio++ is a set of C++ libraries for Bioinformatics. |
| bpp-popgen |
2.4.1 |
|
|
CeCILL |
X | X | | | Bio++ is a set of C++ libraries for Bioinformatics. |
| bpp-seq |
2.4.1 |
|
|
CeCILL |
X | X | | | Bio++ is a set of C++ libraries for Bioinformatics. |
| bracken |
3.1 |
doc |
dev |
GPL-3.0-or-later |
X | X | | X | Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly... |
| braid-mrf |
1.0.9 |
|
dev |
MIT |
| | | X | Predicting protein complexes |
| braker |
1.9 |
|
|
Artistic |
X | | | X | BRAKER1: Unsupervised RNA-Seq-based genome annotation with GeneMark-ET... |
| braker2 |
2.1.6 |
|
|
Artistic |
X | X | | X | BRAKER2 is an extension of BRAKER1 |
| braker3 |
3.0.8 |
|
|
Artistic |
| | | X | BRAKER3 is the latest pipeline in the BRAKER suite |
| brass |
5.1.6 |
|
|
|
X | | | | None |
| brawn |
1.0.2 |
|
dev |
GPL-3.0 |
| | | X | A tool for handling repetitive insertions into sequence alignments. |
| break-point-inspector |
1.5 |
|
|
MIT |
X | X | | X | BPI uses Manta’s variant calls to re-analyse BAM files and precisely... |
| breakdancer |
1.4.5 |
|
|
GPLv3 |
X | X | | | SV detection from paired end reads mapping |
| breakfast |
0.4.5 |
|
dev |
MIT |
| | | X | breakfast: fast putative outbreak cluster and infection chain detection... |
| breakseq2 |
2.2 |
|
|
BSD-2-Clause |
X | X | | | BreakSeq2: Ultrafast and accurate nucleotide-resolution analysis of... |
| breseq |
0.39.0 |
doc |
dev |
GPL-2.0-or-later |
X | X | | | A computational pipeline for finding mutations relative to a reference... |
| brockman-pipeline |
1.0 |
|
|
GPL-3.0 |
X | X | | X | Brockman Representation Of Chromatin by K-mers in Mark-Associated Nucleotides |
| brooklyn_plot |
0.0.4 |
doc |
dev |
MIT |
| | | X | Gene co-expression and transcriptional bursting pattern recognition... |
| bs-seeker2 |
2.1.7 |
|
|
MIT |
X | X | | X | BS Seeker 2 is a seamless and versatile pipeline for accurately and... |
| bs_call |
2.02 |
|
|
GPL-3.0 |
X | X | | | DNA methylation and variant Caller for Bisulfite Sequencing Data. |
| bsmap |
2.90 |
|
|
GNU |
X | X | | | BSMAP is a short reads mapping software for bisulfite sequencing reads. |
| bte |
0.9.0 |
|
|
MIT |
X | X | | | Cython wrapper enabling use of the MAT library in Python. |
| btllib |
1.7.3 |
doc |
dev |
GPL-3.0-or-later |
X | X | | | Bioinformatics common code library in C++ with Python wrappers, from... |
| btrim |
1.0.1 |
|
|
AGPL-3.0 |
X | | | | This tool is made to remove "tips" (short dead ends) from a... |
| bttcmp |
1.0.3 |
|
dev |
GPLv3 |
| | | X | A toxin minging tool for Bacillus thuringiensis |
| bttoxin_digger |
1.0.10 |
|
dev |
GPLv3 |
| | | X | A toxin minging tool for Bacillus thuringiensis |
| bttoxin_scanner |
2.0.1 |
|
dev |
GPLv3 |
| | | X | A toxin exploration tool for Bacillus thuringiensis |
| btyper3 |
3.4.0 |
|
|
GPL-3 |
| | | X | In silico taxonomic classification of Bacillus cereus group isolates... |
| bubblegun |
1.1.9 |
doc |
dev |
MIT |
| | | X | BubbleGun is a tool for detecting bubbles and superbubbles in GFA... |
| bucketcache |
0.12.0 |
|
|
MIT |
X | X | | | Versatile persisent file cache. |
| bufet |
1.0 |
|
|
file |
X | X | | | Tool that performs the unbiased miRNA functional enrichment analysis... |
| bugseq-porechop |
0.3.4pre |
|
|
GPL3 |
X | X | | | Adapter removal and demultiplexing of Oxford Nanopore reads (fork of... |
| buildh |
1.6.1 |
doc |
|
BSD |
| | | X | Build hydrogen atoms from a united-atom MD of lipids and calculate the... |
| bumbershoot |
3_0_21142_0e4f4a4 |
|
|
Apache |
X | | | | The Bumbershoot tool suite for analyzing shotgun proteomic data |
| burrito |
0.9.1 |
|
|
BSD |
X | X | | X | Framework for wrapping and controlling command-line applications. |
| burrito-fillings |
0.1.1 |
|
|
BSD |
X | X | | X | burrito-fillings: burrito application controllers for bioinformatics |
| burst |
1.0 |
|
|
AGPL3.0 |
| | | X | BURST (formerly known as embalmer) is an optimal, high-speed pairwise... |
| busco |
5.8.3 |
doc |
dev |
MIT |
X | X | | X | Assessment of assembly completeness using Universal Single Copy Orthologs. |
| busco_phylogenomics |
20240919 |
|
|
MIT |
| | | X | Utility script to construct species phylogenies using BUSCO proteins. |
| buscolite |
24.11.3 |
|
dev |
BSD-2-Clause |
| | | X | buscolite: busco analysis for gene predictions |
| bustools |
0.44.1 |
doc |
dev |
BSD-2-Clause |
X | X | | | bustools is a program for manipulating BUS files for single cell... |
| bwa |
0.7.18 |
|
|
GPL3 |
X | X | | | The BWA read mapper. |
| bwa-aln-interactive |
0.7.18 |
|
|
GPL-3.0-only |
X | X | | | Version of the BWA aln read mapper for interactive alignment. |
| bwa-mem2 |
2.2.1 |
|
|
MIT |
X | X | | | The next version of bwa-mem |
| bwa-meme |
1.0.6 |
|
|
MIT |
X | | | | Faster BWA-MEM2 using learned-index |
| bwakit |
0.7.18.dev1 |
|
|
GPLv3 |
X | X | | X | A self-consistent installation-free package of scripts and precompiled... |
| bwameth |
0.2.7 |
|
|
MIT |
X | X | | X | A fast and accurate aligner of BS-seq reads |
| bwapy |
0.1.4 |
|
|
Mozilla |
X | X | | | Bwapy provides python wrappers for bwa. |
| bwise |
1.0.0 |
|
|
AGPL-3.0 |
X | | | | BWISE is a de Bruijn assembly Workflow using Integral information of... |
| bwread |
0.0.5 |
|
|
MIT |
X | X | | | Read bigwig files quickly into PyRanges or DataFrames |
| bx-python |
0.13.0 |
doc |
dev |
MIT |
X | X | | | Tools for manipulating biological data, particularly multiple sequence... |
| bxtools |
0.1.0 |
|
|
GPLv3 |
X | X | | | Tools for analyzing 10X Genomics data |
| byobu |
5.98 |
|
|
GPLv3 |
X | | | | Byobu is a GPLv3 open source text-based window manager and terminal multiplexer. |
| c-ares |
1.11.0 |
|
|
MIT |
X | X | | | c-ares is a C library for asynchronous DNS requests (including name resolves) |
| c4counter |
0.0.2 |
|
|
MIT |
| | | X | returns the number and types of human C4 regions in a fasta file |
| cactus |
2019.03.01 |
|
|
https://github. |
X | | | | Cactus is a reference-free whole-genome multiple alignment program... |
| cadd-scripts |
1.7.2 |
|
|
Restricted. |
| | | X | CADD scripts release for offline scoring |
| cafe |
5.1.0 |
|
|
IU |
X | | | | Computational Analysis of gene Family Evolution (CAFE) |
| cage |
2016.05.13 |
|
|
Apache |
X | | | | Changepoint Analysis for Efficient Variant Calling |
| cagee |
1.2 |
doc |
dev |
ECL |
X | X | | | Analyzes changes in gene expression in a way that accounts for... |
| calcs |
0.0.0.9999 |
|
|
MIT |
| | | X | Append minimap2's CS tag to a SAM file. |
| calib |
0.3.4 |
|
|
MIT |
X | X | | | Clustering without alignment using (locality sensitive hashing) LSH and... |
| calisp |
3.1.1 |
|
dev |
MIT |
| | | X | Estimate isotopic composition of peptides from proteomics mass... |
| calitas |
1.0 |
|
|
BSD-3-Clause-Clear |
| | | X | A CRISPR/Cas-aware ALigner for In silico off-TArget Search |
| callerpp |
0.1.6 |
|
|
MIT |
X | X | | | A simple consensus caller based on partial order alignment with spoa |
| callingcardstools |
1.8.1 |
doc |
dev |
MIT |
| | | X | An API and collection of cmd line tools to work with calling cards... |
| callstate |
0.0.2 |
|
|
MIT |
X | | | | A replacement for GATK3 CallableLoci |
| calour |
2020.8.6 |
doc |
dev |
BSD-3-Clause |
| | | X | exploratory and interactive microbiome analyses based on heatmaps |
| cameo |
0.13.6 |
|
|
Apache |
| | | X | cameo - computer aided metabolic engineering & optimization |
| cami-amber |
2.0.7 |
|
dev |
GPL-3.0-or-later |
| | | X | AMBER: Assessment of Metagenome BinnERs |
| cami-opal |
1.0.13 |
|
dev |
Apache-2.0 |
| | | X | OPAL assesses and compares the performance of taxonomic metagenome profilers. |
| camlhmp |
1.1.0 |
|
|
MIT |
| | | X | Classification through yAML Heuristic Mapping Protocol |
| campyagainst |
0.1.0 |
|
|
GPL-3.0-or-later |
| | | X | Accurate assignment of ANI genomic species to Campylobacter genomes. |
| campygstyper |
0.1.1 |
|
|
GPL-3.0-or-later |
| | | X | Accurate assignment of ANI genomic species to Campylobacter genomes. |
| cancerit-allelecount |
4.3.0 |
|
|
GPL-3.0-only |
X | | | | Support code for NGS copy number algorithms |
| cannoli |
1.0.1 |
|
|
Apache-2.0 |
X | X | | X | Distributed execution of bioinformatics tools on Apache Spark |
| canopy |
0.25 |
|
|
GPL-2.0-or-later |
X | X | | | Canopy - Metagenomics Canopy Clustering Implementation |
| cansam |
3489bc1 |
|
|
BSD-3-Clause |
X | X | | | C++ binding for SAM/BAM files |
| cansnper |
1.0.10 |
|
|
GPLv3 |
X | X | | X | A hierarchical genotype classifier of clonal pathogens. |
| cansnper2 |
2.0.6 |
|
|
GPLv3 |
| | | X | A toolkit for SNP-typing bacterial genomes. |
| canu |
2.3 |
doc |
dev |
GPL-2.0-or-later |
X | X | | | Canu is a fork of the Celera Assembler designed for high-noise... |
| canvas |
1.35.1.1316 |
|
|
GPLv3 |
X | | | | Copy number variant (CNV) calling from DNA sequencing data |
| cap-mirseq |
version |
|
|
GPL |
X | | | | None |
| cap3 |
10.2011 |
|
|
Michigan |
X | X | | | DNA sequence assembly program. |
| capc-map |
1.1.3 |
|
|
GNU |
X | X | | | Analysis software for Capture-C data |
| capcruncher |
0.3.14 |
doc |
dev |
GPL-3.0-or-later |
| | | X | An end-to-end solution for processing Capture-C, Tri-C and Tiled-C data. |
| caper |
1.1.0 |
|
|
MIT |
| | | X | Cromwell Assisted Pipeline ExecutoR |
| captus |
1.2.0 |
|
|
GPL3 |
| | | X | Captus: Assembly of Phylogenomic Datasets from High-Throughput Sequencing data |
| card_trick |
0.2.1 |
|
|
MIT |
| | | X | Utility package to find gene <-> drug relationships within CARD |
| carna |
1.3.3 |
|
|
GPL |
X | X | | | Constraint-based Alignment of RNA Ensembles |
| carnac-lr |
1.0.0 |
|
|
GNU |
X | X | | | Clustering coefficient-based Acquisition of RNA Communities in Long Read |
| carpedeam |
1.0.0 |
|
|
GPL-3.0-only |
X | X | | | CarpeDeam - A metagenomic assembler for heavily damaged ancient datasets |
| cartools |
1.1.3 |
doc |
|
MIT |
| | | X | Coverage Analysis Report tool CAR tool is a tool for assessment of per... |
| carveme |
1.6.2 |
doc |
dev |
Apache-2.0 |
| | | X | CarveMe: automated genome-scale metabolic model reconstruction |
| cas-offinder |
2.4 |
|
|
BSD-3-Clause |
X | X | | | Cas-OFFinder is OpenCL based, ultrafast and versatile program that... |
| cascade-config |
0.4.0 |
|
|
Apache-2.0 |
| | | X | Cascading configuration from the CLI and config files. |
| caspeak |
1.1.0 |
|
|
GPL-3.0-or-later |
| | | X | A pipeline for finding non-reference mobile element insertions |
| cassiopee |
1.0.9 |
|
|
GPL-3+ |
X | X | | | scan an input genomic sequence (dna/rna/protein) and search for a... |
| cassiopeia |
2.0.0 |
|
dev |
MIT |
X | X | | | An end-to-end pipeline for single-cell lineage tracing experiments. |
| cassis |
0.0.20120106 |
|
|
GPL3 |
| | | X | Detection of genomic rearrangement breakpoints |
| cat |
6.0.1 |
|
dev |
MIT |
X | X | | X | CAT/BAT: tool for taxonomic classification of contigs and... |
| catch |
1.5.2 |
|
|
MIT |
X | X | | X | A package for designing compact and comprehensive capture probe sets. |
| catch_chimera |
1.0 |
|
|
GPL3 |
| | | X | CATCh is an ensemble classifier for chimera detection in 16S rRNA... |
| catfasta2phyml |
1.2.1 |
|
|
MIT |
| | | X | Concatenates FASTA formatted files to one "phyml" (PHYLIP)... |
| cath-tools |
0.16.5 |
|
dev |
GPLv3 |
X | X | | | Protein structure comparison tools such as SSAP, as used by the Orengo... |
| cayman |
0.10.1 |
|
dev |
MIT |
| | | X | A command-line profiling tool for profiling CAZyme abundances in... |
| cazy_webscraper |
2.3.0.4 |
doc |
dev |
MIT |
| | | X | A tool to automate retrieving data from CAZy, build a local CAZyme SQL... |
| cblaster |
1.3.20 |
doc |
dev |
MIT |
| | | X | Find clustered hits from a BLAST search. |
| ccat |
3.0 |
|
|
unknown |
X | X | | | CCAT is a software package for the analysis of ChIP-seq data with... |
| ccmetagen |
1.5.0 |
|
|
GPL3 |
| | | X | CCMetagen: comprehensive and accurate identification of eukaryotes and... |
| ccne |
1.1.2 |
|
|
GPL-3.0 |
| | | X | Carbapenemase-encoding gene copy number estimator |
| ccphylo |
0.8.2 |
|
|
Apache-2.0 |
X | X | | | CCPhylo enables phylogenetic analysis of samples based on overlaps... |
| ccsmeth |
0.5.0 |
|
dev |
BSD-3-Clause-Clear |
| | | X | Detecting DNA methylation from PacBio CCS read |
| cctk |
1.0.3 |
|
dev |
GPL-3.0-or-later |
| | | X | Tools to identify and compare CRISPR arrays. |
| cd-hit |
4.8.1 |
doc |
dev |
GPL-2.0-or-later |
X | X | | | Clusters and compares protein or nucleotide sequences. |
| cd-hit-auxtools |
4.8.1 |
|
|
GPLv2 |
X | X | | | Clusters and compares protein or nucleotide sequences |
| cdbtools |
0.99 |
|
|
Public |
X | X | | | CDB (Constant DataBase) indexing and retrieval tools for FASTA files |
| cdhit-reader |
0.2.0 |
|
|
MIT |
| | | X | Parse CD-HIT cluster files |
| cdk-inchi-to-svg |
0.9 |
|
|
BSD-2-Clause |
| | | X | Convert an InChI string to a SVG file |
| cdna_cupcake |
29.0.0 |
|
|
BSD-3-Clause-Clear |
X | X | | | cDNA_Cupcake is a miscellaneous collection of Python and R scripts used... |
| ceas |
1.0.2 |
|
|
Artistic |
X | | | X | CEAS: Cis-regulatory Element Annotation System |
| cell-types-analysis |
0.1.11 |
|
|
MIT |
| | | X | A suite of scripts for analysis of scRNA-seq cell type classification... |
| cell2cell |
0.7.4 |
|
|
BSD-3-Clause |
X | X | | | Inferring cell-cell interactions from transcriptomes with cell2cell |
| cellbender |
0.3.2 |
doc |
dev |
BSD-3-Clause |
| | | X | A software package for eliminating technical artifacts from... |
| cellprofiler |
4.2.8 |
doc |
dev |
BSD-3-Clause |
X | X | | X | CellProfiler is free, open-source software for quantitative analysis of... |
| cellprofiler-core |
4.2.8 |
doc |
dev |
BSD-3-Clause |
| | | X | Dependency for CellProfiler v4. |
| cellqc |
0.0.8 |
|
|
MIT |
| | | X | Cellqc standardizes the qualiy control of single-cell RNA-Seq (scRNA)... |
| cellrank |
1.5.1 |
doc |
dev |
BSD |
| | | X | CellRank for directed single-cell fate mapping |
| cellrank-krylov |
1.5.1 |
doc |
dev |
BSD |
| | | X | CellRank for directed single-cell fate mapping |
| cellsnake |
0.2.0.12 |
|
|
MIT |
| | | X | cellsnake, a user-friendly tool for single cell RNA sequencing analysis |
| cellsnp-lite |
1.2.3 |
doc |
dev |
Apache-2.0 |
X | X | | | Efficient genotyping bi-allelic SNPs on single cells. |
| celltypist |
1.6.3 |
|
dev |
MIT |
| | | X | A tool for semi-automatic cell type annotation |
| cellxgene |
1.3.0 |
doc |
dev |
MIT |
| | | X | Web application for exploration of large scale scRNA-seq datasets |
| cenote-taker3 |
3.3.2 |
doc |
dev |
MIT |
| | | X | Cenote-Taker 3: Discover and annotate the virome |
| centreseq |
0.3.8 |
|
dev |
MIT |
| | | X | Fast generation of core genome from bacterial strains |
| centrifuge |
1.0.4.2 |
|
|
GPL-3.0-only |
X | X | | | Classifier for metagenomic sequences. Supports classifier scripts |
| centrifuge-core |
1.0.4.2 |
doc |
dev |
GPL-3.0-only |
X | X | | | Classifier for metagenomic sequences. Does not include evaluation scripts |
| centrifuger |
1.0.7 |
|
|
MIT |
X | X | | | Lossless compression of microbial genomes for efficient and accurate... |
| centroid_rna_package |
0.0.16 |
|
|
GPL-V2 |
X | | | | Collection of RNA secondary structure prediction programs based on... |
| centrosome |
1.3.0 |
|
|
BSD |
X | X | | | An open source image processing library. Dependency for CellProfiler |
| cesar |
1.01 |
|
|
MIT |
X | X | | | CESAR 2.0 is a method to realign coding exons or genes to DNA sequences... |
| cesm |
2.1.3 |
doc |
|
BSD |
X | | | | The Community Earth System Model (CESM) is a coupled climate model for... |
| cfm |
33 |
|
|
GPL-2 |
X | X | | | Tools for applying Competitive Fragmentation Modeling (CFM) to spectrum... |
| cgat-apps |
0.7.10 |
doc |
dev |
MIT |
X | X | | | Computational Genomics Analysis Toolkit. |
| cgat-daisy |
0.1.12 |
|
|
MIT |
| | | X | A system to design and execute benchmarks |
| cgat-pipelines-nosetests |
0.0.4 |
|
|
MIT |
X | | | | Metapackage to test CGAT Pipelines |
| cgat-report |
0.9.1 |
|
|
BSD |
X | X | | X | A report generator in python based on sphinx |
| cgat-scripts |
0.3.2 |
|
|
BSD |
X | X | | | Computational Genomics Analysis Toolkit |
| cgat-scripts-nosetests |
0.0.4 |
|
|
BSD |
X | | | | Computational Genomics Analysis Toolkit |
| cgatcore |
0.6.16 |
|
|
MIT |
X | X | | X | CGAT : the Computational Genomics Analysis Toolkit |
| cgcloud-lib |
1.6.0 |
|
|
Apache |
X | X | | X | Components shared between cgcloud-core and cgcloud-agent |
| cgecore |
2.0.0 |
|
dev |
Apache-2.0 |
| | | X | Center for Genomic Epidemiology Core Module |
| cgelib |
0.7.5 |
|
dev |
Apache-2.0 |
| | | X | This package will in time replace the cgecore package. The package... |
| cgmlst-dists |
0.4.0 |
|
|
GPL3 |
X | X | | | Convert cgMLST table to distance matrix |
| cgpbigwig |
1.7.0 |
|
|
GPL-3.0-only |
X | | | | BigWig manpulation tools using libBigWig and htslib |
| cgranges |
0.1.1 |
|
|
MIT |
X | X | | | cgranges is a small C library for genomic interval overlap queries |
| cgt |
1.0.0 |
|
|
Apache-2.0 |
X | X | | | Calculate a core genome threshold (cgt) from metagenome data |
| cgview |
1.0 |
|
|
GNU |
X | X | | X | CGView is a Java package for generating high quality, zoomable maps of... |
| chado-tools |
0.2.15 |
|
|
GPL-3.0 |
| | | X | Tools to access CHADO databases |
| chain2paf |
0.1.1 |
|
dev |
MIT |
X | X | | | convert CHAIN format to PAF format |
| chainmap |
1.0.3 |
|
|
Python |
X | X | | X | Backport/clone of ChainMap for py26, py32, and pypy3. |
| changeo |
1.3.0 |
|
|
Creative |
| | | X | A bioinformatics toolkit for processing high-throughput lymphocyte... |
| chanjo |
3.3.0 |
|
|
MIT |
X | X | | | None |
| chap |
0.9.1 |
|
|
MIT |
X | | | | CHAP is a tool for the functional annotation of ion channel structures |
| check-sort-order |
0.0.7 |
|
|
MIT |
X | X | | | check sort-order of genomic files according to a genomefile |
| checkatlas |
0.4.17 |
doc |
dev |
BSD |
| | | X | One liner tool to check the quality of your single-cell atlases. |
| checkm-genome |
1.2.3 |
doc |
dev |
GPL-3.0-or-later |
X | X | | X | Assess the quality of microbial genomes recovered from isolates, single... |
| checkm2 |
1.1.0 |
|
dev |
GPL-3.0-only |
| | | X | Assessing the quality of metagenome-derived genome bins using machine learning. |
| checkqc |
4.0.5 |
doc |
dev |
GPLv3 |
| | | X | A simple program to parse Illumina NGS data and check it for quality criteria. |
| checkv |
1.0.3 |
|
|
Modified |
| | | X | Assess the quality of metagenome-assembled viral genomes. |
| chemfp |
1.6.1 |
|
|
MIT |
X | | | | chemfp is a set of command-lines tools for generating cheminformatics... |
| cherri |
0.8 |
|
|
GPL-3.0-or-later |
| | | X | Accurate detection of functional RNA-RNA Interactions sites |
| chewbbaca |
3.3.10 |
doc |
|
GPL-3.0-or-later |
X | X | | X | A complete suite for gene-by-gene schema creation and strain identification. |
| chewiesnake |
3.0.0 |
|
|
BSD-3 |
| | | X | ChewieSnake is a snakemake workflow that performs cgMLST allele calling... |
| chexalign |
0.12 |
|
|
MIT |
| | | X | ChExAlign is used for alignment and quantification of ChIP-exo... |
| chexmix |
0.52 |
|
|
MIT |
| | | X | ChExMix aims to characterize protein-DNA binding subtypes in ChIP-exo... |
| chia-rep |
3.1.1 |
|
|
MIT |
X | X | | | A package for measuring reproducibility of ChIA-PET data. |
| chicagotools |
1.2.0 |
|
|
artistic |
X | X | | X | chicagoTools are an assorted set of scripts associated with the Chicago... |
| chip-r |
1.2.0 |
|
|
GPL3 |
| | | X | ChIP-R is a method for assessing the reproducibility of replicated... |
| chips |
2.4 |
|
|
GNU |
X | X | | | ChIPs is a tool for simulating ChIP-sequencing experiments. |
| chipseq-greylist |
1.0.2 |
|
|
MIT |
X | X | | X | Python implementation of GreyListChIP Bioconductor package. |
| chira |
1.4.3 |
|
|
GNU |
| | | X | An integrated framework for annotation and visualization of chimeric reads. |
| chiron |
0.6.1.1 |
|
|
Mozilla |
| | | X | A deep neural network basecaller for nanopore sequencing. |
| chisel |
1.1.4 |
|
|
BSD-3 |
| | | X | Copy-number Haplotype Inference in Single-cell by Evolutionary Links |
| chiton |
1.1.0 |
|
|
GNU |
| | | X | Chiton provides a Python wrapper to commonly used bioinformatics programs. |
| chopper |
0.9.1 |
doc |
dev |
MIT |
X | X | | | A rust command line for filtering and trimming long reads. |
| chorus2 |
2.01 |
doc |
dev |
MIT |
X | X | | X | A pipeline to select oligonucleotides for fluorescence in situ... |
| chromap |
0.2.7 |
doc |
|
MIT |
X | X | | | Fast alignment and preprocessing of chromatin profiles |
| chromatiblock |
1.0.0 |
|
|
GPL-3.0-only |
| | | X | Scalable, whole-genome visualisation of structural changes in prokaryotes. |
| chromeister |
1.5.a |
|
|
GPL-3.0 |
X | X | | | An ultra fast, heuristic approach to detect conserved signals in... |
| chromhmm |
1.26 |
|
|
GPLv3 |
X | X | | X | ChromHMM is software for learning and characterizing chromatin states.... |
| chromimpute |
1.0.3 |
|
|
GPLv2 |
| | | X | ChromImpute is software for large-scale systematic epigenome imputation. |
| chromograph |
1.3.1 |
|
|
MIT |
X | | | X | Chromograph is a python package to create PNG images from genetics data... |
| chromosight |
1.6.3 |
|
|
Artistic |
| | | X | Detect loops (and other patterns) in Hi-C contact maps. |
| chromosomer |
0.1.4a |
|
|
MIT |
X | X | | X | A reference-assisted assembly tool for producing draft chromosome sequences. |
| chromsize |
0.0.2 |
|
|
MIT |
X | X | | | just get your chrom sizes |
| chronumental |
0.0.65 |
|
|
MIT |
| | | X | Make time trees from large phylogenetic divergence trees |
| chunked-scatter |
1.0.0 |
|
|
MIT |
| | | X | Chunk and scatter the regions in a bed or sequence dict file |
| cialign |
1.1.4 |
|
|
MIT |
| | | X | Toolkit for cleaning and interpreting multiple sequence alignments |
| cigar |
0.1.3 |
|
|
MIT |
| | | X | manipulate SAM cigar strings |
| circexplorer |
1.1.10 |
|
|
MIT |
X | X | | X | A combined strategy to identify circular RNAs (circRNAs and ciRNAs) |
| circexplorer2 |
2.3.8 |
|
|
MIT |
X | X | | X | Circular RNA analysis toolkits |
| circlator |
1.5.5 |
|
|
GNU |
X | X | | X | circlator: a tool to circularise genome assemblies |
| circle-map |
1.1.4 |
|
|
MIT |
| | | X | Circular DNA analysis tools |
| circle-map-cpp |
0.5.0 |
|
|
GPL-3.0-only |
X | X | | | Circle-Map-cpp is the C++ version of Circle-Map |
| circminer |
0.4.2 |
|
|
GPLv3 |
X | X | | | Sensitive and fast computational tool for detecting circular RNAs... |
| circos |
0.69.9 |
|
|
GNU |
X | X | | X | Circos is a software package for visualizing data and information. It... |
| circos-tools |
0.23 |
|
|
GNU |
X | X | | X | circos-tools provides several utility add-on scripts, such as for bundling links |
| circrna_finder |
1.2 |
|
|
MIT |
| | | X | Scripts required for running the pipeline to find circular RNAs from... |
| circtools |
2.0 |
doc |
dev |
GPL-3.0-or-later |
| | | X | circtools - a circular RNA toolbox. |
| circularmapper |
1.93.5 |
|
|
GPLv3 |
X | X | | X | A method to improve mappings on circular genomes, using the BWA mapper. |
| circulocov |
0.1.20240104 |
doc |
|
GPL-3.0 |
| | | X | CirculoCov is a Python tool designed for circular-aware coverage... |
| ciri-full |
2.1.2 |
doc |
dev |
unknown |
| | | X | Full length circRNA reconstruction and quantification using BSJ and... |
| ciriquant |
1.1.2 |
|
|
MIT |
| | | X | circular RNA quantification pipeline |
| cirtap |
0.3.1 |
|
dev |
MIT |
| | | X | A CLI to handle PATRIC data from the FTP |
| ciso8601 |
1.0.5 |
|
|
MIT |
X | X | | | Fast ISO8601 date time parser for Python written in C |
| cistrome-ceas |
1.0.2b1 |
doc |
dev |
Artistic |
X | X | | X | Cistrome-CEAS -- Cis-regulatory Element Annotation System |
| cistrome_beta |
1.0.7 |
|
|
This |
X | X | | | Binding and Expression Target Analysis of ChIP-seq TF with differential... |
| cite-seq-count |
1.4.5 |
doc |
dev |
MIT |
| | | X | A python package to map reads from CITE-seq or hashing data for single... |
| cityhash |
0.2.3.post9 |
|
|
MIT |
X | X | | | Python-bindings for CityHash, a fast non-cryptographic hash algorithm |
| civicpy |
4.0.0 |
doc |
dev |
MIT |
| | | X | CIViC variant knowledgebase analysis toolkit. |
| cladebreaker |
0.2.3 |
|
|
MIT |
| | | X | Nextflow pipeline for phylogenetic analysis. |
| cladeomatic |
0.1.1 |
doc |
dev |
Apache-2.0 |
| | | X | Clade-O-Matic: Automatic recognition of population structures based on... |
| clair |
2.1.1 |
|
|
AGPLv3 |
| | | X | Single-molecule sequencing technologies have emerged in recent years... |
| clair3 |
1.0.10 |
|
|
BSD-3-Clause |
X | | | X | Clair3 is a small variant caller for long-reads. Compare to PEPPER... |
| clair3-illumina |
1.0.10 |
|
dev |
BSD-3-Clause |
X | | | | Clair3 with libraries to support variant calling using Illumina... |
| clair3-trio |
0.7 |
|
|
BSD-3-Clause |
X | | | | Clair3-Trio is a variants caller tailored for family trios from... |
| clairvoyante |
1.02 |
|
|
AGPLv3 |
X | | | X | Identifying the variants of DNA sequences sensitively and accurately is... |
| clame |
1.0 |
|
|
GPL-3.0 |
X | | | | CLAME is a binning software for metagenomic reads. It immplements a... |
| clan |
0.05 |
|
|
Creative |
X | | | | CLAN - the CrossLinked reads ANalysis tool |
| clark |
1.2.6.1 |
|
|
GPL3 |
X | X | | | Fast, accurate and versatile k-mer based classification system |
| classpro |
1.0.2 |
|
|
https://github. |
| | | X | A K-mer classifier for HiFi reads . |
| cleanifier |
0.1.3 |
|
dev |
MIT |
| | | X | A fast lightweight tool to remove contamination using k-mers. |
| clearcnv |
0.306 |
|
|
MIT |
| | | X | CNV calling package |
| clearcut |
1.0.9 |
|
|
BSD |
X | | | | The reference implementation for Relaxed Neighbor Joining (RNJ). |
| clermontyping |
24.02 |
|
|
GPL-3.0-only |
| | | X | determine the Clermont E coli phylotype |
| clever-toolkit |
2.4 |
doc |
dev |
GPL-3.0-only |
X | X | | | The CLEVER Toolkit |
| clinker |
1.33 |
|
|
MIT |
| X | | X | Clinker is a bioinformatics pipeline that generates a... |
| clinker-py |
0.0.31 |
doc |
dev |
MIT |
| | | X | Gene cluster comparison figure generator |
| clinod |
1.3 |
|
|
Apache |
X | | | X | Command line NoD (clinod), for predicting nucleolar localization sequences. |
| clinvar-this |
0.18.5 |
|
dev |
MIT |
| | | X | ClinVar Submission API Made Easy. |
| clinvar-tsv |
0.6.3 |
|
|
MIT |
| | | X | A Snakemake-based program to download ClinVar and convert to... |
| clipandmerge |
1.7.9 |
|
|
GPLv3 |
X | X | | X | Clip&Merge is a tool to clip off adapters from sequencing reads and... |
| clipcontext |
0.7 |
|
|
MIT |
| | | X | Extract CLIP-seq binding regions with both genomic and transcript context |
| clipkit |
2.4.1 |
doc |
|
MIT |
| | | X | Alignment trimming software for phylogenetics. |
| clippy |
1.5.0 |
|
|
GPL-3.0-only |
| | | X | An intuitive and interactive peak caller for CLIP data |
| cliquesnv |
2.0.3 |
|
|
MIT |
| | | X | Scalable Reconstruction of Intra-Host Viral Populations from NGS Reads |
| cloci |
0.3.1 |
|
dev |
AGPL-3.0-only |
| | | X | Co-occurrence Locus and Orthologous Cluster Identifier. |
| clonalframeml |
1.13 |
doc |
|
GPL-3.0-or-later |
X | X | | | Efficient inferencing of recombination in bacterial genomes |
| cloudspades |
3.16.0 |
doc |
dev |
GPL-2.0-only |
X | | | | A module of the SPAdes assembler aimed at genome assembly from linked... |
| clove |
0.17 |
|
|
GPL-2.0 |
X | X | | X | CLOVE: Classification of genomic fusions into structural variation events. |
| clsify |
0.1.1 |
|
|
MIT |
| | | X | Haplotyping of C. Liberibacter solanacearum from Sanger data. |
| clust |
1.18.0 |
|
|
LGPL-3.0 |
X | X | | X | Optimised consensus clustering of multiple heterogeneous datasets. |
| clustalo |
1.2.4 |
|
|
GPLv2 |
X | X | | | Latest version of Clustal: a multiple sequence alignment program for... |
| clustalw |
2.1 |
doc |
|
LGPL-3.0-or-later |
X | X | | | ClustalW2 is a general purpose multiple sequence alignment program for... |
| cluster-picker |
1.2.3 |
|
|
GPLv3 |
X | X | | | The Cluster Picker identifies clusters in newick-formatted trees... |
| cluster_vcf_records |
0.13.3 |
|
|
MIT |
| | | X | Package to cluster VCF records. For use by gramtools and minos |
| clusterfunk |
0.0.2 |
|
|
MIT |
| | | X | Miscellaneous clustering manipulation tools for phylogenetic trees |
| clustergrammer |
1.13.6 |
|
|
MIT |
X | X | | X | A python module for the Clustergrammer visualization project |
| clusterone |
1.0 |
|
|
GPL-3.0 |
| | | X | Graph clustering algorithm |
| clusterpicker |
1.2.5 |
|
|
GPLv3 |
| | | X | The Cluster Picker identifies clusters in newick-formatted trees... |
| clusty |
1.1.5 |
doc |
dev |
GPL-3.0-or-later |
X | X | | | Clusty is a tool for large-scale data clustering. |
| cmaple |
1.1.0 |
doc |
dev |
GPL-2.0 |
X | X | | | MAximum Parsimonious Likelihood Estimation in C/C++. |
| cmappy |
4.0.1 |
|
|
BSD |
X | X | | | Assorted tools for interacting with .gct, .gctx, .grp, and .gmt files... |
| cmash |
0.5.2 |
doc |
dev |
BSD-3-Clause |
| | | X | Fast and accurate set similarity estimation via containment min hash... |
| cmat |
3.3.2 |
|
dev |
Apache-2.0 |
| | | X | ClinVar Mapping and Annotation Toolkit |
| cmfinder |
0.4.1.9 |
|
|
GPL3 |
X | X | | | CMfinder - A Covariance Model Based RNA Motif Finding Algorithm |
| cmip |
2.7.0 |
|
|
Apache |
X | X | | | CMIP Classical Molecular Interaction Potentials |
| cmph |
2.0 |
|
|
LGPL |
X | X | | | CMPH - C Minimal Perfect Hashing Library |
| cmsearch_tblout_deoverlap |
0.09 |
|
|
Public |
| | | X | cmsearch-deoverlap.pl: remove lower scoring overlaps from cmsearch |
| cmseq |
1.0.4 |
|
|
MIT |
| | | X | Set of utilities on sequences and BAM files |
| cmsip |
0.0.3.0 |
|
|
MIT |
| | | X | A package for detecting differential 5hmC regions from CMS-IP sequencing data. |
| cmv |
1.0.8 |
|
|
GPL-3 |
X | | | | A collection of tools for the visualisation of Hidden Markov Models... |
| cnasim |
1.3.4 |
|
|
GPL-3.0-only |
| | | X | Improved simulation of single-cell copy number profiles and DNA-seq... |
| cnmf |
1.6.0 |
|
dev |
MIT |
| | | X | Consensus NMF for scRNA-Seq data. |
| cnv_facets |
0.16.1 |
|
|
MIT |
X | | | | Detect somatic copy number variants (CNV) in tumour-normal samples... |
| cnvetti |
0.2.0 |
|
|
GPL3 |
X | | | | CNVetti is a CNV caller from HTS data. |
| cnvkit |
0.9.12 |
doc |
dev |
Apache-2.0 |
X | X | | X | Copy number variant detection from high-throughput sequencing. |
| cnvnator |
0.4.1 |
|
|
MIT |
X | | | | Tool for calling copy number variations. |
| cnvpytor |
1.3.1 |
|
|
MIT |
X | X | | X | Python extension of CNVnator |
| coast |
0.2.2 |
|
dev |
MIT |
| | | X | Alignment search tool that identifies similar proteomes. |
| coatran |
0.0.4 |
|
dev |
GPL-3.0-or-later |
X | X | | | Coalescent tree simulation along a transmission network |
| cobra |
0.21.0 |
|
|
GNU |
X | X | | X | COBRApy is a package for constraint-based modeling of biological networks. |
| cobra-meta |
1.2.3 |
|
|
MIT |
| | | X | COBRA is a tool to get higher quality viral genomes assembled from metagenomes. |
| cobs |
0.3.1 |
|
|
MIT |
X | X | | | Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams) |
| coconet-binning |
1.1.0 |
doc |
dev |
Apache |
| | | X | A contig binning tool from viral metagenomes |
| cocoscore |
1.0.0 |
|
|
MIT |
X | X | | X | CoCoScore: context-aware co-occurrence scores for biomedical text... |
| codan |
1.2 |
doc |
|
GPLv3 |
X | X | | X | CDS prediction in eukaryotic transcripts. |
| codingorf |
1.0.0 |
|
|
AGPL-3.0 |
| | | X | codingorf: The codingorf finds translatable ORFs from an input sequence |
| codingquarry |
2.0 |
|
|
GPL-3 |
X | X | | | CodingQuarry: highly accurate hidden Markov model gene prediction in... |
| codoff |
1.1.8 |
|
dev |
BSD-3-Clause |
| X | | X | codoff: program to measure the irregularity of the codon usage for a... |
| codonw |
1.4.4 |
|
|
GPLv2 |
X | X | | | CodonW is a programme designed to simplify the Multivariate analysis... |
| cofold |
2.0.4 |
|
|
MIT-like |
X | | | | An RNA secondary structure prediction method that takes... |
| cogclassifier |
1.0.5 |
|
|
MIT |
| | | X | Classify prokaryote protein sequences into COG functional category |
| cogent |
1.9 |
|
|
GNU |
X | X | | | COmparative GENomics Toolkit |
| cogent3 |
2024.12.19a2 |
doc |
dev |
BSD-3-Clause |
| | | X | COmparative GENomics Toolkit 3: genomic sequence analysis within... |
| cogtriangles |
2012.04 |
|
|
Public |
X | | | | low-polynomial algorithm for assembling clusters of orthologous groups... |
| coidb |
0.4.8 |
|
|
MIT |
| | | X | A tool to obtain and maintain a database of COI metabarcode references |
| coils |
2.2.1 |
|
|
GPL |
X | X | | | A generalized profile syntax for biomolecular sequence motifs and its... |
| coinfinder |
1.2.1 |
doc |
dev |
GPL-3.0-only |
X | X | | | A tool for the identification of coincident (associating and... |
| cojac |
0.9.3 |
|
|
GNU |
| | | X | Command-line tools to analyse co-occurrence of mutations on amplicons. |
| colabfold |
1.5.5 |
|
|
MIT |
| | | X | ColabFold: making protein folding accessible to all |
| collect-columns |
1.0.0 |
|
|
MIT |
| | | X | Retrieve a column for each in a set of tables, placing them in a single... |
| collect_mgf |
1.0 |
|
|
GPL-3.0 |
X | X | | | Collects MGF files and dd_results from an XMass setup_QDD.tcl... |
| collectl |
4.0.4 |
|
|
Artistic |
X | X | | | collectl monitoring tool |
| colombo |
4.0 |
|
|
Creative |
X | X | | X | A software framework equipped with a GUI for the prediction of genomic... |
| colorbrewer |
0.3 |
|
dev |
Apache-2.0 |
X | X | | X | An easy way to get access to ColorBrewer schemes from within a Python program. |
| colord |
1.1.0 |
|
|
GPL-3 |
X | X | | | A versatile compressor of third generation sequencing reads. |
| colorid_bv |
0.1.0 |
|
|
MIT |
X | X | | | Experiments with using BIGSI data structure for metagenomic and QC applications |
| colormap |
0.9.8 |
|
|
GNU |
X | X | | | Utilities to ease manipulation of matplotlib colormaps and color codecs... |
| combined-pvalues |
0.50.6 |
|
|
MIT |
X | X | | X | A library to combine, analyze, group and correct p-values in BED files.... |
| comebin |
1.0.4 |
|
|
BSD |
| | | X | COMEBin allows effective binning of metagenomic contigs using... |
| comet-ms |
2024011 |
|
|
Apache |
X | X | | | Comet is a command line tool that does MS/MS database search. |
| commec |
0.3.1 |
doc |
dev |
MIT |
| | | X | commec: a free, open-source, globally available tool for DNA sequence screening |
| commet |
24.7.14 |
|
|
GNU |
X | X | | | Comparing and combining multiple metagenomic datasets |
| compalignp |
1.0 |
|
|
GPL |
X | | | | Compute fractional "identity" between trusted alignment and... |
| comparative-annotation-toolkit |
0.1 |
|
|
Apache |
X | X | | X | A straightforward end-to-end pipeline that takes as input a HAL-format... |
| compare-reads |
0.0.1 |
|
|
MIT |
X | X | | | cythonized function to compare reads by name. |
| comparem |
0.1.2 |
|
|
GPL-3 |
| | | X | A toolbox for comparative genomics. |
| comparem2 |
2.13.1 |
doc |
dev |
GPL-3.0-or-later |
| | | X | CompareM2 genomes-to-report pipeline |
| comparems2 |
1 |
|
|
GPL3 |
X | X | | | A simple tool developed to compare, globally, all MS/MS spectra between... |
| compleasm |
0.2.7 |
|
dev |
Apache |
| | | X | Compleasm: a faster and more accurate reimplementation of BUSCO |
| complexcgr |
0.8.0 |
|
|
MIT |
| | | X | Encoders and Image representation of DNA/RNA sequences based on the... |
| comut |
0.0.3 |
|
|
MIT |
| | | X | A Python library for creating comutation plots to visualize genomic and... |
| concoct |
1.1.0 |
|
|
FreeBSD |
X | X | | | Clustering cONtigs with COverage and ComposiTion |
| concoord |
2.1.2 |
|
|
Apache |
X | X | | | CONCOORD is a method to generate protein conformations around a known... |
| condiga |
0.2.2 |
doc |
dev |
MIT |
| | | X | ConDiGA: Contigs Directed Gene Annotation for accurate protein sequence... |
| conduit-assembler |
0.1.2 |
|
|
GPL-2.0 |
X | X | | | Long- and short-read hybrid de novo transcriptome assembly |
| confindr |
0.8.2 |
doc |
dev |
MIT |
X | X | | X | Detect intra- and inter-species bacterial contamination in NGS reads. |
| conifer |
1.0.2 |
|
|
BSD-2-Clause |
X | X | | | Calculate confidence scores from Kraken2 output |
| conipher |
2.2.0 |
|
dev |
BSD-3-Clause |
| | | X | CONIPHER is an R package for clustering mutation data and... |
| connectome-workbench |
1.3.2 |
|
dev |
GPL-2.0 |
X | | | | Connectome Workbench is an open source, freely available visualization... |
| connor |
0.6.1 |
|
|
Apache-2.0 |
X | X | | X | A command-line tool to deduplicate bam files based on custom, inline barcoding. |
| consan |
1.2 |
doc |
dev |
GPL-2.0-or-later |
X | X | | | Pairwise RNA structural alignment, both unconstrained and constrained... |
| consel |
0.20 |
|
|
GNU |
X | | | | CONSEL calculates the probability value (i.e., p-value) to assess the... |
| consensify |
2.4.0 |
doc |
dev |
GPL-3.0-or-later |
X | X | | | A method for generating a consensus pseudohaploid genome sequence |
| consensusfixer |
0.4 |
|
|
GPL-3.0 |
X | X | | X | Computes a consensus sequence with wobbles, ambiguous bases, and... |
| consent |
2.2.2 |
doc |
dev |
AGPL-3.0-or-later |
X | X | | | Scalable long read self-correction and assembly polishing with multiple... |
| consplice |
0.0.6 |
|
|
MIT |
| | | X | The Constrained Splicing (ConSplice) python module |
| constava |
1.1.0 |
doc |
dev |
GPL-3.0-or-later |
| | | X | Calculate conformational states probability and variability from a... |
| constax |
2.0.20 |
doc |
|
MIT |
| | | X | A software for accurate taxonomic classification of environmental DNA markers |
| constellations |
0.1.12 |
|
|
CC-BY-ND-4.0 |
| | | X | Descriptions of constellations of mutations for the SARS-CoV-2 virus |
| contammix |
1.0.11 |
|
|
GPL-3 |
X | X | | | estimation of mtDNA contamination from a set of potential contaminant genomes. |
| contatester |
1.0.0 |
|
|
CeCILL |
X | X | | | Compute the Allelic Balance of a sample from a VCF file. |
| conterminator |
1.c74b5 |
|
|
GPL3 |
X | | | | Conterminator: software to detect contamination in large sequence sets |
| contignet |
1.0.1.post3 |
|
|
USC-RL |
| | | X | ContigNet, a deep learning based phage-host interaction prediction tool |
| contigtax |
0.5.10 |
|
|
MIT |
| | | X | Assign taxonomy to metagenomic contigs (previously know as tango) |
| contrafold |
2.02 |
|
|
BSD |
X | | | | CONditional TRAining for RNA Secondary Structure Prediction |
| control-freec |
11.6 |
|
|
GPL |
X | X | | | Copy number and genotype annotation from whole genome and whole exome... |
| conus |
1.0 |
|
|
file |
X | X | | | CONUS is an implementation of simple stochastic context-free grammars... |
| convert_zero_one_based |
0.0.1 |
|
|
MIT |
| | | X | Convert between zero and one based coordinate systems |
| coolbox |
0.3.9 |
|
dev |
GPL-3.0-or-later |
| | | X | Jupyter notebook based genomic data visulization toolkit. |
| cooler |
0.10.3 |
doc |
dev |
BSD-3-Clause |
X | X | | X | Sparse binary format for genomic interaction matrices. |
| coolpuppy |
1.1.0 |
doc |
|
MIT |
| | | X | A versatile tool to perform pile-up analysis on Hi-C data in .cool format |
| cooltools |
0.7.1 |
doc |
|
MIT |
X | X | | | Analysis tools for genomic interaction data stored in .cool format |
| coprarna |
2.1.4 |
|
|
MIT |
X | | | X | Target prediction for prokaryotic trans-acting small RNAs |
| coptr |
1.1.4 |
|
dev |
GPL-3.0-or-later |
| | | X | Accurate and robust inference of microbial growth dynamics from... |
| coral |
1.0.0 |
|
|
BSD |
X | X | | | Coral is an efficient tool to bridge paire-end RNA-seq reads. |
| core-snp-filter |
0.2.0 |
|
|
GPLv3 |
X | X | | | Filtering sites (i.e. columns) in a FASTA-format whole-genome pseudo-alignment. |
| corekaburra |
0.0.5 |
doc |
dev |
MIT |
| | | X | A commandline bioinformatics tool made to utilize syntenic information... |
| coreutils |
8.25 |
|
|
GPL |
X | X | | | The GNU Core Utilities are the basic file, shell and text manipulation... |
| corgi |
0.4.0 |
doc |
dev |
Apache-2.0 |
| | | X | Classifier for ORganelle Genomes Inter alia |
| corneto |
1.0.0a0 |
|
|
GPL-3.0-or-later |
| | | X | CORNETO: A Unified Framework for Omics-Driven Network Inference |
| corona_lineage_dynamics |
0.1.6 |
|
dev |
ASL |
X | X | | | Analyzing and visualizing pangolin lineages of GISAID metadata. |
| correlationplus |
0.2.1 |
doc |
dev |
GNU |
| | | X | A Python package to calculate, visualize and analyze dynamical... |
| corset |
1.09 |
|
|
GPLv3 |
X | X | | | Software for clustering de novo assembled transcripts and counting... |
| corsid |
0.1.3 |
|
dev |
MIT |
| | | X | Core Sequence Identifier |
| cortex_con |
0.04c |
|
|
GPL3 |
X | X | | | cortex_con (primary contact Mario Caccamo) is for consensus genome assembly |
| cortexpy |
0.46.5 |
doc |
dev |
Apache-2.0 |
X | X | | | A Python API for manipulating (Mc)Cortex de novo assembly graph and link data. |
| cosap |
0.1.0 |
doc |
dev |
MIT |
| | | X | COSAP - Comparative Sequencing Analysis Platform |
| cosg |
1.0.3 |
|
dev |
BSD-3-Clause |
| | | X | Accurate and fast cell marker gene identification with COSG. |
| cosi2 |
2.3.0rc4 |
|
|
GPLv3 |
X | X | | | cosi2 is an efficient coalescent simulator with support for selection,... |
| cosigt |
0.1.3 |
|
dev |
GNU |
X | X | | | Cosigt (COsine SImilarity-based GenoTyper) |
| cospar |
0.4.1 |
|
|
MIT |
| | | X | A toolkit for dynamic inference of cell fate by integrating state and... |
| count_constant_sites |
0.1.1 |
|
|
MIT |
X | X | | | Compute the count of cases in constant sites in a (FASTA) multiple... |
| counterr |
0.1 |
|
|
GPL-3.0 |
| | | X | Counterr is a light-weight command line tool that computes errors in... |
| cov-lineages |
2020.05.19.2 |
|
|
GPL-3.0 |
| | | X | A dynamic nomenclature proposal for SARS-CoV-2 to assist genomic epidemiology |
| coverageanomalyscanner |
0.2.3 |
|
|
GPL-3.0 |
X | | | | Application to find local anomalies in read coverage and to predict... |
| coverm |
0.7.0 |
|
|
GPL3 |
X | | | | CoverM aims to be a configurable, easy to use and fast DNA read... |
| covid-spike-classification |
0.6.4 |
|
|
Apache |
| | | X | Detect interesting SARS-CoV-2 spike protein variants from Sanger... |
| covsonar |
2.0.0a1 |
|
|
GPL-3.0 |
| | | X | A database-driven system for handling genomic sequences and screening... |
| covtobed |
1.3.5 |
|
|
MIT |
X | X | | | covtobed - generate a BED file of covered regions from a BAM file |
| cpat |
3.0.5 |
|
|
GPL-2.0-or-later |
X | X | | X | Coding Potential Assessment Tool |
| cpc2 |
1.0.1 |
|
|
MIT |
| | | X | Coding Potential Calculator 2 (CPC2) |
| cpgeneprofiler |
2.1.1 |
|
|
GPL2 |
| | | X | Generate a profile of carbapenamase genes from the genome assemblies. |
| cpinsim |
0.5.2 |
|
|
MIT |
X | X | | X | CPINSim is a package for the simulation of protein complex assembly... |
| cpstools |
2.5 |
|
dev |
MIT |
| | | X | CPStools is a package for analyzing chloroplast genome sequences. |
| cpt_gffparser |
1.2.2 |
|
|
BSD |
| | | X | A Biopython extension package for I/O of GFF files |
| cptac |
1.5.13 |
doc |
dev |
Apache-2.0 |
| | | X | Python packaging for CPTAC data |
| crabs |
1.0.7 |
|
dev |
MIT |
| | | X | Crabs (Creating Reference databases for Amplicon-Based Sequencing) is a... |
| cramino |
0.16.0 |
|
|
MIT |
X | | | | A tool for very fast quality assessment of long read cram/bam files. |
| cramtools |
3.0.b127 |
|
|
Apache |
X | X | | X | A set of Java tools and APIs for efficient compression of sequence read data |
| craq |
1.0.9 |
doc |
dev |
MIT |
| | | X | Pinpoint assembly errors for genomic assessing and correcting. |
| crass |
1.0.1 |
|
|
GNU |
X | | | | Crass (The CRISPR Assembler) is a program that searches through raw... |
| crb-blast |
0.6.9 |
|
|
MIT |
X | | | X | Conditional Reciprocal Best BLAST - high confidence ortholog assignment. |
| crimson |
1.1.1 |
|
|
BSD |
X | X | | X | Bioinformatics tool outputs converter to JSON or YAML. |
| crispector |
1.0.7 |
|
|
free |
| | | X | Accurate estimation of off-target editing activity from comparative NGS data |
| crispector2 |
2.1.2 |
|
|
free |
| | | X | Accurate estimation of off-target editing activity from comparative NGS data |
| crisper_recognition_tool |
1.2 |
|
|
Public |
X | X | | X | A tool for automatic detection of clustered regularly interspaced... |
| crispr_studio |
1 |
|
|
GPL-3.0 |
| | | X | CRISPRStudio is a program developed to facilitate and accelerate CRISPR... |
| crisprbact |
0.3.11 |
|
|
GNU |
| | | X | Tools to design and analyse CRISPRi experiments |
| crispresso |
1.0.13 |
|
|
GPLv3 |
X | X | | | A software pipeline for the analysis of targeted CRISPR-Cas9 sequencing data |
| crispresso2 |
2.3.2 |
doc |
dev |
CC0-1.0 |
X | X | | | A software pipeline designed to enable rapid and intuitive... |
| crispritz |
2.6.6 |
|
|
GPL3 |
X | X | | | CRISPRitz, tool package for CRISPR experiments assessment and analysis. |
| crisprlungo |
0.1.14 |
|
|
Partners |
| | | X | A software pipeline for analyzing single-anchor amplicon sequencing and... |
| crisprme |
2.1.7 |
doc |
dev |
AGPL-3.0-or-later |
| | | X | CRISPRme, tool package for CRISPR experiments assessment and analysis. |
| crnsimulator |
0.9 |
|
|
MIT |
| | | X | Simulate chemical recation networks (CRNs) using ordinary differential... |
| crocodeel |
1.0.6 |
|
|
GPL-3.0-or-later |
| | | X | CroCoDeEL is a tool that detects cross-sample contamination in shotgun... |
| cromshell |
2.1.1 |
|
|
BSD-3-Clause |
| | | X | Command-line interface to the Cromwell workflow manager |
| cromwell |
0.40 |
|
|
BSD |
X | X | | X | A Workflow Management System geared towards scientific workflows... |
| cromwell-tools |
2.4.1 |
doc |
dev |
BSD |
| | | X | Utilities for interacting with the Cromwell workflow engine |
| croo |
0.6.0 |
|
|
MIT |
| | | X | CRomwell Output Organizer |
| crossmap |
0.7.0 |
doc |
dev |
GPL-3.0-or-later |
X | X | | X | CrossMap is a program for convenient conversion of genome coordinates... |
| crumble |
0.9.1 |
|
|
multiple |
X | X | | | Controllable lossy compression of BAM/CRAM files |
| crussmap |
1.0.0 |
|
|
MIT |
X | X | | | crussmap is a faster tool to convert genome coordinates between... |
| crux-toolkit |
4.2 |
|
dev |
Apache-2.0 |
X | X | | | A cross-platform suite of analysis tools for interpreting protein mass... |
| cryfa |
20.04 |
|
|
GPL3 |
X | X | | | A secure encryption tool for genomic data |
| cryptkeeper |
1.0.1 |
|
dev |
GPL-3.0-only |
| | | X | A negative design tool for predicting and visualizing undesired gene expression |
| crypto_typer |
1.0.0 |
|
|
Apache |
| | | X | This package crypto_typer: tool to subtype the parasite,... |
| cryptogenotyper |
1.0 |
|
|
Apache |
| | | X | This package crypto_typer: tool to subtype the parasite,... |
| csb |
1.2.5 |
|
|
MIT |
X | X | | X | Computational Structural Biology Toolbox |
| csblast |
2.2.3 |
|
|
GPL3 |
X | X | | | Context-specific extension of BLAST that significantly improves... |
| cstag |
1.1.0 |
doc |
|
MIT |
| | | X | Python module to manipulate the minimap2's CS tag |
| cstag-cli |
1.0.0 |
|
|
MIT |
| | | X | Command line interface of cstag to manipulate the minimap2's CS tag |
| csvtk |
0.31.0 |
|
|
MIT |
X | X | | | A cross-platform, efficient, practical CSV/TSV toolkit |
| ctat-lncrna |
1.0.1 |
|
|
BSD-3-Clause |
X | X | | X | ctat-lncrna uses slncky |
| ctat-metagenomics |
1.0.1 |
|
|
BSD-3-Clause |
X | X | | X | ctat-metagenomics uses centrifuge |
| ctat-mutations |
2.1.0 |
|
|
BSD-3-Clause |
X | X | | X | Mutation detection in RNA-Seq using GATK-v4.0 in RNA-Seq variant... |
| ctc-scite |
1.0.2 |
|
dev |
GPL-3.0-or-later |
X | X | | | CTC-SCITE is a software package to infer cell lineages of single-cells... |
| cthreepo |
0.1.3 |
|
|
MIT |
| | | X | A python script to interconvert seq-ids in gff3, gtf, bed and other files. |
| ctseq |
0.0.2 |
|
|
MIT |
| | | X | ctSeq is a pipeline to analyze methylation patch PCR data |
| ctxcore |
0.2.0 |
doc |
dev |
GPL-3.0-or-later |
| | | X | Core functions for pycisTarget and the SCENIC tool suite. |
| ctyper |
1.0.1 |
|
dev |
USC-RL |
X | X | | | Genotyping sequence-resolved copy-number variation using pangenomes. |
| cufflinks |
2.2.1 |
|
|
Boost |
X | X | | | Transcriptome assembly and differential expression analysis for RNA-Seq. |
| curare |
0.6.0 |
|
|
GPL3 |
| | | X | A Customizable and Reproducible Analysis Pipeline for RNA-Seq Experiments. |
| cured |
1.05 |
|
dev |
GPLv3 |
| | | X | Classification Using Restriction Enzyme Diagnostics |
| curesim |
1.3 |
|
|
unknown |
X | X | | X | CuReSim (Customized Read Simulator) is a customized tool which... |
| curlywhirly |
1.17.08.31 |
|
|
BSD-2-Clause |
X | X | | X | CurlyWhirly is an application for viewing multi-dimensional data, with... |
| curves |
3.0.3 |
|
|
Apache |
X | X | | | CURVES+: Conformational analysis of single nucleic acid structures or... |
| customtkinter |
5.2.2 |
|
|
MIT |
| | | X | Create modern looking GUIs with Python |
| cutadapt |
5.0 |
|
dev |
MIT |
X | X | | | Trim adapters from high-throughput sequencing reads |
| cutefc |
1.0.0 |
|
|
MIT |
| | | X | Regenotyping structural variants through an accurate and efficient... |
| cutesv |
2.1.1 |
|
|
MIT |
| | | X | cuteSV is a long-read based human genomic structural variation detection tool |
| cutqc |
0.07 |
|
|
MIT |
| | | X | generate aggregated fastqc report of both before and after trimming. |
| cuttlefish |
2.2.0 |
doc |
dev |
BSD-3-Clause |
X | X | | | Construction of the compacted de Bruijn graph efficiently. |
| cvbio |
3.0.0 |
doc |
|
MIT |
| | | X | Tools for working with genomic and sequencing data, including... |
| cvlr |
1.0 |
|
|
MIT |
X | X | | | Clustering and Visualization of Long Reads |
| cwl2wdl |
0.1dev44 |
|
|
MIT |
X | X | | X | Proof of concept converter from Common Workflow Language (CWL) to the... |
| cwltest |
2.2.20220521103021 |
|
|
Apache-2.0 |
X | X | | X | Common workflow language testing framework |
| cwltool |
1.0.20180225105849 |
|
|
Apache |
X | X | | X | Common Workflow Language reference implementation |
| cycle_finder |
1.0.0 |
|
|
GPL-3.0 |
X | | | | A de novo analysis tool for tandem and interspersed repeats based on... |
| cyntenator |
0.0.r2326 |
|
|
GPL |
X | X | | | progressive gene order alignments |
| cyordereddict |
0.2.2 |
|
|
BSD |
X | X | | | Cython implementation of Python's collections.OrderedDict |
| cyrcular |
0.3.0 |
|
dev |
MIT |
X | | | | Tool for calling circles from nanopore reads |
| cytocad |
1.0.3 |
|
|
GPL-3.0-or-later |
X | | | | Large copy-number variation detector with low-depth whole-genome sequencing data |
| cytoscape |
3.10.3 |
|
dev |
LGPL |
X | | | X | Cytoscape: an open source platform for network analysis and visualization. |
| cytosnake |
0.0.2 |
doc |
|
CC-BY-4.0 |
| | | X | Orchestrating high-dimensional cell morphology data processing pipelines |
| cytotrace2-python |
1.1.0 |
doc |
dev |
Custom |
| | | X | CytoTRACE 2 is an interpretable AI method for predicting cellular... |
| cyushuffle |
1.1.2 |
doc |
|
BSD |
X | X | | | A Cython wrapper over uShuffle - a useful tool for shuffling biological... |
| cyvcf |
0.8.0 |
|
|
MIT |
X | X | | | A cython wrapper around htslib built for fast parsing of Variant Call... |
| cyvcf2 |
0.31.1 |
doc |
dev |
MIT |
X | X | | | A cython wrapper around htslib built for fast parsing of Variant Call... |
| czlab_perl_lib |
1.0.1 |
|
|
MIT |
| | | X | mCross Perl script |
| d4binding |
0.3.11 |
|
dev |
MIT |
X | X | | | The C/C++ binding for the D4 file format. |
| d4tools |
0.3.11 |
|
dev |
MIT |
X | X | | | The D4 command line utility program. |
| dadaist2 |
1.3.1 |
|
dev |
MIT |
| | | X | Command line wrapper to run DADA2 on a set of paired-end reads |
| dadaist2-full |
2.0 |
|
|
The |
| | | X | Meta-package for Dadaist2 with full R packages, VSEARCH, CD-HIT and MultiQC |
| dadi |
2.0.5 |
|
|
BSD-3-Clause |
X | X | | | Fit population genetic models using diffusion approximations to the... |
| dagchainer |
r120920 |
|
|
MIT |
X | X | | | DAGchainer identifies syntenic regions. |
| daisysuite |
1.3.0 |
|
|
GNU |
X | | | X | DaisySuite - mapping-based pipeline for horizontal gene transfer (HGT)... |
| dajin2 |
0.6.0 |
|
|
MIT |
| | | X | One-step genotyping tools for targeted long-read sequencing |
| daligner |
1.0.20230620 |
|
|
Custom |
X | X | | | DALIGNER: Find all significant local alignments between reads |
| damageprofiler |
1.1 |
|
|
GPL-3.0 |
X | X | | X | A Java based tool to determine damage patterns on ancient DNA as a... |
| damasker |
1.0p1 |
|
|
Custom |
X | X | | | DAMASKER: Module to determine where repeats are and make soft-masks of said |
| damidseq_pipeline |
1.6 |
doc |
dev |
GPL-2.0-or-later |
X | X | | X | An automated pipeline for processing DamID sequencing datasets. |
| dammet |
1.0.4 |
|
|
MIT |
X | X | | | Software to reconstruct methylomes from HTS data from ancient specimen |
| dammit |
1.2 |
|
dev |
BSD |
X | X | | X | simple de novo transcriptome annotator |
| danbing-tk |
1.3.2.5 |
|
|
BSD-3-Clause |
X | | | | Toolkit for VNTR genotyping and repeat-pan genome graph construction |
| danpos |
2.2.2 |
|
|
Unknown |
| | | X | A toolkit for Dynamic Analysis of Nucleosome and Protein Occupancy by... |
| dapcy |
1.0.1 |
|
dev |
MIT |
| | | X | An sklearn implementation of discriminant analysis of principal... |
| dart |
1.4.6 |
|
|
MIT |
X | X | | | Dart: a fast and accurate RNA-seq mapper |
| das_tool |
1.1.7 |
|
|
BSD |
X | | | X | Recovery of genomes from metagenomes via a dereplication, aggregation... |
| dascrubber |
0.0.1a2 |
|
|
Custom |
X | X | | | Alignment-based Scrubbing pipeline |
| dashing |
1.0 |
|
|
GPL-3 |
X | X | | | Fast and accurate genomic distances using HyperLogLog |
| dastk |
1.0.1 |
|
dev |
BSD-3 |
| | | X | Differential ATAC-seq toolkit |
| data_hacks |
0.3.1 |
|
|
Apache |
X | | | X | Command line utilities for data analysis. |
| datafunk |
0.1.0 |
|
|
MIT |
| | | X | Miscellaneous data manipulation tools for fasta and sam files |
| datamash |
1.1.0 |
|
|
GPL3 |
X | X | | | None |
| datma |
2.0 |
|
|
GPL-3.0 |
| | | X | DistributedAuTomaticMetagenomicAssembly andAnnotation framework |
| dawg |
2.0.beta1 |
|
|
GPL-2 |
X | X | | | DNA Assembly with Gaps (Dawg) is an application designed to simulate... |
| dazz_db |
1.0 |
|
|
Custom |
X | X | | | DAZZ_DB: The Dazzler Data Base |
| dbcan |
4.1.4 |
doc |
dev |
GPL-3.0-or-later |
| | | X | Standalone version of dbCAN annotation tool for automated CAZyme annotation. |
| dbcanlight |
1.1.0 |
doc |
dev |
MIT |
| | | X | A lightweight CAZyme annotation tool |
| dbg2olc |
20200723 |
|
|
unknown |
X | X | | | Efficient Assembly of Large Genomes Using Long Erroneous Reads of the... |
| dbghaplo |
0.0.2 |
|
|
MIT |
X | X | | | Haplotyping small sequences from heterogeneous long-read sequencing... |
| dbgraph |
1.0.0 |
|
|
GNU |
X | | | | A graph-centric approach for metagenome-guided peptide identification... |
| dca |
0.3.4 |
|
|
Apache |
| | | X | Count autoencoder for scRNA-seq denoising |
| dcc |
0.5.0 |
|
|
GPL-3.0 |
| | | X | DCC is a python package intended to detect and quantify circRNAs with... |
| dcmtk |
3.6.7 |
|
dev |
BSD |
X | X | | | DCMTK is a collection of libraries and applications implementing large... |
| dcplib |
3.12.0 |
|
|
MIT |
| | | X | Modules shared among multiple Data Coordination Platform components. |
| ddipy |
0.0.5 |
|
|
Apache |
| | | X | Python client for OmicsDI Restful API |
| ddocent |
2.9.8 |
doc |
dev |
MIT |
X | X | | X | dDocent is an interactive bash wrapper to QC, assemble, map, and call... |
| ddrage |
1.8.1 |
|
|
MIT |
X | X | | X | Simulator for ddRADseq (double digest restriction site associated DNA... |
| deap |
1.0.2 |
|
|
GNU |
X | X | | X | Distributed Evolutionary Algorithms in Python |
| debarcer |
2.1.4 |
|
|
MIT |
| | | X | A package for De-Barcoding and Error Correction of sequencing data... |
| deblur |
1.1.1 |
|
|
BSD |
X | X | | X | Deblur is a greedy deconvolution algorithm based on known read error profiles. |
| debreak |
1.3 |
|
|
MIT |
X | | | X | DeBreak, Deciphering the exact breakpoints of structural variations... |
| debwt |
1.0.1 |
|
|
Unknown |
X | X | | | A efficient method to construct BWT index of a given DNA sequence,... |
| dechat |
1.0.1 |
|
dev |
MIT |
X | X | | | Repeat and haplotype aware error correction in nanopore sequencing... |
| decifer |
2.1.4 |
|
|
BSD-3 |
X | X | | | DeCiFer simultaneously selects mutation multiplicities and clusters... |
| decom |
0.0.32 |
doc |
dev |
MIT |
| | | X | decOM: Microbial source tracking of ancient oral samples using k-mers. |
| decoupler |
1.5.0 |
|
|
GPL-3.0 |
| | | X | Ensemble of methods to infer biological activities from omics data |
| decoypyrat |
1.0.1 |
|
|
MIT |
| | | X | Fast Hybrid Decoy Sequence Database Creation for Proteomic Mass... |
| dedup |
0.12.9 |
|
|
GPLv3 |
X | X | | X | DeDup is a tool for read deduplication in paired-end read merging (e.g.... |
| deepac |
0.14.1 |
doc |
dev |
MIT |
| | | X | Predicting pathogenic potentials of novel DNA with reverse-complement... |
| deepaccess |
0.1.3 |
doc |
dev |
MIT |
| | | X | A package for training and interpreting an ensemble of neural networks... |
| deepaclive |
0.3.2 |
doc |
dev |
MIT |
| | | X | Detecting novel pathogens from NGS reads in real-time during a sequencing run. |
| deepacstrain |
0.2.1 |
doc |
dev |
MIT |
| | | X | Predicting pathogenic potentials of novel strains of known bacterial species. |
| deepacvir |
0.2.2 |
doc |
dev |
MIT |
| | | X | Detecting novel human viruses from DNA reads with reverse-complement... |
| deeparg |
1.0.4 |
|
|
MIT |
| | | X | A deep learning based approach to predict Antibiotic Resistance Genes... |
| deepbgc |
0.1.31 |
|
|
MIT |
| | | X | DeepBGC - Biosynthetic Gene Cluster detection and classification |
| deepbinner |
0.2.0 |
|
|
GPL3 |
X | X | | X | A signal-level demultiplexer for Oxford Nanopore reads. |
| deepblast |
1.0.2 |
|
dev |
BSD-3-Clause |
| | | X | Neural Networks for Protein Sequence Alignment. |
| deepchopper |
1.2.6 |
doc |
dev |
Apache-2.0 |
X | X | | | A Genomic Language Model for Chimera Artifact Detection in Nanopore... |
| deepchopper-cli |
1.2.6 |
doc |
dev |
Apache-2.0 |
X | X | | | A CLI for Genomic Language Model for Chimera Artifact Detection in... |
| deepdirect |
0.2.5 |
|
|
GPL-2.0 |
| | | X | In silico approach to generate mutations for protein complexes towards... |
| deepfplearn |
2.1 |
|
|
GPL-3.0-or-later |
| | | X | Link molecular structures of chemicals (in form of topological... |
| deeplc |
3.1.8 |
doc |
dev |
Apache-2.0 |
| | | X | DeepLC: Retention time prediction for (modified) peptides using Deep Learning. |
| deeplcretrainer |
1.0.2 |
|
|
Apache-2.0 |
| | | X | Evaluating DeepLC performance and retraining prediction models. |
| deeplift |
0.6.13.0 |
doc |
dev |
MIT |
| | | X | DeepLIFT (Deep Learning Important FeaTures) |
| deepmased |
0.3.1 |
doc |
dev |
MIT |
| | | X | Deep learning for Metagenome Assembly Error Detection |
| deepmedic |
0.6.1 |
|
|
BSD |
X | | | X | Efficient Multi-Scale 3D Convolutional Neural Network for Brain Lesion... |
| deepmei |
1.6.24 |
|
|
GPL-3.0-only |
| | | X | A tool to detect mobile elements insertion |
| deepmicro |
1.4 |
doc |
dev |
MIT |
| | | X | Deep representation learning framework |
| deepmicroclass |
1.0.3 |
|
|
BSD-2-Clause |
| | | X | DeepMicroClass, a deep learning based contig prediction tool (CPU version) |
| deepmod |
0.1.3 |
|
|
GPL3 |
| | | X | A deep-learning method for DNA modifcation (5mC and 6mA) prediction. |
| deepnog |
1.2.3 |
doc |
dev |
BSD |
| | | X | Deep learning tool for protein orthologous group assignment |
| deepsig |
1.2.5 |
|
dev |
GPLv3 |
| | | X | Predictor of signal peptides in proteins based on deep learning |
| deepsignal-plant |
0.1.6 |
|
dev |
GNU |
| | | X | A deep-learning method for detecting DNA methylation state from Oxford... |
| deepstats |
0.4 |
|
|
GPL3 |
| | | X | A statistical and dataviz toolbox for deeptools, genomic signals, and more. |
| deepsvr |
0.1.0 |
|
|
MIT |
| | | X | DeepSVR stands for deep somatic variant refinement. It uses deep... |
| deeptools |
3.5.6 |
doc |
dev |
MIT |
X | X | | X | A set of user-friendly tools for normalization and visualzation of... |
| deeptoolsintervals |
0.1.9 |
|
|
MIT |
X | X | | | A python module creating/accessing GTF-based interval trees with... |
| deepvariant |
1.5.0 |
|
|
MIT |
X | | | | DeepVariant is an analysis pipeline that uses a deep neural network to... |
| defense-finder |
2.0.0 |
|
dev |
GPL-3.0-or-later |
| | | X | Defense Finder: allow for a systematic search of all known anti-phage systems. |
| defiant |
1.1.4 |
|
|
GPL-2.0 |
X | X | | | Differential methylation, Easy, Fast, Identification and ANnoTation. |
| degenotate |
1.3 |
doc |
dev |
MIT |
| | | X | Annotation of degeneracy of sites in coding regions of a genome |
| dehomopolymerate |
0.4.0 |
|
|
GPL3 |
X | X | | | Collapse homopolymer runs in FASTQ files |
| delegation |
1.1 |
doc |
dev |
BSD |
| | | X | Simple implementation of the delegate pattern. |
| delly |
1.3.3 |
|
|
BSD-3-Clause |
X | X | | | Structural variant discovery by integrated paired-end and split-read analysis |
| deltabs |
0.1 |
|
|
GPL3 |
X | X | | X | Quantifying the significance of genetic variation using probabilistic... |
| deltamsi |
1.0.1 |
|
|
GNU |
| | | X | DeltaMSI: AI-based modeling of microsatellite instability scoring on NGS data |
| deltapd |
0.1.5 |
|
|
AGPL-3.0-only |
X | X | | | DeltaPD is a tool used to determine outliers in a gene tree when... |
| demultiplex |
1.2.2 |
doc |
|
MIT |
| | | X | Demultiplex any number of FASTA or a FASTQ files based on a list of barcodes |
| demultiplexer |
1.2.1 |
|
|
MIT |
| | | X | python tool to demultiplex illumina reads tagged with the leeselab... |
| demuxem |
0.1.7.post1 |
doc |
|
BSD-3-Clause |
| | | X | DemuxEM is the demultiplexing module of Pegasus, which works on... |
| demuxlet |
1.0 |
doc |
dev |
GPL3 |
X | | | | Genetic multiplexing of barcoded single cell RNA-seq |
| dendropy |
5.0.6 |
doc |
dev |
BSD-3-Clause |
X | X | | X | A Python library for phylogenetics and phylogenetic computing: reading,... |
| denovogear |
1.1.1 |
|
|
GPL3 |
X | | | | None |
| deploid |
0.5 |
|
|
GPLv3 |
X | X | | | A software that deconvolutes mixed genomes with unknown proportions. |
| derna |
1.0.4 |
doc |
dev |
BSD-3-Clause |
X | X | | | RNA sequence design for a target protein sequence. |
| desalt |
1.5.6 |
|
|
MIT |
X | X | | | De Bruijn graph-based Spliced Aligner for Long Transcriptome reads |
| desman |
2.1 |
|
|
BSD |
X | X | | | De novo Extraction of Strains from MetAgeNomes |
| detonate |
1.11 |
|
|
GPL |
X | X | | | DETONATE (DE novo TranscriptOme rNa-seq Assembly with or without the... |
| devider |
0.0.1 |
|
|
MIT |
X | X | | | Haplotyping small sequences from heterogeneous long-read sequencing... |
| dextractor |
1.0p2 |
|
|
Custom |
X | X | | | Bax File Decoder and Data Compressor |
| dfam |
3.7 |
doc |
|
Creative |
X | | | X | The Dfam database is a collection of Repetitive DNA element sequence... |
| dfast |
1.3.6 |
|
dev |
GPLv3 |
X | X | | X | DDBJ Fast Annotation and Submission Tool - Prokaryotic genome... |
| dfast_qc |
1.0.6 |
|
dev |
GPLv3 |
| | | X | DFAST_QC: Taxonomy and completeness check for prokaryotic genomes |
| dgenies |
1.5.0 |
doc |
dev |
GPL-3 |
| | | X | Dotplot large Genomes in an Interactive, Efficient and Simple way |
| dia_umpire |
2.1.6 |
|
|
Apache |
X | X | | X | DIA-Umpire is an open source Java program for computational analysis of... |
| dialign-tx |
1.0.2 |
doc |
|
LGPL-2.1-or-later |
X | X | | | DIALIGN-TX is a greedy and progressive approaches for segment-based... |
| dialign2 |
2.2.1 |
|
|
LGPL |
X | | | | DIALIGN multiple sequence alignment using various sources of external... |
| diamond |
2.1.11 |
doc |
dev |
GPL-3.0-or-later |
X | X | | | Accelerated BLAST compatible local sequence aligner. |
| diamond_add_taxonomy |
0.1.2 |
|
|
MIT |
X | X | | | Utility to work with NCBI taxonomy database including tool to annotate... |
| diapysef |
1.0.10 |
|
|
MIT |
| | | X | Analysis, conversion and visualization of diaPASEF data. |
| dice |
1.1.0 |
|
|
GPL-3.0-only |
| | | X | Cell lineage reconstruction from single-cell CNA data |
| dicey |
0.3.3 |
|
|
GPL-3 |
X | X | | | In-silico PCR and variant primer design |
| diego |
0.1.2 |
|
|
GNU |
| | | X | Detection of differential alternative splicing using Aitchinson`s geometry |
| difcover |
3.0.1 |
|
|
MIT |
X | | | | Pipeline to identify genomic regions with read coverage differences... |
| diffacto |
1.0.7 |
|
dev |
Apache-2.0 |
| | | X | A protein summarization method for shotgun proteomics experiments |
| dig2 |
1.0 |
|
|
GPL3 |
X | X | | | dig2 is a simple but flexible in silico digester of protein sequences... |
| digest |
0.2.0 |
|
|
MIT |
X | X | | | Fast, multi-use k-mer sub-sampling library |
| digestiflow-cli |
0.5.8 |
|
|
MIT |
X | | | | Command line client for Digestiflow. |
| digestiflow-demux |
0.5.3 |
|
|
MIT |
| | | X | Digestiflow Command Line Client. |
| dimet |
0.2.4 |
|
|
MIT |
| | | X | A tool for Differential Isotope-labeled targeted Metabolomics data |
| dimspy |
2.0.0 |
|
|
GNU |
X | X | | X | Python package for data processing of direct-infusion mass... |
| dinamo |
1.0 |
|
|
GPLv3 |
X | | | | An exact and efficient method for IUPAC motif discovery in DNA sequences |
| dinf |
0.5.0 |
|
|
MIT |
| | | X | discriminator-based inference for population genetics |
| dingii |
0.0.1 |
doc |
dev |
MIT |
| | | X | Computing the Rearrangement Distance of Natural Genomes. |
| dinopy |
3.0.0 |
|
|
MIT |
X | X | | | DNA input and output library for Python and Cython. Includes reader and... |
| dinosaur |
1.2.0 |
|
|
Apache-2.0 |
| | | X | Feature finding algorithm for detection of isotope patterns in HPLC... |
| dipcall |
0.3 |
doc |
dev |
MIT |
| | | X | Dipcall is a reference-based variant calling pipeline for a pair of... |
| diphase |
1.0.3 |
|
|
MIT |
X | | | | A diploid genome phasing tool |
| dirseq |
0.4.3 |
|
|
MIT |
| | | X | Work out whether RNAseq reads in general agree with the direction of... |
| discasm |
0.1.3 |
|
|
BSD-3-Clause |
X | | | X | DISCASM aims to extract reads that map to reference genomes in a... |
| disco |
1.2 |
|
|
GPL-3.0 |
X | X | | | Multi-threaded Distributed Memory Overlap-Layout-Consensus (OLC)... |
| discosnp |
2.6.2 |
|
|
GNU |
X | X | | | reference-free small variant caller for short read sequencing data |
| discovar |
52488 |
|
|
MIT |
X | | | | Suitable for variant calling with reference and de novo assembly of... |
| discovardenovo |
52488 |
|
|
MIT |
X | | | | Suitable for de novo assembly of large and small genomes. |
| dist_est |
1.1 |
|
|
GNU |
X | X | | | Estimation of Rates-Across-Sites Distributions in Phylogenetic... |
| distle |
0.2.0 |
|
|
GPL-3.0-only |
X | X | | | Fast distance matrix calculations on fasta and cgmlst files |
| disty |
0.1.0 |
|
|
MIT |
X | X | | | Disty McMatrixface - compute a distance matrix from a core genome... |
| ditasic |
0.2 |
|
|
MIT |
X | X | | | DiTASiC is designed as a comprehensive approach for abundance... |
| divvier |
1.01 |
|
dev |
GPL-3.0-or-later |
X | X | | | A program for removing MSA uncertainty. |
| dkfz-bias-filter |
1.2.3a |
|
|
GPLv3 |
X | X | | X | The DKFZ bias filter flags SNVs that appear to be biased based on the... |
| dlcpar |
1.0 |
|
|
GPLv3 |
X | X | | X | Accurate inference of orthogroups, orthologues, gene trees and rooted... |
| dligand2 |
0.1.0 |
|
|
MIT |
X | | | | DLIGAND2 is a knowledge-based method to predict protein-ligand binding... |
| dmbiolib |
0.4.3 |
doc |
|
GPL-3.0 |
| | | X | Library of Python functions for bioinformatics |
| dms |
1.1 |
|
|
GPL3 |
X | X | | | Comprehensive taxonomic and phylogenetic comparison of shotgun... |
| dmtools |
0.2.6 |
doc |
|
MIT |
X | | | | BS-seq, WGBS, NOMe-Seq, RRBS data storage and analysis tool dmtools |
| dna-nn |
0.1 |
|
dev |
Unknown |
X | X | | | Model and predict short DNA sequence features with neural networks. |
| dna_features_viewer |
3.1.3 |
doc |
dev |
MIT |
| | | X | Plot features from DNA sequences (e.g. Genbank) with Python |
| dnaapler |
1.2.0 |
doc |
dev |
MIT |
| | | X | Reorients assembled microbial sequences |
| dnacauldron |
2.0.9 |
|
|
MIT |
| | | X | Cloning simulation for DNA assembly (Golden Gate, Gibson...) |
| dnachisel |
3.2.13 |
|
|
MIT |
| | | X | Optimize DNA sequences under constraints. |
| dnaio |
1.2.3 |
|
|
MIT |
X | X | | | Read and write FASTA and FASTQ files efficiently |
| dnamarkmaker |
1.0 |
|
|
GPL-3.0-or-later |
| | | X | DNAMarkMaker: pipeline to development ARMS and CAPS marker |
| dnapi |
1.1 |
|
|
MIT |
X | X | | X | De novo adapter prediction (iterative) algorithm for small RNA sequencing data. |
| dnarrange |
1.6.3 |
|
|
GPL-3.0-or-later |
| | | X | Find rearrangements in "long" DNA reads relative to a genome sequence |
| dnaweaver |
v0.3.7 |
|
|
MIT |
| | | X | Python library to find optimal strategies for assembling large DNA constructs. |
| dnaweaver_synbiocad |
1.0.2 |
|
|
MIT |
| | | X | Build the genetic designs generated by the SynBioCAD project using... |
| dnmtools |
1.4.4 |
doc |
dev |
GPL-3.0-or-later |
X | X | | | dnmtools is a set of tools for analyzing DNA methylation data from... |
| dnoise |
1.4.1 |
|
|
GPL-3.0-only |
| | | X | Denoise sequence data sets from Illumina using distance corrected... |
| dnp-binstrings |
1.0 |
|
|
MIT |
X | X | | | Convert fasta strings into dinucleotide binary indicator string as 00101... |
| dnp-corrprofile |
1.0 |
|
|
MIT |
X | X | | | Profile of correlations between the patterns of dinucleotide frequency... |
| dnp-diprofile |
1.0 |
|
|
MIT |
X | X | | | Dinucleotide frequency of occurrence in a batch of fasta sequences |
| dnp-fourier |
1.0 |
|
|
MIT |
X | X | | | Periodogram of dinucleotide frequency pattern |
| dnp-mapping |
1.0 |
|
|
MIT |
X | X | | | Mapping of a nuclesome position in sequence by pattern |
| docking_py |
0.2.3 |
doc |
dev |
GPL-2.0-only |
| | | X | Docking_py is a python library allowing a simplified use of the Smina,... |
| dockq |
2.1.3 |
doc |
dev |
MIT |
X | X | | | A Quality Measure for Protein, Nucleic Acids and Small Ligand Docking Modelsc |
| dodge |
1.0.1 |
|
|
GPL-3.0-or-later |
| | | X | Dynamic Outbreak Detection for Genomic Epidemiology. Automated point... |
| doit |
0.29.0 |
|
|
MIT |
X | | | | None |
| domclust |
1.2.8a |
|
|
GPL3 |
X | X | | | Effective tool for orthologous grouping in multiple genomes |
| dominate |
2.1.16 |
|
|
GNU |
X | X | | | Dominate is a Python library for creating and manipulating HTML... |
| domino |
1.0.0 |
|
|
MIT |
| | | X | AMI algorithm with low rate of false calls |
| dosage_score |
1.0.0 |
|
|
GPL-3.0-or-later |
| | | X | Dosage-score: pipline to estimate dosage of each genomic region |
| doubletd |
0.1.0 |
|
|
BSD-3 |
| | | X | doubletD is a method to detect doublets in single-cell DNA sequencing data |
| doubletdetection |
4.2 |
doc |
dev |
MIT |
| | | X | Method to detect and enable removal of doublets from single-cell RNA-sequencing. |
| downpore |
0.3.4 |
|
|
MIT |
X | X | | | Suite of tools for use in genome assembly and consensus. |
| dr-disco |
0.18.3 |
|
|
GPL-3.0+ |
X | X | | X | Dr. Disco: fusion gene and genomic breakpoint detection in random... |
| dragmap |
1.3.0 |
|
|
GPL-3 |
X | | | | Dragmap is the Dragen mapper/aligner Open Source Software. |
| dragonflye |
1.2.1 |
|
|
GPL2 |
| | | X | Microbial assembly pipeline for Nanopore reads |
| dram |
1.5.0 |
doc |
dev |
GPL-3.0 |
| | | X | Distilled and Refined Annotation of Metabolism: A tool for the... |
| drax |
0.0.0 |
|
|
MIT |
X | X | | X | A pipeline for Detecting Resistome Associated taXa. |
| dreamtools |
1.3.0 |
|
|
BSD |
X | X | | | Scoring functions for the DREAM / SAGE challenges |
| drep |
3.5.0 |
doc |
dev |
MIT |
X | X | | X | De-replication of microbial genomes assembled from multiple samples |
| drive |
0.3.9 |
|
|
Apache |
X | X | | | Google Drive client for the commandline |
| drop |
1.4.0 |
doc |
dev |
MIT |
| | | X | Detection of RNA Outlier Pipeline |
| dropbox |
5.2.1 |
|
|
https://raw.git |
X | X | | | Official Dropbox API Client |
| dropest |
0.8.6 |
|
|
GPL3 |
X | | | | Pipeline for initial analysis of droplet-based single-cell RNA-seq data |
| dropkick |
1.2.8 |
|
|
MIT |
X | | | | Automated scRNA-seq filtering |
| dropletutils-scripts |
0.0.5 |
|
dev |
Apache |
| | | X | CLI scripts for the DropletUtils package |
| dropseq_tools |
3.0.2 |
doc |
dev |
MIT |
X | X | | X | Package for the analysis of Drop-seq data developed by Jim Nemesh in... |
| drprg |
0.1.1 |
|
|
MIT |
X | | | | Drug resistance prediction with reference graphs |
| drtransformer |
1.0 |
|
|
MIT |
| | | X | Heuristic cotranscriptional folding using the nearest neighbor energy model. |
| drug2cell |
0.1.2 |
|
|
non-commercial |
| | | X | This is a collection of utility functions for gene group activity... |
| dscr |
2014.12.17 |
|
|
GNU |
X | | | | high-performance compression of sequencing reads stored in FASTQ format |
| dsh-bio |
2.4 |
|
|
LGPL |
X | X | | X | Tools for BED, FASTA, FASTQ, GAF, GFA1/2, GFF3, PAF, SAM, and VCF files |
| dsk |
2.3.3 |
|
|
AGPL-3.0 |
X | X | | | DSK is a k-mer counter for reads or genomes. |
| dsrc |
2015.06.04 |
|
|
GNU |
X | X | | | high-performance compression of sequencing reads stored in FASTQ format |
| dudes |
0.10.0 |
|
|
MIT |
X | X | | X | DUDes: a top-down taxonomic profiler for metagenomics and metaproteomics |
| duet |
1.0 |
|
|
BSD-3-Clause |
| | | X | SNP-Assisted Structural Variant Calling and Phasing Using Oxford... |
| dunovo |
3.0.2 |
|
|
GPL2 |
X | | | | Du Novo: A pipeline for processing duplex sequencing data. |
| duphold |
0.2.1 |
|
|
MIT |
X | | | | SV callers like lumpy look at split-reads and pair distances to find... |
| duplex-tools |
0.3.3 |
doc |
dev |
MPL-2.0 |
| | | X | Duplex Tools contains a set of utilities for dealing with ONT Duplex... |
| duplomap |
0.9.5 |
|
|
MIT |
X | X | | | Tool designed to improve precision and recall of long-read alignments... |
| dupre |
0.1 |
|
|
MIT |
X | X | | X | Duplicate rate estimation using linear programming and the... |
| dupsifter |
1.3.0.20241113 |
|
dev |
MIT |
X | X | | | A tool for PCR duplicate marking of WGBS (and WGS) data. |
| dvorfs |
1.0.1 |
|
|
MIT |
| | | X | DVORFS tool for mining endogenous viral elements |
| dwgsim |
1.1.14 |
|
|
GNU |
X | X | | | Whole Genome Simulator for Next-Generation Sequencing |
| dx-cwl |
0.1.0a20180905 |
|
|
Apache |
X | X | | X | Import and run CWL workflows on DNAnexus |
| dxpy |
0.392.0 |
doc |
dev |
Apache-2.0 |
X | X | | X | DNAnexus Platform API bindings for Python |
| dxua |
1.5.31 |
|
|
Apache |
X | X | | | command-line tool for uploading files to the DNAnexus Platform |
| dysgu |
1.8.0 |
|
dev |
MIT |
X | X | | | A collection of tools for calling structural variants using short or long reads |
| e-pcr |
2.3.12 |
|
|
GPLv2 |
X | | | | None |
| ea-utils |
1.1.2.779 |
|
|
MIT |
X | | | | Command-line tools for processing biological sequencing data. |
| eagle |
0.9.4.6 |
|
|
MIT |
X | X | | X | Eagle is a webtool for genome variants and snp analysis |
| eagle2 |
2.4.1 |
|
|
GPL-3.0-or-later |
X | X | | | The Eagle software estimates haplotype phase either within a genotyped... |
| earlgrey |
5.1.1 |
doc |
dev |
OSL-2.1 |
X | X | | | Earl Grey: A fully automated TE curation and annotation pipeline |
| easel |
0.49 |
|
dev |
BSD |
X | X | | | Easel is an ANSI C code library for computational analysis of... |
| eastr |
1.1.2 |
doc |
dev |
MIT |
X | X | | | Tool for emending alignments of spuriously spliced transcript reads. |
| easypqp |
0.1.51 |
|
dev |
BSD-3-Clause |
| | | X | EasyPQP: Simple library generation for OpenSWATH |
| ebcsgen |
2.2.0 |
doc |
dev |
MIT |
| | | X | eBSCgen is a tool for development and analysis of models written in... |
| ebfilter |
0.2.2 |
|
|
GNU |
X | | | X | EBFilter (Empirical Bayesian Mutation Filtering) |
| ebi-eva-common-pyutils |
0.6.14 |
|
|
Apache-2.0 |
| | | X | EBI EVA - Common Python Utilities |
| ebisearch |
0.0.3 |
|
|
MIT |
X | X | | X | A Python library for interacting with EBI Search's API |
| ebolaseq |
0.1.3 |
doc |
dev |
GPL-3.0-or-later |
| | | X | Tool for downloading and analyzing Ebola virus sequences |
| echidna |
1.0.2 |
|
|
MIT |
| | | X | Mapping genotype to phenotype through joint probabilistic modeling of... |
| ecmwfapi |
1.4.1 |
|
|
Apache |
X | X | | X | ECMWF API is a set of services developed by ECMWF http://www.ecmwf.int... |
| ecopcr |
0.5.0 |
|
|
CeCill |
X | X | | | ecoPCR is an electronic PCR software that helps you estimate Barcode... |
| ecoprimers |
1.0 |
|
|
CeCill |
X | X | | | ecoPrimers is a software that finds primers from a set of sequence. |
| ecopy |
0.1.2.2 |
|
|
MIT |
X | X | | | EcoPy: Ecological Data Analysis in Python |
| ectyper |
2.0.0 |
|
|
Apache |
X | X | | X | ECtyper is a python program for serotyping E. coli genomes |
| edd |
1.1.19 |
|
|
MIT |
X | X | | | Enriched domain detector for ChIP-seq data |
| eden |
2.0 |
|
|
MIT |
X | | | X | The Explicit Decomposition with Neighborhoods (EDeN) is a... |
| edena |
3.131028 |
|
|
GPL3 |
X | X | | | de novo short reads assembler |
| edittag |
1.1 |
|
|
http://www.open |
X | X | | X | Design and check sets of edit metric sequence tags. |
| edlib |
1.2.3 |
|
|
MIT |
X | X | | | C/C++ library and program for sequence alignment using edit... |
| edta |
2.2.2 |
doc |
dev |
GPL-3.0-only |
| | | X | Extensive de-novo TE Annotator. |
| effectivet3 |
1.0.1 |
|
|
Apache |
X | X | | | Command line NoD (clinod), for predicting nucleolar localization sequences. |
| efishent |
0.0.5 |
|
|
MIT |
| | | X | A tool to design RNA FISH oligos/probes |
| ega-cryptor |
2.0.0 |
|
|
Apache-2.0 |
| | | X | EGA Cryptor v2.0.0 is a tool designed to encrypt files compliant with... |
| ega2 |
2.2.2 |
|
|
unknown |
| | | X | EGA download client v2 |
| egap |
2.6.6 |
|
|
BSD |
| | | X | EGAP pipeline for genome assembly and QC analysis |
| egglib |
3.3.5 |
doc |
dev |
GPL-3.0-or-later |
X | X | | | Evolutionary Genetics and Genomics Library. EggLib is a C++/Python... |
| eggnog-mapper |
2.1.12 |
doc |
|
AGPL-3.0-only |
X | X | | X | Fast genome-wide functional annotation through orthology assignment. |
| eigen |
3.2 |
|
|
MPL2 |
X | X | | | None |
| eigensoft |
8.0.0 |
|
|
Custom |
X | X | | | The EIGENSOFT package implements methods for analzing population... |
| eigenstratdatabasetools |
1.1.0 |
|
|
GPL-3.0-only |
| | | X | A set of tools to compare and manipulate the contents of EingenStrat... |
| eklipse |
1.8 |
|
|
GNU |
| | | X | eKLIPse is a sensitive and specific tool allowing the detection and... |
| el_gato |
1.21.0 |
doc |
dev |
MIT |
| | | X | Perform Legionella pneumophila Sequence Based Typing (SBT) from short... |
| elastic-blast |
1.3.1 |
|
dev |
Public |
| | | X | ElasticBLAST is a cloud-based tool to perform your BLAST searches... |
| elasticluster |
0.1.3bcbio |
|
|
GPL |
X | X | | | Create, manage and setup computing clusters hosted on a public or... |
| elector |
1.0.4 |
|
|
AGPL-3.0 |
X | | | | ELECTOR EvaLuator of Error Correction Tools for lOng Reads |
| elprep |
5.1.3 |
|
|
AGPL-3.0-only |
X | X | | X | elPrep is a high-performance tool for preparing .sam/.bam files for... |
| ema |
0.7.0 |
doc |
dev |
MIT |
X | X | | | Fast & accurate alignment of barcoded short-reads |
| embassy-phylip |
3.69.650 |
|
|
GPL |
X | X | | | embassy/emboss wrappers for phylip functions |
| embl-api-validator |
1.1.180 |
|
|
Apache-2-0 |
X | X | | X | ENA flat file validator for submission |
| emblmygff3 |
2.3 |
|
dev |
GPLv3 |
| | | X | An efficient way to convert gff3 annotation files into EMBL format... |
| emboss |
6.6.0 |
|
|
GPL |
X | X | | | The European Molecular Biology Open Software Suite |
| emerald |
1.2.1 |
|
|
AGPL-3.0 |
X | X | | | Unlocking the suboptimal pairwise alignment space for protein sequences |
| emeraldbgc |
0.2.4.1 |
|
|
Apache-2.0 |
| | | X | SMBGC detection tool |
| emirge |
0.61.1 |
|
|
GNU |
X | X | | | EMIRGE reconstructs full length sequences from short sequencing reads |
| emmix |
1.3 |
|
|
Available |
X | | | | A tool that fits a mixture model of multivariate normal or... |
| emmtyper |
0.2.0 |
|
|
GNU |
| | | X | Streptococcus pyogenes in silico EMM typer |
| emperor |
0.9.51 |
|
|
BSD |
X | X | | | EMPeror a tool for visualizing high-throughput microbial community data |
| emptydrops |
0.0.5 |
|
dev |
MIT |
| | | X | Python implementation of emptydrops from 10X Cellranger v3.0.2 |
| emu |
3.5.1 |
|
|
MIT |
| | | X | Emu is a relative abundance estimator for 16s genomic data. |
| emu-pca |
1.2.1 |
|
dev |
GPL-3.0-only |
X | X | | | EM-PCA for Ultra-low Coverage Sequencing Data. |
| emvc-2 |
1.0 |
|
|
MIT |
X | X | | | An efficient SNV variant caller based on the expectation maximization algorithm. |
| ena-dl |
1.0.0 |
|
|
MIT |
| | | X | A tool to download FASTQs associated with Study, Experiment, or Run accessions. |
| ena-upload-cli |
0.8.0 |
|
|
MIT |
| | | X | Command Line Interface to upload data to the European Nucleotide Archive |
| ena-webin-cli |
8.1.1 |
|
|
Apache-2.0 |
| | | X | Data submissions to ENA can be made using the Webin command line... |
| enabrowsertools |
1.5.4 |
|
|
Apache-2.0 |
| | | X | enaBrowserTools is a set of scripts that interface with the ENA web... |
| enano |
1.0 |
|
|
MIT |
X | X | | | ENANO is a FASTQ compression tool especially designed for nanopore... |
| enasearch |
0.2.2 |
|
|
MIT |
X | X | | X | A Python library for interacting with ENA's API |
| encode-blacklist |
2.0 |
|
|
GPL3 |
X | X | | | The ENCODE Blacklist: Identification of Problematic Regions of the Genome |
| encyclopedia |
2.12.30 |
|
|
Apache |
| | | X | EncyclopeDIA is library search engine comprised of several algorithms... |
| endorspy |
1.3 |
|
|
MIT |
| | | X | endorS.py calculates endogenous DNA from samtools flagstat files and... |
| enrichm |
0.6.5 |
|
|
GPL3+ |
| | | X | EnrichM is a toolbox for comparing the functional composition of... |
| ensembl-genomio |
1.6.1 |
doc |
dev |
Apache-2.0 |
| | | X | Ensembl GenomIO - tools to convert basic genomic data into Ensembl... |
| ensembl-py |
2.1.3 |
doc |
dev |
Apache-2.0 |
| | | X | Ensembl Python base library |
| ensembl-utils |
0.7.0 |
doc |
dev |
Apache-2.0 |
| | | X | Ensembl Python general-purpose utils |
| ensembl-vep |
113.3 |
doc |
dev |
Apache-2.0 |
X | | | X | Ensembl Variant Effect Predictor |
| entrez-direct |
22.4 |
|
|
PUBLIC |
X | X | | X | Entrez Direct (EDirect) is an advanced method for accessing the... |
| entrezpy |
2.1.3 |
doc |
|
LGPLv3 |
| | | X | Entrezpy is a dedicated Python library to interact with NCBI Entrez databases |
| enviroampdesigner |
0.1.2 |
|
|
GPL-3.0-only |
| | | X | Tool for training model and classifying reads from environmental ONT... |
| eoulsan |
2.5 |
|
dev |
LGPL |
X | | | X | A pipeline and a framework for NGS analysis (RNA-Seq and Chip-Seq) |
| epa-ng |
0.3.8 |
|
|
GNU |
X | X | | | Massively parallel phylogenetic placement of genetic sequences |
| ephemeris |
0.10.10 |
doc |
|
Academic |
X | X | | X | Ephemeris is an opinionated library and set of scripts for managing the... |
| epic |
0.2.12 |
|
|
GNU |
X | X | | X | Chip-Seq broad peak/domain finder. |
| epic2 |
0.0.52 |
|
|
MIT |
X | | | | Ultraperformant Chip-Seq broad domain finder based on SICER. |
| epicseg |
1.0 |
|
|
GPL-3 |
X | X | | | EpiCSeg (Epigenome Count-based Segmentation) is a software for... |
| epik |
0.2.0 |
|
|
MIT |
X | X | | | EPIK is a tool for fast alignement-free phylogenetic placements. |
| epimuller |
0.0.8 |
|
|
MIT |
| | | X | Visualize lineages overtime, with phylogentic context, based on viral genomes |
| episcanpy |
0.4.0 |
|
|
BSD-3-Clause |
| | | X | Epigenomics Single-Cell Analysis in Python. |
| epiweeks |
2.3.0 |
|
|
MIT |
| | | X | Epidemiological weeks calculation based on the US CDC (MMWR) and ISO... |
| epydoc |
3.0.1 |
|
|
MIT |
X | | | X | Edward Loper's API Documentation Generation Tool |
| epytope |
3.3.1 |
doc |
dev |
BSD |
| | | X | A Framework for Epitope Detection and Vaccine Design |
| eqtlbma |
1.3.3 |
|
|
GPLv3 |
X | X | | | Package to detect eQTLs jointly in multiple subgroups (e.g. tissues)... |
| equirep |
1.0.0 |
|
|
BSD-3-Clause |
X | X | | | EquiRep is tool to identify tandem repeats. |
| erds |
1.1 |
|
|
Free |
X | | | | Inferring copy number variants in high-coverage human genomes with... |
| ericscript |
0.5.5 |
|
|
GPL3 |
X | | | X | EricScript is a computational framework for the discovery of gene... |
| erne |
2.1.1 |
|
|
GPLv3 |
X | X | | | ERNE - Extended Randomized Numerical alignEr |
| ervdetective |
1.0.8 |
|
|
LGPL-2.1-or-later |
| | | X | An efficient pipeline for identification and annotation of endogenous... |
| escher |
1.7.3 |
|
|
MIT |
| | | X | Escher: A Web Application for Building, Sharing, and Embedding... |
| esimsa |
1.0 |
|
|
GPL3 |
X | X | | | Simple deconvolution of electrospray ionization peak lists |
| eskrim |
1.0.9 |
|
|
GPL-3.0-or-later |
| | | X | ESKRIM: EStimate with K-mers the RIchness in a Microbiome |
| esme |
1.0.0 |
|
|
BSD-3-Clause |
X | | | | Earth System Modelling Environment (ESME) - A bundle for scientific... |
| esme_esmf_mpich_4_2_3 |
8.8.0 |
|
|
ESMF |
X | | | | ESMF - Earth System Modeling Framework |
| esme_esmf_openmpi_4_1_6 |
8.8.0 |
|
|
ESMF |
X | | | | ESMF - Earth System Modeling Framework |
| esme_esmf_openmpi_5_0_6 |
8.8.0 |
|
|
ESMF |
X | | | | ESMF - Earth System Modeling Framework |
| esme_esmf_openmpi_5_0_7 |
8.8.0 |
|
|
ESMF |
X | | | | ESMF - Earth System Modeling Framework |
| esme_hdf5_mpich_4_2_3 |
1.14.5 |
|
|
BSD-3-Clause |
X | | | | HDF5 - Hierarchical Data Format 5 |
| esme_hdf5_openmpi_4_1_6 |
1.14.5 |
|
|
BSD-3-Clause |
X | | | | HDF5 - Hierarchical Data Format 5 |
| esme_hdf5_openmpi_5_0_6 |
1.14.5 |
|
|
BSD-3-Clause |
X | | | | HDF5 - Hierarchical Data Format 5 |
| esme_hdf5_openmpi_5_0_7 |
1.14.5 |
|
|
BSD-3-Clause |
X | | | | HDF5 - Hierarchical Data Format 5 |
| esme_mpich_4_2_3 |
1.0.0 |
|
|
BSD-3-Clause |
X | | | | Earth System Modelling Environment (ESME) - A bundle for scientific... |
| esme_netcdf-c_mpich_4_2_3 |
4.9.2 |
|
|
MIT |
X | | | | NetCDF-C - netCDF interface for C |
| esme_netcdf-c_openmpi_4_1_6 |
4.9.2 |
|
|
MIT |
X | | | | NetCDF-C - netCDF interface for C |
| esme_netcdf-c_openmpi_5_0_6 |
4.9.2 |
|
|
MIT |
X | | | | NetCDF-C - netCDF interface for C |
| esme_netcdf-c_openmpi_5_0_7 |
4.9.2 |
|
|
MIT |
X | | | | NetCDF-C - netCDF interface for C |
| esme_netcdf-fortran_mpich_4_2_3 |
4.6.1 |
|
|
MIT |
X | | | | NetCDF-Fortran - netCDF interface for Fortran |
| esme_netcdf-fortran_openmpi_4_1_6 |
4.6.1 |
|
|
MIT |
X | | | | NetCDF-Fortran - netCDF interface for Fortran |
| esme_netcdf-fortran_openmpi_5_0_6 |
4.6.1 |
|
|
MIT |
X | | | | NetCDF-Fortran - netCDF interface for Fortran |
| esme_netcdf-fortran_openmpi_5_0_7 |
4.6.1 |
|
|
MIT |
X | | | | NetCDF-Fortran - netCDF interface for Fortran |
| esme_omb_mpich_4_2_3 |
7.5 |
|
|
BSD-3-Clause |
X | | | | OSU Micro Benchmarks |
| esme_omb_openmpi_4_1_6 |
7.5 |
|
|
BSD-3-Clause |
X | | | | OSU Micro Benchmarks |
| esme_omb_openmpi_5_0_6 |
7.5 |
|
|
BSD-3-Clause |
X | | | | OSU Micro Benchmarks |
| esme_omb_openmpi_5_0_7 |
7.5 |
|
|
BSD-3-Clause |
X | | | | OSU Micro Benchmarks |
| esme_openmpi_4_1_6 |
1.0.0 |
|
|
BSD-3-Clause |
X | | | | Earth System Modelling Environment (ESME) - A bundle for scientific... |
| esme_openmpi_5_0_6 |
1.0.0 |
|
|
BSD-3-Clause |
X | | | | Earth System Modelling Environment (ESME) - A bundle for scientific... |
| esme_openmpi_5_0_7 |
1.0.1 |
|
|
BSD-3-Clause |
X | | | | Earth System Modelling Environment (ESME) - A bundle for scientific... |
| esme_pio_mpich_4_2_3 |
2.6.2 |
|
|
Apache-2.0 |
X | | | | ParallelIO - High-level parallel I/O library |
| esme_pio_openmpi_4_1_6 |
2.6.2 |
|
|
Apache-2.0 |
X | | | | ParallelIO - High-level parallel I/O library |
| esme_pio_openmpi_5_0_6 |
2.6.2 |
|
|
Apache-2.0 |
X | | | | ParallelIO - High-level parallel I/O library |
| esme_pio_openmpi_5_0_7 |
2.6.5 |
|
|
Apache-2.0 |
X | | | | ParallelIO - High-level parallel I/O library |
| esme_pnetcdf_mpich_4_2_3 |
1.14.0 |
|
|
PnetCDF |
X | | | | PnetCDF - Parallel netCDF |
| esme_pnetcdf_openmpi_4_1_6 |
1.14.0 |
|
|
PnetCDF |
X | | | | PnetCDF - Parallel netCDF |
| esme_pnetcdf_openmpi_5_0_6 |
1.14.0 |
|
|
PnetCDF |
X | | | | PnetCDF - Parallel netCDF |
| esme_pnetcdf_openmpi_5_0_7 |
1.14.0 |
|
|
PnetCDF |
X | | | | PnetCDF - Parallel netCDF |
| esmf_mpich |
8.8.0 |
|
|
ESMF |
X | | | | ESMF - Earth System Modeling Framework |
| esmre |
0.3.1 |
|
|
GNU |
X | | | X | Regular expression accelerator |
| espresso |
1.5.0 |
|
|
Free |
X | | | X | ESPRESSO (Error Statistics PRomoted Evaluator of Splice Site Options)... |
| est-sfs |
2.04 |
|
|
Free |
X | X | | | est-sfs ( Keightley and Jackson, 2018) is a stand-alone implementation... |
| estmapper |
2008 |
|
|
GPL |
X | X | | | Software package for the high-throughput alignment of large cDNA (EST,... |
| estscan |
3.0 |
|
|
open |
X | | | | Detects coding regions in DNA sequences even if they are of low quality |
| esviritu |
0.2.3 |
|
dev |
MIT |
| | | X | EsViritu: Read mapping pipeline for detection and measurement of virus... |
| eta |
0.9.7 |
|
|
BSD |
X | X | | X | ETA Progress bar for command-line utilities |
| ete2 |
2.3.10 |
|
|
GPLv3 |
X | X | | X | Phylogenetic tree analyses and exploration |
| ete3 |
3.1.1 |
|
|
GPLv3 |
X | X | | X | A Python framework for the analysis and visualization of trees |
| eternafold |
1.3.1 |
doc |
dev |
BSD-3-Clause |
X | X | | | RNA structure prediction algorithm improved through crowdsourced training data |
| etoki |
1.2.3 |
|
|
GNU |
| | | X | EToKi (Enterobase Tool Kit) includes methods related to Enterobase data... |
| eukcc |
2.1.3 |
doc |
dev |
GPL-3.0-or-later |
| | | X | Check eukaryotic genomes or MAGs for completeness and contamination. |
| eukfinder |
1.2.3 |
|
|
MIT |
X | X | | | Eukfinder is a tool for detecting eukaryotic sequences in metagenomic data. |
| eukrep |
0.6.7 |
|
|
MIT |
| | | X | Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets |
| eukulele |
2.0.9 |
doc |
dev |
MIT |
| | | X | Easy taxonomic annotation for eukaryotic microbes. |
| eva-sub-cli |
0.4.4 |
|
|
Apache-2.0 |
| | | X | EVA Submission Command Line Interface |
| eval |
2.2.8 |
doc |
|
BSD |
| | | X | Eval is a flexible tool for analyzing the performance of gene-structure... |
| evidencemodeler |
2.1.0 |
|
|
BSD |
X | X | | X | Evidence Modeler combines ab intio gene predictions, protein... |
| evigene |
23.7.15 |
|
|
Don |
| | | X | A genome informatics project for Evidence Directed Gene Construction... |
| evofold2 |
0.1 |
|
|
GPL |
X | | | | Identifies functional RNA-structure in multiple sequence alignments. |
| evofr |
0.1.26 |
|
dev |
AGPL-3.0 |
| | | X | Tools for evolutionary forecasting |
| examine |
1.0.1 |
|
dev |
GPL-2.0 |
| | | X | A graphical application to visually analyze network modules. |
| excludonfinder |
0.1.4 |
|
dev |
MIT |
| | | X | A tool for identifying and analyzing excludons in genomic data using... |
| exomiser-rest-prioritiser |
14.1.0 |
doc |
dev |
AGPL-3.0-or-later |
| | | X | Exomiser prioritiser REST API |
| exonerate |
2.4.0 |
|
|
GPL-3.0-or-later |
X | X | | | Exonerate - A generic tool for pairwise sequence comparison / alignment |
| expam |
1.4.0.6 |
doc |
dev |
BSD-3-Clause |
X | X | | | Metagenomic profiling using a reference phylogeny |
| expansionhunter |
5.0.0 |
|
|
APACHE |
X | X | | | A tool for estimating repeat sizes |
| expansionhunterdenovo |
0.9.0 |
|
|
Apache |
X | | | | ExpansionHunter Denovo (EHdn) is a suite of tools for detecting novel... |
| exparna |
1.0.1 |
|
|
GPL-2.0 |
X | | | | The program finds the longest common subsequence of exact pattern... |
| export2graphlan |
0.22 |
|
|
MIT |
X | X | | X | Conversion software tool for annotating tree with GraPhlAn |
| express |
1.5.1 |
|
|
Artistic |
X | X | | | eXpress is a streaming DNA/RNA sequence quantification tool. |
| expressbetadiversity |
1.0.10 |
doc |
dev |
GPL-3 |
X | | | | Taxon- and phylogenetic-based beta diversity measures. |
| extern |
0.2.1 |
|
|
MIT |
X | X | | | Extern is an opinionated version of Pythons subprocess, making it just... |
| extract-codon-alignment |
0.0.1 |
|
|
GNU |
| | | X | To extract some codon positions (1st, 2nd, 3rd) from a CDS alignment. |
| extract-sv-reads |
1.3.0 |
|
|
MIT |
X | | | | Tool for extracting splitter or discordant reads from a BAM or CRAM file. |
| extract_fasta_seq |
0.0.1 |
|
|
GNU |
| | | X | To extract specific fasta sequences from a fasta file. |
| extract_fullseq |
3.101 |
|
|
Public |
X | X | | | extract_fullseq is part of BMTagger aka Best Match Tagger, for removing... |
| extract_genome_region |
0.0.3 |
|
|
BSD |
X | X | | X | Given a CSV file of variable information defining the regions of... |
| extract_vcf |
0.5 |
|
|
BSD |
| | | X | Tool to extract information from vcf file. |
| extracthifi |
1.0.0 |
|
|
BSD-3-Clause-Clear |
X | | | X | PacBio utility to extract HiFi reads from CCS reads |
| ezaai |
1.2.3 |
doc |
dev |
GNU |
| | | X | EzAAI is a suite of workflows for improved AAI calculation performance... |
| ezcharts |
0.11.2 |
doc |
dev |
BSD-4-Clause |
| | | X | eCharts plotting API. |
| ezclermont |
0.7.0 |
|
dev |
MIT |
| | | X | easily determine the Clermont 2013 E coli phylotype |
| ezomero |
3.1.0 |
|
|
GPL-2.0-only |
| | | X | A module with convenience functions for writing Python code that... |
| f5c |
1.5 |
|
|
MIT |
X | X | | | An optimised re-implementation of the call-methylation and eventalign... |
| fadapa |
0.3.1 |
|
|
uncopyrighted |
X | X | | X | FAstqc DAta PArser - A minimal parser to parse FastQC output data |
| fade |
0.6.0 |
|
|
MIT |
X | X | | | fade is a D program that provides fast identification and removal of... |
| fairease-source |
1.4.4 |
|
dev |
CC-BY-NC-4.0 |
| | | X | SOURCE: Sea Observations Utility for Reprocessing, Calibration and Evaluation |
| fairy |
0.5.7 |
|
|
MIT |
X | X | | | fairy calculates all-to-all approximate coverage for multi-sample... |
| falco |
1.2.5 |
doc |
dev |
GPL-3.0-only |
X | X | | | falco is a drop-in C++ implementation of FastQC to assess the quality... |
| famsa |
2.2.3 |
|
dev |
GPL-3.0-only |
X | X | | | Algorithm for large-scale multiple sequence alignments. |
| famseq |
1.0.3 |
|
|
GPL-3 |
X | X | | | Peng G, Fan Y, Palculict TB, Shen P, Ruteshouser EC, Chi A, Davis RW,... |
| fanc |
0.9.23b |
doc |
dev |
ACADEMIC |
X | X | | | Framework for the ANalysis of C-data. |
| fann |
2.2.0 |
|
|
LGPL-2.1 |
X | X | | | Fast Artificial Neural Network Library |
| faqcs |
2.10 |
|
|
BSD |
X | X | | | Quality Control of Next Generation Sequencing Data. |
| fargene |
0.1 |
|
|
MIT |
X | X | | X | Fragmented Antibiotic Resistance Gene iENntifiEr takes either... |
| fast-edit-distance |
1.2.2 |
doc |
dev |
MIT |
X | X | | | A implementation of edit distance with improved runtime. |
| fast2q |
2.7.7 |
|
dev |
GPL-3.0-or-later |
| | | X | A Python3 program that counts sequence occurrences in FASTQ files. |
| fast5 |
0.6.5 |
|
|
MIT |
X | X | | X | A C++ header-only library for reading Oxford Nanopore Fast5 files. |
| fast5-research |
1.2.22 |
|
|
Mozilla |
X | X | | X | ONT Research fast5 read/write package |
| fast5seek |
0.1.1 |
|
|
MIT |
X | X | | X | Get paths for fast5 files contained in BAM, SAM, or fastq. |
| fasta-splitter |
0.2.6 |
|
|
zlib/libpng |
X | X | | X | Divides a large FASTA file into a set of smaller, approximately equally... |
| fasta3 |
36.3.8 |
|
|
Apache |
X | X | | | The FASTA package - protein and DNA sequence similarity searching and... |
| fasta_ushuffle |
0.2 |
|
|
custom |
X | X | | | a wrapper for uShuffle |
| fasta_windows |
0.2.4 |
|
|
MIT |
X | X | | | Generate fast sequence statistics in windows for each record in a fasta file. |
| fastafunk |
0.1.2 |
|
|
MIT |
| | | X | Miscellaneous fasta manipulation tools |
| fastagap |
1.0.1 |
|
|
MIT |
| | | X | Count and remove missing data in fasta-formatted sequence data |
| fastahack |
2016.07.2 |
doc |
dev |
MIT |
X | X | | | fastahack --- *fast* FASTA file indexing, subsequence and sequence extraction |
| fastaindex |
0.11c |
|
|
GPLv3 |
X | X | | X | FastA indexing and sequence retrival. |
| fastalite |
0.4.1 |
|
|
MIT |
| | | X | Simplest possible fasta parser |
| fastani |
1.34 |
|
|
Apache-2.0 |
X | X | | | FastANI is developed for fast alignment-free computation of... |
| fastaptamer |
1.0.16 |
|
|
GPL-3.0-or-later |
| | | X | A Bioinformatic Toolkit for High-Throughput Sequence Analysis of... |
| fastdtw |
0.2.0 |
|
|
MIT |
X | X | | X | Dynamic Time Warping (DTW) algorithm with an O(N) time and memory complexity |
| fasten |
0.8.5 |
|
|
MIT |
X | X | | | Perform random operations on fastq files, using unix streaming. Secure... |
| fastg2protlib |
1.0.2 |
|
|
MIT |
| | | X | FASTG sequences to a protein library. |
| fastindep |
1.0.0 |
|
|
MIT |
X | X | | | A fast random heuristic algorithm for identifying large sets of... |
| fastk |
1.1.0 |
|
|
https://github. |
X | | | | FastK is a k‑mer counter that is optimized for processing high quality... |
| fastkit |
1.0.2 |
|
|
MIT |
| | | X | Routine pre-processing of biological data e.g. FASTA/FASTQ files |
| fastlin |
0.4.1 |
|
|
MIT |
X | X | | | fastlin, ultra-fast MTBC lineage typing |
| fastlmm |
0.2.32 |
|
|
Apache |
X | X | | | Fast GWAS |
| fastme |
2.1.6.3 |
doc |
dev |
GPL-3.0-only |
X | X | | | a comprehensive, accurate and fast distance-based phylogeny inference program. |
| fastml |
3.11 |
|
|
GNU |
X | | | | FastML is a bioinformatics tool for the reconstruction of ancestral... |
| fastmlst |
0.0.16 |
|
|
LGPL-3.0-only |
| | | X | A Fast Multilocus Sequence Typing scan against PubMLST typing schemes |
| fastobo |
0.13.0 |
doc |
|
MIT |
X | | | | Faultless AST for Open Biomedical Ontologies in Python |
| fastoma |
0.3.5 |
|
|
Mozilla |
| | | X | FastOMA - a package to infer orthology information among proteomes |
| fastool |
0.1.4 |
|
|
MIT |
X | X | | | A simple and quick tool to read huge FastQ and FastA files (both normal... |
| fastools |
1.1.5 |
|
|
MIT |
| | | X | FASTA/FASTQ analysis and manipulation toolkit. |
| fastp |
0.24.0 |
doc |
dev |
MIT |
X | X | | | A ultra-fast FASTQ preprocessor with full features... |
| fastphylo |
1.0.3 |
|
|
MIT |
X | X | | | Fastphylo is software project containing the implementations of the... |
| fastplong |
0.2.2 |
doc |
dev |
MIT |
X | X | | | Ultra-fast preprocessing and quality control for long-read sequencing data. |
| fastq |
2.0.4 |
doc |
dev |
GPL-3.0-or-later |
| | | X | A simple FASTQ toolbox for small to medium size projects without dependencies. |
| fastq-and-furious |
0.3.2 |
|
|
MIT |
X | X | | | Fast handling of FASTQ files |
| fastq-anonymous |
1.0.1 |
|
|
MIT |
X | X | | X | Change the sequence of a fastq file to enable sharing of confidential... |
| fastq-count |
0.1.0 |
|
|
MIT |
X | X | | | Simple fastq read and base counter for paired data. |
| fastq-dl |
3.0.0 |
|
|
MIT |
| | | X | A tool to download FASTQs associated with Study, Experiment, or Run accessions. |
| fastq-filter |
0.3.0 |
|
|
MIT |
X | X | | | A fast FASTQ filter program. |
| fastq-join |
1.3.1 |
|
|
MIT |
X | X | | | Similar to audy's stitch program, but in C, more efficient and... |
| fastq-multx |
1.4.2 |
|
|
MIT |
X | X | | | Demultiplexes a fastq. Capable of auto-determining barcode id's... |
| fastq-pair |
1.0 |
|
|
MIT |
X | X | | | fastq-pair: efficient synchronization of paired-end fastq files |
| fastq-scan |
1.0.1 |
|
|
MIT |
X | X | | | FASTQ summary statistics in JSON format |
| fastq-screen |
0.16.0 |
|
dev |
GPL-3.0-or-later |
X | X | | X | FastQ Screen allows you to screen a library of sequences in FastQ... |
| fastq-tools |
0.8.3 |
|
|
MIT |
X | X | | | A collection of fastq manipulation scripts written in C for speed. |
| fastq_utils |
0.25.2 |
|
dev |
GPL-3.0-only |
X | X | | | Validation and manipulation of FASTQ files, scRNA-seq barcode... |
| fastqc |
0.12.1 |
|
|
GPL |
X | X | | X | A quality control tool for high throughput sequence data. |
| fastqc-rs |
0.3.4 |
|
dev |
MIT |
X | X | | | A fast quality control tool for FASTQ files written in rust. |
| fastqe |
0.3.3 |
|
|
BSD-3-Clause |
X | X | | X | A emoji based bioinformatics command line tool. |
| fastqmetrics |
0.1.0 |
|
|
MIT |
X | X | | X | Extract metrics from a fastq file, streaming |
| fastqpuri |
1.0.7 |
|
|
GPL3.0 |
X | X | | | fastq quality assessment and filtering tool |
| fastqsplitter |
1.2.0 |
doc |
|
MIT |
X | X | | X | Splits FASTQ files evenly. |
| fastqtk |
0.27 |
|
|
MIT |
X | X | | | fastqtk is a fast and lightweight tool for... |
| fastquast |
1.0.2 |
doc |
|
MIT |
| | | X | Fast and simple Quality Assessment Tool for Large Genomes |
| fastremap-bio |
1.0.0 |
|
|
MIT |
X | | | | FastRemap, a C++ tool for quickly remapping reads between genome... |
| fastsimbac |
1.0.1_bd3ad13d8f79 |
|
|
GPL |
X | X | | | Models bacterial recombination |
| fastsimcoal2 |
27093 |
|
|
GPL |
| | | X | fast sequential markov coalescent simulation of genomic data under... |
| fastspar |
1.0.0 |
|
|
GPLv3 |
X | X | | | Rapid and scalable correlation estimation for compositional data |
| faststructure |
1.0 |
|
|
MIT |
X | X | | | A variational framework for inferring population structure from SNP... |
| fasttree |
2.1.11 |
|
|
GPL-2 |
X | X | | | FastTree infers approximately-maximum-likelihood phylogenetic trees... |
| fastuniq |
1.1 |
|
|
Creative |
X | X | | | FastUniq, A Fast De Novo Duplicates Removal Tool for Paired Short Reads |
| fastutils |
0.3 |
|
|
GPL-3.0 |
X | X | | | A light toolkit for parsing, manipulating and analysis of FASTA and FASTQ files |
| fastv |
0.10.0 |
|
|
MIT |
X | X | | | An ultra-fast tool for identification of SARS-CoV-2 and other microbes... |
| fastx_toolkit |
0.0.14 |
doc |
dev |
AGPL-3.0-or-later |
X | X | | | 'The FASTX-Toolkit is a collection of command line tools for... |
| favites_lite |
1.0.3 |
|
dev |
GPL-3.0-or-later |
| X | | X | FAVITES-Lite: A lightweight framework for viral transmission and... |
| fba |
0.0.13 |
doc |
dev |
MIT |
| | | X | Tools for single-cell feature barcoding analysis. Citation: Duan, et al... |
| fc |
1.0.1 |
|
dev |
MIT |
X | | | | Accurate Assembly of Full-length Consensus for Viral Quasispecies. |
| fcp |
1.0.7 |
|
|
GPL3 |
X | X | | | Homology- and composition-based classifiers for assigning a taxonomic... |
| fcsparser |
0.2.8 |
|
|
MIT |
| | | X | A python package for reading raw fcs files |
| feature_merge |
1.3.0 |
doc |
dev |
MIT |
| | | X | Merge features in GFF files |
| fec |
1.0.1 |
|
|
MIT |
X | | | | An error correction tool |
| feelnc |
0.2 |
|
|
GNU |
X | X | | X | FlExible Extraction of LncRNA |
| feems |
1.0.0 |
|
|
MIT |
| | | X | Fast Estimation of Effective Migration Surfaces |
| fegenie |
1.2 |
|
|
AGPL-3.0 |
| | | X | HMM-based identification and categorization of iron genes and iron gene... |
| feht |
1.1.0 |
|
|
BSD |
X | | | | A commandline program to automatically identify markers predictive of... |
| fermi |
1.1_r751_beta |
|
|
Unknown |
X | X | | | A WGS de novo assembler based on the FMD-index for large genomes |
| fermi-lite |
0.1 |
|
|
MIT |
X | X | | | Fermi-lite is a standalone C library as well as a command-line tool for... |
| fermi2 |
r193 |
|
|
Unknown |
X | X | | | Fermi2 focuses on the exploration of FMD-index as a graph. |
| fermikit |
0.14.dev1 |
|
|
Unknown |
X | X | | | FermiKit is a de novo assembly based variant calling pipeline for deep... |
| ffgc |
2.4.2 |
doc |
|
BSD |
| | | X | Family Free Genome Comparison (FFGC) workflow |
| ffindex |
0.98 |
|
|
CC-BY-SA-3.0 |
X | X | | | FFindex - A database wrapped around mmap. |
| ffindex-dbkit |
0.2 |
|
|
GPL-2.0-only |
| | | X | Tools to create ffindex files |
| ffq |
0.3.1 |
|
|
MIT |
| | | X | A command line tool that makes it easier to find sequencing data from... |
| fgap |
1.8.1 |
|
|
MIT |
X | X | | | FGAP: an automated gap closing tool |
| fgbio |
2.5.0 |
|
|
MIT |
X | X | | X | A set of tools for working with genomic and high throughput sequencing... |
| fgbio-minimal |
2.5.0 |
|
|
MIT |
| | | X | A set of tools for working with genomic and high throughput sequencing... |
| fgmp |
1.0.3 |
|
|
MIT |
X | X | | X | FGMP: assessing fungal genome completeness and gene content. |
| fgpyo |
1.0.0 |
doc |
dev |
MIT |
| | | X | Python bioinformatics and genomics library |
| fgsv |
0.2.1 |
|
|
MIT |
| | | X | Tools to find evidence for structural variation. |
| fgwas |
0.3.6 |
|
dev |
GPL2 |
X | X | | | fgwas is a command line tool for integrating functional genomic... |
| fibertools-rs |
0.6.4 |
doc |
dev |
MIT |
X | X | | | Mitchell Vollger's rust tools for fiberseq data. |
| ficus |
0.5 |
|
|
BSD-3-Clause |
X | X | | X | provides a context manager for matplotlib figures. |
| fido |
1.0 |
|
|
MIT |
X | | | | A method for protein identification in MS/MS proteomics. Think of it... |
| figaro |
1.1.2 |
|
|
GPLv3 |
| | | X | An efficient and objective tool for optimizing microbiome rRNA gene... |
| figtree |
1.4.4 |
|
|
GPLv2 |
| | | X | FigTree is designed as a graphical viewer of phylogenetic trees and as... |
| fiji |
20250206 |
|
|
GPL-3.0-or-later |
X | X | | | Fiji is an image processing package—a "batteries-included"... |
| fiji-max_inscribed_circles |
2.1.0 |
|
dev |
GPLv3 |
| | | X | ImageJ / Fiji plugin implementing an iterative Largest Inscribed Circle... |
| fiji-morpholibj |
1.6.1 |
|
|
LGPL3 |
| | | X | MorphoLibJ is a collection of mathematical morphology methods and... |
| fiji-omero_ij |
5.8.6 |
|
dev |
GPLv2 |
| | | X | ImageJ / Fiji plugin to visualize and manipulate both image data and... |
| fiji-simple_omero_client |
5.19.0 |
|
dev |
GPLv2 |
| | | X | Java library to simplify API to put/get objects on an OMERO server from... |
| filechunkio |
1.6 |
|
|
MIT |
X | X | | | FileChunkIO represents a chunk of an OS-level file containing bytes data |
| filtlong |
0.2.1 |
|
|
GPL-3.0 |
X | X | | | Filtlong is a tool for filtering long reads. It can take a set of long... |
| find_circ |
1.2 |
|
|
GPL-3 |
| | | X | Detect head-to-tail spliced (back-spliced) sequencing reads, indicative... |
| find_differential_primers |
0.1.4 |
|
|
MIT |
X | X | | X | Scripts to aid the design of differential primers for diagnostic PCR. |
| finemap |
1.4.2 |
|
|
Custom |
X | | | X | Program for identifying causal SNPs and their effect sizes and... |
| fineradstructure |
0.3.2r109 |
|
|
Attribution-Non |
X | | | | Inference of population structure from RAD datasets |
| finestructure |
4.1.1 |
|
|
OTHER |
X | X | | X | fineSTRUCTURE is a fast and powerful algorithm for identifying... |
| fingerprintscan |
3_597 |
|
dev |
GPL |
X | X | | | Search against FingerPRINTScan with a protein query sequence to... |
| fings |
1.7.1 |
|
|
Apache |
| | | X | Filters for Next Generation Sequencing |
| firecloud |
0.16.37 |
doc |
dev |
BSD-3-Clause |
X | X | | X | API and CLI for Broad Institute's Firecloud workspace/workflow... |
| fisher |
0.1.4 |
|
|
BSD |
X | X | | | Fast Fisher's Exact Test |
| fishtaco |
1.0.5 |
|
|
BSD-3-Clause |
X | X | | X | FishTaco: a metagenomic computational framework, aiming to identify the... |
| fit_nbinom |
1.2 |
|
|
GPL-3.0-or-later |
| | | X | Script to fit negative binomial distributions via maximum likelihood estimation. |
| fithic |
2.0.8 |
|
|
MIT |
| | | X | Fit-Hi-C is a tool for assigning statistical confidence estimates to... |
| fitter |
1.4.1 |
|
|
GPL-3.0-only |
X | X | | X | A tool to fit data to many distributions and best one(s) |
| flaimapper |
3.0.0 |
|
|
GNU |
X | X | | X | FlaiMapper: Detecting small ncRNA derived fragments in small RNA-Seq data |
| flair |
2.0.0 |
|
|
BSD-3 |
| | | X | Correction, isoform definition, and alternative splicing analysis of... |
| flams |
1.1.5 |
|
|
MIT |
| | | X | Find Lysine Acylation & other Modification Sites |
| flanker |
0.1.5 |
|
|
MIT |
| | | X | Gene-flank analysis tool |
| flapjack |
1.20.10.07 |
|
|
BSD-2-Clause |
X | X | | X | Flapjack provides interactive visualizations of high-throughput genotyping data. |
| flash |
1.2.11 |
|
|
GPLv3+ |
X | X | | | Merge mates from fragments that are shorter than twice the read length |
| flash2 |
2.2.00 |
|
|
GPLv3+ |
X | X | | | Merge paired-end reads from fragments that are shorter than twice the... |
| flashlfq |
2.0.0 |
doc |
dev |
LGPL-3.0-only |
X | X | | X | Ultrafast label-free quantification algorithm for mass-spectrometry proteomics. |
| flask-admin |
1.4.0 |
|
|
BSD |
X | X | | | Simple and extensible admin interface framework for Flask |
| flask-bootstrap |
3.3.5.7 |
|
|
BSD |
X | X | | | An extension that includes Bootstrap in your project, without any... |
| flask-bower |
1.3.0 |
|
|
GNU |
X | X | | | An extension to manage and serve your javascript assets with bower |
| flask-markdown |
0.3 |
|
|
BSD |
X | X | | | Small extension to make using markdown easy |
| flask-nav |
0.5 |
|
|
MIT |
X | X | | | Easily create navigation for Flask applications. |
| flask-potion |
0.12.1 |
|
|
MIT |
X | X | | | Powerful REST API framework for Flask and SQLAlchemy |
| flexbar |
3.5.0 |
|
|
BSD-3-Clause |
X | X | | | Flexible barcode and adapter removal |
| flexi-formatter |
1.0.1 |
|
|
MIT |
| | | X | Moving flexiplex barcode and UMI to bam tags |
| flexiformatter |
1.0.2 |
|
|
MIT |
| | | X | Moving flexiplex barcode and UMI to bam tags |
| flexiplex |
1.01 |
|
|
MIT |
X | X | | | flexiplex: the flexible demultiplexer |
| flexserv |
1.0.2 |
|
|
Apache |
X | X | | | FlexServ protein structure conformational ensemble generation tools |
| flexsweep |
1.0 |
|
|
MIT |
| | | X | A versatile tool for detecting selective sweeps |
| flextaxd |
0.4.4 |
|
|
GPLv3 |
| | | X | Script that allows the creation of custom kraken databases from various... |
| flexynesis |
0.2.17 |
doc |
dev |
OTHER |
| | | X | A deep-learning-based multi-omics bulk sequencing data integration... |
| flight-genome |
1.6.3 |
|
|
BSD-3 |
| | | X | flight - python component of Rosella and Lorikeet |
| flippyr |
0.6.1 |
doc |
|
MIT |
| | | X | This package is designed to align a PLINK fileset with a FASTA reference genome. |
| flock |
1.0 |
|
|
unknown |
X | X | | | FLOCK - Flow Cytometry Clustering without K. |
| flopp |
0.2.0 |
|
|
MIT |
X | X | | | flopp is a software package for single individual haplotype phasing of... |
| floria |
0.0.1 |
|
|
MIT |
X | X | | | Floria is method for recovering strain-level haplotypes and clusters of... |
| flowcraft |
1.4.1 |
doc |
dev |
GPL3 |
X | X | | X | A Nextflow pipeline assembler for genomics. Pick your modules. Assemble... |
| flumut |
0.6.3 |
|
|
AGPL-3.0-or-later |
| | | X | A tool to search for molecular markers with potential impact on the... |
| flumutdb |
6.4 |
|
dev |
AGPL-3.0-or-later |
| | | X | Utility module for FluMut database. |
| flux-simulator |
1.2.1 |
|
|
BSD |
X | X | | X | Tool for modeling RNA-Seq experiments in silico |
| flye |
2.9.5 |
doc |
dev |
BSD-3-Clause |
X | X | | | A fast and accurate de novo assembler for single molecule sequencing... |
| fmlrc |
1.0.0 |
|
|
MIT |
X | X | | | A long-read error correction tool using the multi-string Burrows... |
| fmlrc2 |
0.1.7 |
|
|
MIT |
X | X | | | A rust implementation of fmlrc with faster run times. |
| fmsi |
0.4.0 |
doc |
dev |
MIT |
X | X | | | FMSI - memory efficient k-mer set index based on masked superstrings... |
| focus |
1.8 |
|
dev |
GPL-3.0 |
| | | X | FOCUS is an innovative and agile model to profile and report organisms... |
| foldcomp |
0.0.7 |
|
|
GPL-3.0-or-later |
X | X | | | Foldcomp: a library and format for compressing and indexing large... |
| foldmason |
2.7bd21ed |
|
|
GPL-3 |
X | X | | | Multiple Protein Structure Alignment at Scale with FoldMason |
| foldseek |
10.941cd33 |
|
|
GPL-3 |
X | X | | | Foldseek: fast and accurate protein structure search |
| footprint |
1.0.1 |
|
|
GPL-2.0-or-later |
X | | | X | This is a pipeline to find transcription factor footprints in ATAC-seq... |
| forceatlas2-python |
1.1 |
|
dev |
GNU |
| | | X | Multithreaded Gephi Force Atlas2 Layout algorithm in 2D and 3D. |
| forgi |
2.2.3 |
|
dev |
GPL-3.0-or-later |
X | X | | X | RNA Graph Library |
| forked-path |
0.2.3 |
|
|
Public |
X | X | | | An object oriented file path module |
| forwardgenomics |
1.0 |
|
|
MIT |
| | | X | Forward Genomics is a framework to associate phenotypic differences... |
| fpa |
0.5.1 |
|
|
MIT |
X | X | | | Filter Pairwise Alignment filter long read mapping information to save... |
| fq |
0.12.0 |
|
|
MIT |
X | X | | | fq is a library to generate and validate FASTQ file pairs. |
| fqgrep |
1.0.3 |
|
|
MIT |
X | X | | | Search a pair of fastq files for reads that match a given ref or alt sequence |
| fqtk |
0.3.1 |
doc |
dev |
MIT |
X | X | | | A toolkit for working with FASTQ files. |
| fqtools |
2.0 |
|
|
GPLv3 |
X | X | | | An efficient FASTQ manipulation suite. |
| fqtrim |
0.9.7 |
|
|
Artistic |
X | X | | | fqtrim is a versatile stand-alone utility that can be used to trim... |
| fqzcomp |
4.6 |
|
|
BSD |
X | | | | Fqzcomp is a basic fastq compressor, designed primarily for high performance. |
| frag_gene_scan_rs |
1.1.0 |
|
|
GPL-3.0-or-later |
X | X | | | Rust implementation of the gene prediction model for short and error-prone reads |
| fragbuilder |
1.0.1 |
|
|
GPL |
| | | X | FragBuilder is a tool to create, setup and analyze QM calculations on peptides. |
| fraggenescan |
1.32 |
|
|
BSD |
X | X | | | FragGeneScan is an application for finding (fragmented) genes in short reads. |
| fragpipe |
22.0 |
|
|
GPL-3.0 |
| | | X | Pipeline for comprehensive analysis of shotgun proteomics data |
| fraposa-pgsc |
1.0.2 |
|
|
MIT |
| | | X | Tools to perform ancestry projection to a reference dataset within the... |
| frc |
5b3f53e |
|
|
GPLv3 |
X | X | | | Computes FRC from SAM/BAM file and not from afg files |
| fred2 |
2.0.7 |
|
|
BSD |
X | X | | X | Python-based framework for computational immunomics. |
| freddie |
0.4 |
|
|
MIT |
| | | X | Annotation-independent detection of splicing isoforms using RNA long-reads |
| freebayes |
1.3.9 |
doc |
dev |
MIT |
X | X | | | Bayesian haplotype-based polymorphism discovery and genotyping. |
| freyja |
1.5.3 |
|
dev |
BSD-2-Clause |
| | | X | Freyja recovers relative lineage abundances from mixed SARS-CoV-2... |
| frogs |
5.0.1 |
|
|
GNU |
X | X | | | FROGS is a workflow designed to metabarcoding sequence analysis |
| fsa |
1.15.9 |
|
|
GPL-3 |
X | X | | | FSA is a probabilistic multiple sequence alignment algorithm which uses... |
| fseq |
1.84 |
|
|
GPL |
X | X | | | F-Seq: A feature density estimator for high-throughput sequence tags |
| fsm-lite |
1.0 |
|
|
GPL-3 |
X | X | | | Frequency-based String Mining (lite) |
| fsnviz |
0.3.0 |
|
|
BSD |
X | X | | X | Tool for plotting gene fusion events detected by various tools using Circos. |
| ftputil |
3.2 |
|
|
BSD |
X | X | | | High-level FTP client library (virtual file system and more) |
| fuc |
0.38.0 |
doc |
dev |
MIT |
| | | X | Frequently used commands in bioinformatics |
| fuma |
4.0.0 |
|
|
GNU |
X | X | | X | FuMa: reporting overlap in RNA-seq detected fusion genes |
| funannotate |
1.8.17 |
doc |
dev |
BSD-2-Clause |
X | X | | X | funannotate: eukaryotic genome annotation pipeline |
| funcannot |
v2.8 |
|
|
GPLv3 |
X | X | | | Annotates cDNA, protein, mutation type, and other funcational changes... |
| funnel |
0.9.0 |
|
|
MIT |
X | X | | | Funnel is a toolkit for distributed task execution via a simple, standard API |
| fununifrac |
0.0.1 |
doc |
dev |
BSD-3-Clause |
| | | X | A repository to implement UniFrac, but on functional profiles of... |
| fusepy |
2.0.4 |
|
|
ISC |
X | X | | | Simple ctypes bindings for FUSE |
| fusion-filter |
0.5.0 |
|
|
BSD-3-Clause |
X | X | | X | FusionFilter provides a common fusion-finding, filtering, and... |
| fusion-inspector |
2.10.0 |
|
|
BSD-3-Clause |
X | | | X | FusionInspector is a component of the Trinity Cancer Transcriptome... |
| fusion-report |
3.1.1 |
|
|
GPL-3.0-only |
| | | X | Tool for parsing outputs from fusion detection tools. Part of a... |
| fusioncatcher |
1.33 |
|
|
GPL-3.0 |
X | X | | X | Finder of Somatic Fusion Genes in RNA-seq data. |
| fusioncatcher-seqtk |
1.2 |
|
|
MIT |
X | X | | | This is modified Seqtk version required for FusionCatcher. |
| fwdpp |
0.5.7 |
|
|
https://raw.git |
X | X | | | A C++ template library for forward-time population genetic simulation. |
| fwdpy |
0.0.4pre1 |
|
|
GNU |
X | X | | | Forward-time population genetic simulation in Python. |
| fwdpy11 |
0.24.3 |
doc |
dev |
GPL-3.0-or-later |
X | X | | | Forward-time population genetic simulation in Python. |
| fxtract |
2.4 |
|
|
MIT |
X | X | | | Extract sequences from a fastx file given a subsequence or identifier. |
| ga4ghmongo |
0.0.1.2 |
|
|
MIT |
X | X | | X | A document based Variant database inspired by ga4gh Variants schema |
| gaas |
1.2.0 |
|
dev |
GPLv3 |
| | | X | Suite of tools related to Genome Assembly Annotation Service tasks at NBIS. |
| gadem |
1.3.1 |
|
|
GPLv3 |
X | X | | | A Genetic Algorithm Guided Formation of Spaced Dyads Coupled with an EM... |
| gadma |
2.0.2 |
doc |
dev |
GNU |
X | X | | X | Genetic Algorithm for Demographic Inference |
| gafpack |
0.1.2 |
|
dev |
MIT |
X | X | | | Convert alignments to pangenome variation graphs to coverage maps |
| gaftools |
1.1.1 |
doc |
dev |
MIT |
| | | X | gaftools is a fast and comprehensive toolkit designed for processing... |
| gait-gm |
21.7.22 |
|
|
MIT |
| | | X | GAIT-GM - Modeling Metabolites as a function of gene expression |
| galah |
0.4.2 |
|
|
GPL-3.0-only |
X | | | | Galah aims to be a more scalable metagenome assembled genome (MAG)... |
| galaxy-containers |
21.9.0 |
doc |
dev |
AFL-3.0 |
| | | X | Galaxy Container Modeling and Interaction Abstractions |
| galaxy-data |
24.2.2 |
doc |
dev |
AFL-3.0 |
| | | X | The Galaxy models, datatype framework, and datatype implementations. |
| galaxy-files |
24.2.2 |
doc |
dev |
AFL-3.0 |
| | | X | The Galaxy file sources framework and default plugins. |
| galaxy-ie-helpers |
0.2.7 |
|
|
MIT |
X | X | | X | Helper scripts to work with Galaxy's Interactive Environments |
| galaxy-lib |
19.5.2 |
doc |
dev |
Academic |
X | X | | X | Subset of Galaxy (http://galaxyproject.org/) core code base designed to... |
| galaxy-ml |
0.10.0 |
|
|
MIT |
X | X | | | APIs for Galaxy machine learning tools |
| galaxy-objectstore |
24.2.2 |
doc |
dev |
AFL-3.0 |
| | | X | The Galaxy object store framework and default implementations |
| galaxy-ops |
1.1.0 |
|
|
Academic |
X | X | | X | Galaxy interval operations |
| galaxy-parsec |
1.16.0 |
|
|
MIT |
X | X | | X | Command-line utilities to assist in interacting with Galaxy servers... |
| galaxy-schema |
24.2.2 |
doc |
dev |
MIT |
| | | X | The Galaxy API schema objects. |
| galaxy-tool-util |
21.9.1 |
doc |
dev |
AFL-3.0 |
| | | X | Galaxy Tool and Tool Dependency Utilities |
| galaxy-upload |
1.0.1 |
doc |
dev |
MIT |
| | | X | Galaxy Command-Line Upload Utility |
| galaxy-util |
21.9.0 |
doc |
dev |
AFL-3.0 |
X | X | | X | Galaxy Generic Utilities |
| galaxy-workflow-executor |
0.2.6 |
|
dev |
Apache-2.0 |
| | | X | Execute workflows on Galaxy through the CLI |
| galaxy_sequence_utils |
1.2.0 |
|
|
Academic |
X | X | | X | Sequence Utilities from the Galaxy project |
| galaxyxml |
0.5.3 |
doc |
dev |
Apache-2.0 |
| | | X | Galaxy XML generation library |
| galitime |
0.2.0 |
doc |
|
MIT |
| | | X | benchmarking of scientific computaional experiments |
| galru |
1.0.0 |
|
|
GPL3 |
| | | X | Rapid spoligotyping for Mycobacterium tuberculosis directly from long... |
| gambit |
1.1.0 |
doc |
dev |
AGPL-3.0-or-later |
X | X | | | Tool for rapid taxonomic identification of microbial pathogens |
| gametes |
2.1 |
|
|
GPL-2.0-only |
| | | X | Tool for the generation of complex single SNP models |
| gamma |
2.2 |
|
|
Apache |
| | | X | Tool for Gene Allele Mutation Microbial Assessment |
| gangstr |
2.5.0 |
|
|
GPL-3.0-or-later |
X | X | | | GangSTR is a tool for genome-wide profiling tandem repeats from short reads. |
| ganon |
2.1.0 |
|
|
MIT |
X | | | | ganon2 classifies genomic sequences against large sets of references... |
| gap2seq |
3.1.1a |
|
|
GPLv3 |
X | X | | | Gap2Seq is a tool for filling gaps between contigs in genome assemblies. |
| gapfiller |
2.1.2 |
|
|
GPLv3 |
X | | | | GapFiller is a seed-and-extend local assembler to fill the gap within... |
| gapless |
0.4 |
|
|
MIT |
| | | X | gapless assembly improvement tool |
| gapmm2 |
23.11.3 |
|
|
BSD-2-Clause |
| | | X | gapmm2: gapped alignment using minimap2 |
| gappa |
0.9.0 |
doc |
dev |
GPL-3.0-only |
X | X | | | Genesis Applications for Phylogenetic Placement Analysis |
| gapseq |
1.4.0 |
|
|
AGPL-3.0-only |
X | | | | Informed prediction and analysis of bacterial metabolic pathways and... |
| gargammel |
1.1.2 |
|
|
GPL-3.0-only |
X | X | | | Tool for simulating ancient DNA datasets |
| gargammel-slim |
1.1.2 |
|
|
GPL-3.0-only |
X | X | | | Tool for simulating ancient DNA datasets |
| garnet |
0.4.5 |
|
|
MIT |
X | X | | | UNKNOWN |
| garnett-cli |
0.0.5 |
doc |
dev |
Apache-2.0 |
| | | X | Collection of wrapper scripts for the Garnett scRNAseq cell type... |
| gassst |
1.28 |
|
|
CeCILL |
X | | | | GASSST : Global Alignment Short Sequence Search Tool |
| gat |
1.3.6 |
|
|
MIT |
X | X | | | Genomic Association Tester |
| gatb |
1.4.2 |
|
|
AGPL |
X | X | | | The Genome Analysis Toolbox with de-Bruijn graph |
| gatk |
3.8 |
|
|
BSD |
X | X | | X | The full Genome Analysis Toolkit (GATK) framework, v3 |
| gatk-framework |
3.6.24 |
|
|
MIT |
X | X | | X | The core MIT-licensed Genome Analysis Toolkit (GATK) framework, free... |
| gatk4 |
4.6.1.0 |
|
dev |
BSD-3-Clause |
X | X | | X | Genome Analysis Toolkit (GATK4) |
| gatk4-spark |
4.6.1.0 |
|
dev |
BSD-3-Clause |
| | | X | Genome Analysis Toolkit (GATK4) |
| gatktool |
0.0.1 |
|
|
MIT |
| | | X | Functions and classes used to extend a GATK tool with Python |
| gb-io |
0.3.3 |
|
dev |
MIT |
X | X | | | A Python interface to gb-io, a fast GenBank parser and serializer... |
| gb_taxonomy_tools |
1.0.1 |
|
|
GNU |
X | X | | | These are four simple utilities which perform certain manipulations and... |
| gbintk |
1.0.0 |
doc |
dev |
GPL-3.0-or-later |
X | X | | X | GraphBin-Tk: assembly graph-based metagenomic binning toolkit |
| gbkviz |
1.2.0 |
|
|
MIT |
| | | X | Simple web application to visualize and compare genomes in Genbank files |
| gblocks |
0.91b |
|
|
The |
X | X | | | Selection of conserved blocks from multiple alignments for their use in... |
| gbmunge |
2018.07.06 |
|
|
MIT |
X | X | | | Munge GenBank files into FASTA and tab-separated metadata. |
| gbsx |
1.3 |
|
|
GPL-3.0 |
| | | X | Toolkit for experimental design and demultiplexing genotyping by... |
| gc-meox-tms |
1.0.1 |
|
dev |
MIT |
| | | X | In-silico MeOX/TMS derivatization of chemical compounds. |
| gcen |
0.6.3 |
|
|
GPL |
X | X | | | GCEN: an easy-to-use toolkit for Gene Co-Expression Network analysis... |
| gclib |
0.0.1 |
|
|
Artistic |
X | X | | | Genomic C libraries by Geo Pertea |
| gcluster |
2.06 |
|
dev |
perl_5 |
| | | X | Gcluster is a simple-to-use tool for visualizing and comparing genome... |
| gcnvkernel |
0.9 |
|
dev |
BSD-3-Clause |
| | | X | Python package to support GATK gCNV calling. |
| gcs-oauth2-boto-plugin |
1.9 |
|
|
Apache |
X | X | | | Auth plugin allowing use the use of OAuth 2.0 credentials for Google... |
| gcta |
1.94.1 |
|
|
GPL-3.0-only |
X | X | | | GCTA (Genome-wide Complex Trait Analysis) estimates the proportion of... |
| gctb |
2.0 |
|
|
MIT |
X | | | | GCTB (Genome-wide Complex Trait Bayesian ) is a software tool that... |
| gdal |
1.9.2 |
|
|
Several |
X | | | | None |
| gdc |
2.0 |
|
|
GPL2 |
X | X | | | Utility designed for compression of genome collections from the same species. |
| gdc-client |
2.3 |
doc |
dev |
Apache-2.0 |
X | X | | X | GDC Data Transfer Tool |
| gdk-pixbuf |
2.32.2 |
|
|
GNU |
X | X | | | The GdkPixbuf Structure — Information that describes an image. |
| gdmicro |
1.0.10 |
|
|
MIT |
| | | X | GDmicro - Use GCN and Deep adaptation network to classify host disease... |
| gdsctools |
1.0.1 |
|
|
BSD |
X | X | | X | Set of tools and pipelines to analyse GDSC data (cancerrxgene.org) |
| gecco |
0.9.10 |
|
|
GPL-3 |
| | | X | Biosynthetic Gene Cluster prediction with Conditional Random Fields. |
| gecko |
1.2 |
|
|
GPL-3.0 |
X | | | | A pairwise genome comparison software for the detection of High-scoring... |
| geco2 |
1.1 |
|
|
GPL3 |
X | | | | A fast tool to compress DNA sequences |
| geco3 |
1.0 |
|
|
GPL3 |
X | | | | An efficient DNA sequence compressor using Neural Networks |
| gecode |
6.2.0 |
|
|
MIT |
X | X | | | Generic constraint development environment |
| gefast |
2.0.1 |
|
|
AGPL |
X | X | | | Clustering tool using Swarm's clustering strategy and... |
| gem2 |
20200110 |
|
|
Custom |
X | | | | GEM2 is a high-performance mapping tool. It also provide a unique tool... |
| gem3-mapper |
3.6.1 |
|
|
GPL-3.0 |
X | X | | | The GEM read mapper (v3). |
| gembs |
3.5.5_IHEC |
|
|
GPL-3.0 |
X | X | | | gemBS is a bioinformatics pipeline designed for high throughput... |
| gemf_favites |
1.0.3 |
|
dev |
GPL-3.0-or-later |
X | X | | | User-friendly epidemic simulations |
| gemini |
0.30.2 |
|
|
MIT |
X | X | | | a lightweight db framework for disease and population genetics. |
| gemma |
0.98.3 |
|
|
GPLv3 |
X | X | | | Linear mixed models (LMMs) for genome-wide association (GWA) |
| gemoma |
1.9 |
|
|
GPL3 |
| | | X | Gene Model Mapper (GeMoMa) is a homology-based gene prediction program.... |
| gempipe |
1.37.7 |
doc |
dev |
GPL-3.0-only |
| | | X | gempipe is a tool for the reconstruction of strain-specific... |
| genbank |
0.119 |
|
|
GPL-3.0-or-later |
X | X | | | Code to work with Genbank files |
| genbank_to |
0.42 |
|
dev |
MIT |
| | | X | genbank_to: convert genbank files to a swath of other formats |
| genblasta |
1.0.4 |
|
|
GNU |
X | X | | | None |
| genblastg |
1.39 |
|
|
GNU |
X | X | | | genBlast is a program suite, consisting of two programs: genBlastA and... |
| genclust |
1.0 |
|
|
GNU |
X | X | | | A genetic algorithm for clustering gene expression data. |
| gencore |
0.17.2 |
|
|
MIT |
X | X | | | Generate consensus reads to reduce sequencing noises and remove duplications |
| gencove |
3.1.0 |
doc |
dev |
Apache-2.0 |
| | | X | Gencove is a high-throughput, cost-effective platform for genome... |
| gene-trajectory-python |
1.0.4 |
doc |
dev |
MIT |
| | | X | Compute gene trajectories |
| genefuse |
0.8.0 |
|
|
MIT |
X | X | | | Gene fusion detection and visualization |
| geneimpacts |
0.3.7 |
|
|
MIT |
X | X | | X | prioritize effects of variant annotations from VEP, SnpEff, et al. |
| genenotebook |
0.3.2 |
|
|
AGPL-3.0 |
X | X | | | A colleborative notebook for comparative genomics |
| genepender |
v2.6 |
|
|
GPLv3 |
X | X | | | Annotates overlapping BED-defined regions to variants in a VCF file.... |
| genepop |
4.8.2 |
doc |
dev |
CeCILL-2 |
X | X | | | Population Genetic Data Analysis package. |
| genera |
1.4.2 |
|
|
GPL-3.0-or-later |
| | | X | Uncovering gene-family founder events during major evolutionary... |
| generax |
2.1.3 |
|
|
AGPL-3.0-only |
X | X | | | GeneRax: a parallel tool for species tree-aware maximum likelihood... |
| genericrepeatfinder |
1.0.2 |
|
dev |
GPLv3 |
X | X | | | Generic Repeat Finder (GRF). |
| genesplicer |
1.0 |
|
|
OSI |
X | | | | GeneSplicer : A computational method for splice site prediction |
| genewalk |
1.6.3 |
doc |
dev |
BSD-2-Clause |
| | | X | Determine gene function based on network embeddings. |
| genform |
r8 |
|
|
GPL-2.0-only |
X | X | | | Generation of molecular formulas by high-resolution MS and MS/MS data |
| genie |
0.7.0 |
|
|
MIT |
X | X | | | A toolkit for working with next-generation sequencing data |
| genin2 |
2.0.1 |
|
|
AGPL-3.0 |
| | | X | Genin2 is a lightining-fast bioinformatic tool to predict genotypes for... |
| genion |
1.2.3 |
|
|
MIT |
X | X | | | Characterizing gene fusions using long transcriptomics reads |
| genmap |
1.3.0 |
doc |
dev |
BSD-3-Clause |
X | X | | | Ultra-fast computation of genome mappability. |
| genmod |
3.9 |
|
|
MIT |
| | | X | Annotate genetic inheritance models in variant files |
| geno2phenotb |
1.0.1 |
doc |
dev |
LGPL-3.0-only |
| | | X | Prediction of Mycobacterium tuberculosis drug resistance from WGS data |
| genoboo |
0.4.16 |
|
|
AGPL-3.0 |
X | X | | | A collaborative notebook for comparative genomics (active fork of GeneNoteBook) |
| genodsp |
0.0.10 |
|
|
GPL-3.0-only |
X | | | | General workbench for processing signals along genomic (chromosomal) intervals |
| genoflu |
1.06 |
|
dev |
GPL-3.0-or-later |
| | | X | Influenza data pipeline to automate genotyping assignment. |
| genologics |
0.4.1 |
|
|
GNU |
X | X | | X | Python interface to the GenoLogics LIMS (Laboratory Information... |
| genomad |
1.11.0 |
doc |
dev |
BSD-4-Clause |
| | | X | Identification of mobile genetic elements. |
| genome_updater |
0.6.4 |
|
|
MIT |
| | | X | genome_updater: bash script to download/update snapshots of refseq/genbank |
| genomebaser |
0.1.2 |
|
|
ECL |
X | | | | GenomeBaser manages complete (bacterial) genomes from NCBI |
| genomeconstellation |
0.21.1 |
|
|
BSD |
X | X | | | Fast, accurate and versatile k-mer based classification system |
| genomedata |
1.7.3 |
doc |
dev |
GPL-2.0 |
X | X | | | Tools for accessing large amounts of genomic data |
| genomelake |
0.1.4 |
|
|
BSD |
X | X | | | Simple and efficient random access to genomic data for deep learning models. |
| genomepy |
0.16.1 |
doc |
|
MIT |
X | X | | X | Install and use genomes & gene annotations the easy way! |
| genomescope2 |
2.0.1 |
|
|
Apache-2.0 |
| | | X | Reference-free profiling of polyploid genomes |
| genomestrip |
2.00.1833 |
|
|
custom |
X | X | | X | Genome STRiP (Genome STRucture In Populations) is a suite of tools for... |
| genometester4 |
4.0 |
|
|
GPL3 |
X | X | | | A toolkit for performing set operations - union, intersection and... |
| genomethreader |
1.7.1 |
|
dev |
ISC |
X | | | | GenomeThreader is a software tool to compute gene structure... |
| genometools |
1.2.1 |
|
|
GNU |
X | X | | | None |
| genometools-genometools |
1.6.5 |
doc |
dev |
BSD |
X | X | | | GenomeTools genome analysis system. |
| genometreetk |
0.1.6 |
|
|
GPL3 |
| | | X | The genome tree toolkit is a collection of methods for working with... |
| genomic_address_service |
0.1.5 |
|
dev |
Apache-2.0 |
| | | X | Genomic Address Service: De novo clustering and cluster address assignment |
| genomic_regions |
0.0.10 |
doc |
dev |
MIT |
| | | X | Consistently handle genomic regions |
| genomicassertions |
0.2.5 |
|
|
MIT |
X | X | | X | A package to test common files in genomics (.vcf.gz, .bam) |
| genomicconsensus |
2.3.3 |
|
|
BSD-3-Clause-Clear |
X | X | | X | PacBio genomic consensus and variant caller for RSII and Sequel |
| genomics-data-index |
0.9.2 |
|
|
Apache-2.0 |
| | | X | Indexes genomics data (nucleotide variants, kmers, MLST) for fast... |
| genonets |
2.0 |
|
|
MIT |
X | X | | X | Framework for creating and analyzing genotype networks from data. |
| genotyphi |
2.0 |
|
|
GPL3 |
| | | X | Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped... |
| genrich |
0.6.1 |
|
|
MIT |
X | X | | | Detecting sites of genomic enrichment. |
| gentle |
1.9.5.alpha1 |
|
dev |
GPL-2.0-or-later |
X | X | | | Software suite for DNA cloning |
| genview |
0.2 |
|
|
GPLv3.0 |
| | | X | Gene-centric visualization tool for genomic sequences |
| geodl |
1.0b5.1 |
|
|
GPL-3-0 |
X | X | | X | Download FASTQ files from GEO-NCBI and ENA with ease |
| geofetch |
0.12.7 |
doc |
|
BSD-2-Clause |
| | | X | Downloads data and metadata from GEO and SRA and creates standard PEPs. |
| geomloss |
0.2.6 |
|
|
MIT |
| | | X | Geometric loss functions between point clouds, images and volumes. |
| geosketch |
1.3 |
|
|
MIT |
| | | X | Geometry-preserving random sampling. |
| gepard |
2.1.0 |
|
dev |
MIT |
| | | X | Genome Pair Rapid Dotter (gepard). |
| gerp |
2.1 |
|
|
GNU |
X | X | | | GERP identifies constrained elements in multiple alignments by... |
| get_fasta_info |
2.5.0 |
|
|
MIT |
X | X | | | get_FAST{A,Q}_info - Get fast info on fasta and fastq files |
| get_homologues |
3.7.2 |
|
|
GPL-3.0-or-later |
X | | | X | A versatile software package for pan-genome analysis, including... |
| get_mnv |
1.0.0 |
doc |
dev |
GPL-3.0-or-later |
X | X | | | Tool to identify Multi-Nucleotide Variants (MNVs) in genomic sequences. |
| get_orfs |
1.1.0 |
|
dev |
MIT |
X | | | | Fast extraction of ORFs in all possible translation tables |
| get_pangenes |
20250123 |
|
|
Apache-2.0 |
| | | X | A versatile software package for calling pangenes from whole genome alignments |
| getorganelle |
1.7.7.1 |
doc |
dev |
GPL-3.0-or-later |
| | | X | Get organelle genomes from genome skimming data |
| gevent |
1.1rc4 |
|
|
MIT |
X | X | | | Coroutine-based network library |
| gfa1 |
0.53.alpha |
|
|
GPL3 |
X | X | | | gfa1 toolkit |
| gfaffix |
0.2.0 |
|
dev |
MIT |
X | X | | | GFAffix identifies and collapses walk-preserving shared affixes in... |
| gfainject |
0.2.0 |
|
dev |
MIT |
X | X | | | Inject alignment into pangenome graphs |
| gfapy |
1.2.3 |
|
|
ISC |
X | X | | X | Library for handling data in the GFA1 and GFA2 formats |
| gfastats |
1.3.10 |
|
|
MIT |
X | X | | | The swiss army knife for genome assembly |
| gfatools |
0.5 |
|
|
Unknown |
X | X | | | Tools for manipulating sequence graphs in the GFA and rGFA formats |
| gff2bed |
1.0.3 |
|
|
MIT |
| | | X | Convert GFF3-formatted data to BED format |
| gff3sort |
0.1.a1a2bc9 |
|
|
GNU |
X | X | | X | A Perl Script to sort gff3 files and produce suitable results for tabix tools |
| gff3toddbj |
0.4.0 |
|
|
GPL-3.0-only |
| | | X | Create a DDBJ annotation file from GFF3 and FASTA files |
| gff3toembl |
1.1.4 |
|
|
GNU |
X | X | | X | Submitting annotated genomes to EMBL is a very difficult and time... |
| gffcompare |
0.12.6 |
|
|
Artistic |
X | X | | | GffCompare by Geo Pertea |
| gfflu |
0.0.2 |
|
|
MIT |
| | | X | Annotate Influenza A virus gene segment sequences and output GFF3 files. |
| gffmunger |
0.1.3 |
|
|
GPL-3.0 |
| | | X | Munges GFF3 files exported from Chado database to make them suitable... |
| gffpandas |
1.2.2 |
doc |
|
MIT |
| | | X | Parse GFF3 into Pandas dataframes |
| gffread |
0.12.7 |
doc |
dev |
MIT |
X | X | | | GFF/GTF utility providing format conversions, region filtering, FASTA... |
| gfftk |
24.10.30 |
|
dev |
BSD-2-Clause |
| | | X | GFFtk: genome annotation GFF3 tool kit |
| gffutils |
0.13 |
doc |
dev |
MIT |
X | X | | X | Work with GFF and GTF files in a flexible database framework |
| gfinisher |
1.4 |
|
|
Unknown |
X | X | | | GFinisher is an application tools for refinement and finalization of... |
| gfmix |
1.0.2 |
|
|
GNU |
X | X | | | Accelerated Estimation of Frequency Classes in Site-heterogeneous... |
| gfold |
1.1.4 |
|
|
MIT |
X | | | | Find differentially expressed genes from RNA-seq data with few... |
| gfviewer |
1.0.4 |
|
|
MIT |
| | | X | A bioinformatics tool for visualizing the localization of multi-gene... |
| ggcaller |
1.3.7 |
|
|
MIT |
X | X | | | A de Bruijn graph-based gene-caller and pangenome analysis tool |
| ggcat |
1.1.0 |
|
dev |
MIT |
X | X | | | Compacted and colored de Bruijn graph construction and querying. |
| ggd |
1.1.3 |
|
|
MIT |
| | | X | GoGetData (GGD) is a genomic data managment system. It provide simple... |
| gget |
0.29.0 |
doc |
dev |
BSD-2-Clause |
| | | X | gget enables efficient querying of genomic databases. |
| ggplot |
0.6.8 |
|
|
BSD |
X | X | | | An extremely un-pythonic package for doing exactly what ggplot2 does |
| ghc |
6.8.3 |
|
|
BSD |
X | | | | None |
| ghm |
3.1 |
|
|
INDIVIDUAL |
X | | | | A MOD-score analysis in which parametric LOD scores are maximized over... |
| ghmm |
0.9 |
|
|
GPL2 |
X | X | | | General Hidden Markov Model library (GHMM) is a freely available C... |
| ghost-tree |
0.2.2 |
|
|
BSD |
| | | X | ghost-tree is a bioinformatics tool that combines sequence data from... |
| ghostscript |
9.18 |
|
|
Affero |
X | X | | | An interpreter for the PostScript language and for PDF. |
| ghostx |
1.3.7 |
|
|
BSD-2-Clause |
X | X | | | GHOSTX is a homology search tool which can detect remote homologues... |
| ghostz |
1.0.2 |
|
|
BSD-2-Clause |
X | X | | | GHOSTZ is a highly efficient remote homologue detection tool |
| gia |
0.2.23 |
|
|
MIT |
X | X | | | Genomic Interval Arithmetic (gia) |
| giatools |
0.3.2 |
|
dev |
MIT |
| | | X | Tools required for Galaxy Image Analysis |
| gifrop |
0.0.9 |
|
|
GPL2 |
| | | X | Identify, classify, and cluster genomic islands from roary pangenomes |
| gimbleprep |
0.0.2 |
doc |
|
GPL-3.0-or-later |
| | | X | Preprocess fasta, bam and vcf files ready to be used by gimble |
| gimmemotifs |
0.18.0 |
|
|
MIT |
X | X | | | Motif prediction pipeline and various motif-related tools |
| gimmemotifs-minimal |
0.18.0 |
|
|
MIT |
X | X | | | Motif prediction pipeline and various motif-related tools |
| ginpipepy |
1.0.0 |
|
dev |
GPLv3 |
| | | X | Package for temporal binning of dated sequences in BAM format and fast... |
| ginpiper |
1.0.0 |
|
dev |
GPLv3 |
| | | X | Package for smooth curve estimation, R_e computation and plotting. |
| glean-gene |
1.0.1 |
|
dev |
Artistic-1.0-Perl |
| | | X | GLEAN is an unsupervised learning system to integrate disparate sources... |
| glimmer |
3.02 |
|
|
Custom |
X | X | | | Glimmer is a system for finding genes in microbial DNA |
| glimmerhmm |
3.0.4 |
doc |
|
Artistic |
X | X | | | GlimmerHMM is a gene finder based on a Generalized Hidden Markov Model (GHMM). |
| glimpse-bio |
2.0.1 |
|
|
MIT |
X | X | | | GLIMPSE is a phasing and imputation method for large-scale low-coverage... |
| glnexus |
1.4.1 |
|
|
Apache |
X | | | | scalable gVCF merging and joint variant calling for population... |
| glob2 |
0.4.1 |
|
|
BSD |
X | X | | | Version of the glob module that can capture patterns and supports... |
| gloome |
VR01.266 |
|
|
GNU |
X | | | | GLOOME is a program that analyzes the evolution of phyletic patterns... |
| glpk |
4.57 |
|
|
GNU |
X | X | | | GNU Linear Programming Kit |
| gmap |
2024.11.20 |
doc |
dev |
Apache-2.0 |
X | X | | | Genomic mapping and alignment program for mRNA and EST sequences. |
| gmap-fusion |
0.4.0 |
|
|
BSD-3-Clause |
X | X | | X | GMAP-fusion is a utility for identifying candidate fusion transcripts... |
| gmcloser |
1.6.2 |
|
|
GPL |
| | | X | GMcloser fills and closes the gaps present in scaffold assemblies,... |
| gmgc-mapper |
0.2.0 |
|
|
MIT |
| | | X | Map genes and genome to the Global Microbial Gene Catalog (GMGC) |
| gmm-demux |
0.2.2.3 |
|
dev |
MIT |
| | | X | GMM-Demux is a Gaussian-Mixture-Model-based software for processing... |
| gmsc-mapper |
0.1.0 |
|
|
MIT |
| | | X | GMSC-mapper is a command line tool to query the Global Microbial smORFs... |
| gmtk |
1.4.4 |
|
|
OSL-3.0 |
X | X | | | A publicly available toolkit for rapidly prototyping statistical models... |
| gmwi2 |
1.6 |
|
|
MIT |
| | | X | Enhanced Health Status Prediction from Gut Microbiome Taxonomic Profiles |
| gnali |
1.1.0 |
|
dev |
Apache-2.0 |
X | | | X | gNALI (gene nonessentiality and loss-of-function identifier) is a tool... |
| gndiff |
0.3.0 |
|
|
MIT |
X | X | | | GNdiff compares scientific names from two files |
| gneiss |
0.4.6 |
|
|
BSD |
| | | X | Compositional data analysis tools and visualizations |
| gnomic |
1.0.1 |
|
|
Apache |
| | | X | A grammar for describing microbial genotypes and phenotypes |
| gnparser |
1.11.4 |
|
dev |
MIT |
X | X | | | GNparser normalises scientific names and extracts their semantic elements |
| gnu-getopt |
1.1.6 |
|
|
GPLv2 |
| X | | | Command-line option parsing library |
| gnu-wget |
1.18 |
|
|
GPLv3 |
X | X | | | Retrieve files using HTTP, HTTPS and FTP |
| gnuplot |
5.0.4 |
|
|
Gnuplot |
X | X | | | Gnuplot, plotting from command line |
| gnuplot-py |
1.8 |
|
|
LGPL |
X | X | | | A Python interface to the gnuplot plotting program. |
| gnuvid |
2.4 |
|
dev |
GPLv3 |
| | | X | GNUVID is Gene Novelty Unit-based Virus IDentification for SARS-CoV-2 |
| go-figure |
1.0.2 |
|
dev |
GPL-3.0-or-later |
| | | X | GO-Figure! offers a simple solution for command-line plotting of... |
| goalign |
0.3.7 |
|
|
GPL-2.0 |
X | X | | | goalign is a set of command line tools to manipulate multiple alignments |
| goat |
0.2.5 |
|
|
MIT |
X | X | | | Query metadata for any taxon across the tree of life. |
| goatools |
1.2.3 |
|
|
BSD-2-Clause |
X | X | | X | Python scripts to find enrichment of GO terms |
| goblin |
1.0.0 |
|
|
MIT |
| | | X | Generate trusted prOteins to supplement BacteriaL annotatIoN |
| gocr |
0.50 |
|
|
GPL |
X | X | | | GOCR is an OCR (Optical Character Recognition) program |
| godmd |
1.0.0 |
|
|
Apache |
X | X | | | GOdMD Conformational Transitions with discrete Molecular Dynamics |
| goenrichment |
2.0.1 |
|
|
Apache |
| | | X | GOEnrichment analyses a set of gene products for GO term enrichment |
| goetia |
0.14 |
|
|
MIT |
X | | | | streaming de Bruijn graph compaction and sketching. |
| gofasta |
1.2.3 |
|
|
MIT |
X | X | | | Genomic epidemiology utilities for short genome alignments |
| gogstools |
0.1.2 |
doc |
dev |
GNU |
| | | X | GenOuest tools for manipulating Official Gene Sets |
| goldrush |
1.2.2 |
|
|
GPL-3.0 |
X | X | | | Linear-time de novo long read assembler, from the Bioinformatics Technology Lab |
| goleft |
0.2.6 |
|
|
MIT |
X | X | | | goleft is a collection of bioinformatics tools distributed under MIT... |
| google-api-python-client |
1.4.2 |
|
|
Apache |
X | X | | | None |
| google-cloud-sdk |
166.0.0 |
|
|
Apache |
X | X | | | Command-line interface for Google Cloud Platform products and services |
| google-sparsehash |
2.0.3 |
|
|
BSD |
X | X | | | None |
| gopeaks |
1.0.0 |
|
dev |
MIT |
X | X | | | Peak caller for CUT&TAG data |
| gor_pyspark |
3.22.6 |
|
|
Apache |
| | | X | Python helper function for gor-spark |
| gorpipe |
4.5.0 |
|
|
AGPL |
| | | X | A query tool for working with sequence data based on a Genomic Ordered... |
| goslimmer |
1.0 |
|
|
Apache |
| | | X | GOSlimmer transforms GO annotations to a slimmed version of GO |
| gothresher |
1.0.29 |
|
|
GPL-3.0-only |
| | | X | GOThresher: a program to remove annotation biases from protein function... |
| gotohscan |
1.3 |
|
|
GPL |
X | | | | a search tool that finds shorter sequences (usually genes) in large... |
| gotree |
0.4.5 |
|
|
GPL-2.0 |
X | X | | | gotree is a set of command line tools to manipulate phylogenetic trees |
| gottcha |
1.0 |
|
|
GNU |
X | | | | Genomic Origin Through Taxonomic CHAllenge (GOTTCHA) |
| gottcha2 |
2.1.8.11 |
doc |
dev |
BSD-3-Clause |
| | | X | Genomic Origin Through Taxonomic CHAllenge (GOTTCHA) v2. |
| gpatch |
0.3.6 |
|
|
MIT |
| | | X | Starting with alignments of contigs to a reference genome, produce a... |
| gplas |
0.6.1 |
|
|
GPL3.0 |
| | | X | gplas is a tool to bin plasmid-predicted contigs based on sequence... |
| gprofiler-official |
1.0.0 |
|
|
BSD |
X | X | | X | Functional enrichment analysis and more via the g:Profiler toolkit |
| gqlib |
2.14.4 |
|
dev |
MIT |
| | | X | A gene quantification library. |
| gqt |
1.1.3 |
|
|
MIT |
X | X | | | GQT is a genotype query interface. |
| grabix |
0.1.8 |
|
|
MIT |
X | X | | | a wee tool for random access into BGZF files. |
| grafimo |
1.1.6 |
|
|
MIT |
X | | | | GRAFIMO, GRAph-based Finding of Indivividual Motif Occurrences |
| graftm |
0.15.1 |
|
|
GPL3+ |
X | X | | X | GraftM is a pipeline used for identifying and classifying marker gene... |
| grampa |
1.4.1 |
doc |
dev |
GPL-3.0-only |
| | | X | GRAMPA is a program to identify and place polyploidy events on a... |
| grapetree |
2.1 |
|
|
GNU |
| | | X | Web interface of GrapeTree, which is a program for phylogenetic analysis. |
| graph-boink |
0.11 |
|
|
MIT |
X | | | | streaming de Bruijn graph compaction and sketching. |
| graph2pro-var |
1.0.0 |
|
|
GPL-3.0 |
X | | | | meta-proteogenomic identification from mass spec and... |
| graph_embed |
2.4 |
doc |
dev |
MIT |
X | X | | X | Compute a 2D embedding of a data matrix given supervised class information. |
| graphaligner |
1.0.20 |
|
|
MIT |
X | X | | | Sequence to graph aligner for long reads |
| graphanalyzer |
1.6.0 |
|
|
GPL-3.0-or-later |
| | | X | A tool to automatically interpret the outputs generated by vConTACT2... |
| graphbin |
1.7.4 |
doc |
dev |
BSD-3 |
| | | X | GraphBin: Refined binning of metagenomic contigs using assembly graphs |
| graphbin2 |
1.3.3 |
doc |
dev |
BSD-3 |
| | | X | GraphBin2: Refined and Overlapped Binning of Metagenomic Contigs Using... |
| graphclust-wrappers |
0.6.0 |
|
|
GPLv3 |
X | | | X | The set of individual perl wrappers extracted from GraphClust pipeline |
| graphembed |
0.1.4 |
|
dev |
MIT |
X | | | | Efficient and Robust Graph Embedding via High-Order Proximity... |
| graphicsmagick |
1.3.26 |
|
|
MIT |
X | X | | | GraphicsMagick is the swiss army knife of image processing |
| graphlan |
1.1.3 |
|
|
MIT |
X | X | | X | GraPhlAn is a software tool for producing high-quality circular... |
| graphlite |
1.0.5 |
|
|
MIT |
X | X | | X | embedded graph datastore |
| graphmap |
0.6.4 |
doc |
dev |
MIT |
X | X | | | A highly sensitive and accurate mapper for long, error-prone reads. |
| graphmb |
0.2.5 |
|
|
MIT |
| | | X | GraphMB is a Metagenomic Binner developed for long-read assemblies,... |
| graphprot |
1.1.7 |
|
|
MIT |
X | | | | GraphProt is a tool for modelling binding preferences of RNA-binding... |
| graphtyper |
2.7.7 |
|
|
MIT |
X | | | | Population-scale genotyping using pangenome graphs |
| greenhill |
1.1.0 |
|
|
GPL-3.0 |
X | | | | A de novo chromosomal-level scaffolding and phasing tool using Hi-C |
| grenedalf |
0.6.3 |
doc |
dev |
GPL-3.0-only |
X | | | | Toolkit for Population Genetic Statistics from Pool-Sequenced Samples,... |
| grep |
3.4 |
|
|
GPL |
X | X | | | Grep searches one or more input files for lines containing a match to a... |
| grepq |
1.5.2 |
doc |
dev |
MIT |
X | X | | | Quickly filter FASTQ files. |
| gretel |
0.0.94 |
|
|
MIT |
X | X | | X | An algorithm for recovering haplotypes from metagenomes |
| gretl |
0.1.1 |
|
dev |
MIT |
X | X | | | gretl is a tool to compute a range of statistics on variation graphs in... |
| grid |
1.3 |
|
|
MIT |
X | | | X | Growth Rate Index (GRiD) measures bacterial growth rate from reference... |
| gridss |
2.13.2 |
|
|
GPL-3.0-only |
X | | | X | GRIDSS: the Genomic Rearrangement IDentification Software Suite |
| grimer |
1.1.0 |
|
|
MIT |
| | | X | GRIMER performs analysis of microbiome studies and generates a portable... |
| gromacs |
2021.3 |
|
|
LGPL-2.1-or-later |
X | X | | | GROMACS is a versatile package to perform molecular dynamics. |
| gromacs_mpi |
2021.1 |
|
|
LGPL-2.1-or-later |
X | X | | | GROMACS is a versatile package to perform molecular dynamics. |
| gromacs_py |
2.0.3 |
doc |
dev |
GPL-2.0-only |
| | | X | Gromacs_py is a python library allowing a simplified use of the gromacs... |
| gromacswrapper |
0.8.2 |
doc |
dev |
GPL-3.0 |
| | | X | GromacsWrapper wraps system calls to GROMACS tools into thin Python classes. |
| groopm |
0.3.4 |
|
|
LGPL-3.0 |
X | | | | Metagenomic binning suite |
| groot |
1.1.2 |
|
|
MIT |
X | X | | | A tool for resistome profiling of metagenomic samples. |
| group_humann2_uniref_abundances_to_go |
1.3.0 |
|
|
Apache |
X | | | X | Group abundances of UniRef50 gene families obtained with HUMAnN2 to... |
| grz-cli |
0.1.4 |
|
|
MIT |
| | | X | Tool for validation, encryption and upload of MV submissions to GDCs. |
| gs-tama |
1.0.3 |
|
|
GPL-3.0 |
| | | X | Gene-Switch Transcriptome Annotation by Modular Algorithms |
| gsalign |
1.0.22 |
|
|
MIT |
X | X | | | GSAlign: an ultra-fast sequence alignment tool |
| gsea |
4.3.2 |
|
|
BSD-3-Clause |
| | | X | Gene Set Enrichment Analysis (GSEA) |
| gseapy |
1.1.6 |
doc |
dev |
BSD-3-Clause |
X | X | | X | Gene Set Enrichment Analysis in Python. |
| gsearch |
0.2.4 |
|
|
MIT |
X | X | | | gsearch is an ultra-fast and scalable microbial genome search program... |
| gsmap |
1.71.2 |
doc |
dev |
MIT |
| | | X | gsMap (genetically informed spatial mapping of cells for complex traits) |
| gsort |
0.1.4 |
|
|
MIT |
X | X | | | sort genomic files according to a genomefile |
| gtdb_to_taxdump |
0.1.9 |
|
|
MIT |
| | | X | GTDB database utility scripts |
| gtdbtk |
2.4.0 |
|
|
GNU |
X | | | X | A toolkit for assigning objective taxonomic classifications to... |
| gtf_to_genes |
1.40 |
|
|
MIT |
X | X | | X | Fast GTF parser |
| gtfparse |
2.5.0 |
|
dev |
Apache-2.0 |
X | X | | X | GTF Parsing |
| gtfsort |
0.2.2 |
|
|
MIT |
X | X | | | A chr/pos/feature GTF sorter that uses a lexicographically-based index... |
| gtftools |
0.9.0 |
doc |
dev |
MIT |
| | | X | gtftools provides a set of functions to compute or extract various... |
| gtotree |
1.8.12 |
doc |
dev |
GPL3 |
X | X | | | GToTree is a user-friendly workflow for phylogenomics. |
| gubbins |
3.4 |
|
|
GPL-2.0 |
X | X | | | Rapid phylogenetic analysis of large samples of recombinant bacterial... |
| guessmylt |
0.2.5 |
|
dev |
GPLv3 |
| | | X | Software to guess the RNA-Seq library type. |
| guide-counter |
0.1.3 |
|
|
MIT |
X | X | | | Fast and accurate guide counting for CRISPR screens |
| guidemaker |
0.4.2 |
doc |
dev |
CC0-1.0 |
| | | X | GuideMaker: Software to design gRNAs pools in non-model genomes and... |
| guidescan |
2.2.1 |
|
|
Unknown |
X | X | | | GuideScan is a tool for genome-wide CRISPR guide RNA (gRNA) design and... |
| gum |
2.0.2 |
|
dev |
MIT |
X | X | | | A header-only library for representation of sequence graphs |
| gunc |
1.0.6 |
doc |
dev |
GNU |
| | | X | Python package for detection of chimerism and contamination in... |
| gustaf |
1.0.8 |
|
|
https://github. |
X | X | | | Gustaf is a tool primarily designed for multi-split mapping of sequencing reads. |
| gvcf-regions |
2016.06.23 |
|
|
GPLv3 |
X | X | | X | Convert a gVCF file in multiple formats into a BED file of callable regions |
| gvcf2bed |
0.3.1 |
doc |
dev |
MIT |
| | | X | Convert gVCF into BED |
| gvcf2coverage |
0.1 |
|
|
MIT |
X | X | | | Coverage extractor from gVCF files. |
| gvcfgenotyper |
2019.02.26 |
|
|
Apache |
X | X | | | A utility for merging and genotyping Illumina-style GVCFs. |
| gvcftools |
0.17.0 |
|
|
MIT |
X | X | | | a set of utilities to help create and analyze Genome VCF (gVCF) files. |
| gw |
1.1.4 |
|
|
MIT |
X | X | | | View genomic sequencing data and vcf files |
| gwama |
2.2.2 |
|
|
BSD-3-clause |
X | X | | | Genome-Wide Association Meta Analysis |
| gxf2bed |
0.2.5 |
|
|
MIT |
X | X | | | Fastest GTF/GFF-to-BED converter chilling around |
| gxf2chrom |
0.1.0 |
|
|
MIT |
X | X | | | Everything in .chrom from GTF/GFF |
| gxformat2 |
0.20.0 |
|
dev |
MIT |
X | X | | X | Galaxy Workflow Format 2 Descriptions |
| gzrt |
0.9.1 |
doc |
dev |
GPL-2.0-only |
X | X | | | Unofficial build of the gzip Recovery Toolkit aka gzrecover. |
| h5sparse |
0.1.0 |
doc |
|
MIT |
| | | X | Scipy sparse matrix in HDF5. |
| hackgap |
1.0.1 |
|
dev |
MIT |
| | | X | hackgap (hash-based counting of k-mers with gaps) provides a fast... |
| haddock_biobb |
3.0.7 |
|
|
Apache |
X | X | | X | HADDOCK3 is the next generation integrative modelling software in the... |
| hafez |
1.0.4 |
doc |
dev |
GPL-3.0-or-later |
| | | X | A tool for identifying active prophage elements through read mapping |
| hail |
0.2.61 |
|
dev |
MIT |
X | X | | | Hail is Python-based data analysis tool for working with genomic data. |
| hairsplitter |
1.9.10 |
|
|
GPL-3.0-or-later |
X | X | | | Recovers collapsed haplotypes from a draft assembly and long reads |
| halfdeep |
0.1.0 |
|
|
BSD-3-Clause |
| | | X | Automated detection of intervals covered at half depth by sequenced reads. |
| hall-lab-svtools |
0.1.1 |
|
|
|
X | | | | None |
| halla |
0.8.17 |
|
|
MIT |
X | X | | | HAllA: Hierarchically All-against-All Association Testing. |
| hamip |
0.0.3.2 |
|
|
License |
| | | X | HaMiP is A scalable, accurate, and efficient solution for... |
| hamroaster |
2.0 |
|
|
CC0 |
| | | X | An analysis pipeline to compare the output of different AMR detection... |
| hamronization |
1.1.4 |
doc |
dev |
GNU |
| | | X | Tool to convert and summarize AMR gene detection outputs using the... |
| handyreadgenotyper |
0.1.24 |
doc |
dev |
GPL-3.0-only |
| | | X | Tool for training model and classifying reads from environmental ONT... |
| hanselx |
0.0.92 |
|
|
MIT |
X | X | | X | A graph-inspired data structure for determining likely chains of... |
| hap-ibd |
1.0.rev20May22.818 |
doc |
|
Apache-2.0 |
| | | X | Hap-ibd Detects identity-by-descent (IBD) segments and... |
| hap.py |
0.3.15 |
|
|
BSD-2-Clause |
X | | | | Haplotype VCF comparison tools |
| hapbin |
1.3.0 |
|
|
GPLv3 |
X | | | | hapbin is a collection of tools for efficiently calculating Extended... |
| hapcut2 |
1.3.4 |
|
dev |
BSD-2-Clause |
X | X | | | Tools for haplotype assembly from sequence data |
| hapflk |
1.3.0 |
|
|
GPLv3 |
X | X | | | hapflk is a software implementing the hapFLK and FLK tests for the... |
| haphpipe |
1.0.3 |
doc |
dev |
GPL |
| | | X | HAplotype and PHylodynamics pipeline for viral assembly, population... |
| haplink |
1.1.0 |
|
|
MIT |
X | | | | Viral haplotype calling via linkage disequilibrium |
| haplocheck |
1.3.3 |
doc |
dev |
MIT |
| | | X | Detects in-sample contamination in mtDNA or WGS sequencing studies by... |
| haploclique |
1.3.1 |
|
|
GPLv3+ |
X | X | | | Viral quasispecies assembly via maximal clique finding. A method to... |
| haploconduct |
0.2.1 |
|
|
GPL3 |
X | | | | HaploConduct is a package designed for reconstruction of individual... |
| haploflow |
1.0 |
|
|
Apache-2.0 |
X | X | | | Strain-aware viral genome assembler for short read sequence data |
| haplogrep |
2.4.0 |
doc |
dev |
MIT |
| | | X | A tool for mtDNA haplogroup classification. |
| haplogrep3 |
3.2.2 |
doc |
dev |
MIT |
| | | X | A tool for mtDNA haplogroup classification. |
| haplomap |
0.1.2 |
|
dev |
MIT |
X | X | | | Haplotype-based computational genetic mapping. |
| haplotaglr |
1.1.10 |
|
|
MIT |
| | | X | Haplotagging individual long reads using known haplotype information. |
| haplotype-lso |
0.4.4 |
|
|
MIT |
| | | X | Haplotype Candidatus Liberibacter solanacearum (Lso) samples from... |
| haploview |
4.2 |
|
|
MIT |
| | | X | Haploview is designed to simplify and expedite the process of haplotype... |
| hapog |
1.3.8 |
doc |
dev |
CECILL-2.1 |
X | X | | | Haplotype-Aware Polishing of Genomes |
| happer |
0.1.1 |
|
dev |
BSD |
| | | X | Minimal Python library for generating haplotype sequences. |
| happy-python |
0.2.1rc0 |
doc |
|
MIT |
| | | X | Haploidy and Size Completeness Estimation with Python |
| haproh |
0.64 |
|
|
GPL-3.0 |
X | X | | | Identify runs of homozygosity (hapROH) and contamination (hapCon) in... |
| hapsolo |
2021.10.09 |
|
dev |
GPL-2.0 |
| | | X | An optimization approach for removing secondary haplotigs during... |
| haptools |
0.5.0 |
doc |
dev |
MIT |
| | | X | Ancestry and haplotype aware simulation of genotypes and phenotypes for... |
| hardklor |
2.3.2 |
|
|
Apache |
X | | | | Analyze mass spectra |
| harmony-pytorch |
0.1.8 |
|
|
BSD-3-Clause |
| | | X | This is a Pytorch implementation of Harmony algorithm on single-cell... |
| harmonypy |
0.0.10 |
|
|
GPL-3.0-or-later |
| | | X | A data integration algorithm. |
| harpy |
1.16.3 |
doc |
dev |
GPL-3.0-or-later |
X | | | X | Process raw haplotagging data, from raw sequences to phased haplotypes. |
| harvest-variants |
1.1.0 |
|
|
MIT |
| | | X | Harvest Variants is a pipeline for variant calling on SARS-CoV-2 samples |
| harvesttools |
1.2 |
|
|
custom; |
X | X | | | HarvestTools is a part of the Harvest software suite and provides file... |
| haslr |
0.8a1 |
|
|
GPL3 |
X | | | | A fast tool for hybrid genome assembly of long and short reads |
| hat-phasing |
0.1.8 |
|
|
GPL-3.0-only |
| | | X | HAT: Haplotype assembly tool that use both long and short reads to... |
| hatchet |
2.1.2 |
doc |
dev |
BSD-3-Clause |
X | X | | | A package to infer allele and clone-specific copy-number aberrations (CNAs). |
| haystac |
0.4.12 |
doc |
|
MIT |
| | | X | Species identification pipeline for both single species and metagenomic samples. |
| haystack_bio |
0.5.5 |
|
|
GPLv3 |
X | X | | X | Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline |
| hca |
7.0.1 |
|
|
Apache |
| | | X | Human Cell Atlas Data Storage System Command Line Interface. This... |
| hca-matrix-downloader |
0.0.4 |
|
|
MIT |
| | | X | Python client for the HCA DCP matrix service |
| hclust2 |
1.0.0 |
|
|
License |
X | X | | X | hclust2 is a handy tool for plotting heat-maps |
| hcluster_sg |
0.5.1 |
|
|
GPLv2 |
X | X | | | A tool for hierarchically clustering on a sparse graph |
| hdf5_mpich |
1.14.5 |
|
|
BSD-3-Clause |
X | | | | HDF5 - Hierarchical Data Format 5 |
| hecatomb |
1.3.3 |
doc |
dev |
MIT |
| | | X | Hecatomb: and end-to-end platform for viral metagenomics |
| heinz |
2.0.1 |
|
|
MIT |
X | | | | The algorithm for identification of the optimal scoring subnetwork. |
| heliano |
1.2.1 |
|
dev |
GNU |
| | | X | HELIANO: A fast and accurate tool for detection of Helitron-like elements |
| helitronscanner |
1.0 |
|
|
GPL-3.0-or-later |
| | | X | HelitronScanner uncovers a large overlooked cache of Helitron... |
| helperlibs |
0.2.1 |
|
|
GPL-3.0 |
X | X | | X | A collection of bioinformatics-related helper functions |
| hera |
1.1 |
|
|
MIT |
X | X | | | hera is a bioinformatics tool that helps analyze RNA-seq data,... |
| hesslab-gambit |
0.5.1 |
doc |
|
AGPL-3.0-or-later |
X | X | | | IMPORTANT: This recipe is out of date. Use "gambit" instead:... |
| hg-color |
1.1.1 |
|
|
GNU |
X | | | | HG-CoLoR (Hybrid Graph for the error Correction of Long Reads) is a... |
| hgtools |
8.2.1 |
|
|
GNU |
X | X | | X | Classes and setuptools plugin for Mercurial and Git repositories |
| hgvs |
1.5.4 |
doc |
|
Apache-2.0 |
| | | X | HGVS Parser, Formatter, Mapper, Validator |
| hhsuite |
3.3.0 |
doc |
|
GPLv3 |
X | X | | | HH-suite3 for fast remote homology detection and deep protein annotation |
| hi-corrector |
1.2 |
|
|
BSD-3-Clause |
X | X | | | Remove biases from chromatin contact matrices generated by genome-wide... |
| hic-straw |
1.3.1 |
doc |
dev |
MIT |
X | X | | | Straw bound with pybind11. |
| hic2cool |
1.0.1 |
|
|
MIT |
X | X | | X | A converter between .hic files (from juicer) and single-resolution or... |
| hicap |
1.0.4 |
doc |
dev |
GPL-3.0-or-later |
| | | X | In silico typing of the H. influenzae capsule locus |
| hicberg |
1.0.0 |
|
dev |
MIT |
| | | X | Statistical profiling based tool for contact data (Hi-C, ChIA-PET,... |
| hicbrowser |
1.0 |
|
|
GPL3 |
X | X | | | A simple web browser to visualize Hi-C and other genomic tracks... |
| hicexplorer |
3.7.6 |
doc |
dev |
GPL-3.0-or-later |
X | X | | X | Set of programs to process, analyze and visualize Hi-C and capture Hi-C data |
| hichipper |
0.7.7 |
|
|
BSD |
X | X | | X | Processing HiChIP data into loops. |
| hicmatrix |
17.2 |
|
dev |
GPL-3.0-or-later |
| | | X | Library to manage Hi-C matrices for HiCExplorer and pyGenomeTracks |
| hicstuff |
3.2.4 |
doc |
dev |
BSD-3-Clause |
| | | X | General purpose stuff to generate and handle Hi-C data in its simplest form. |
| hictk |
2.0.2 |
doc |
dev |
MIT |
X | X | | | Blazing fast toolkit to work with .hic and .cool files |
| hictkpy |
1.1.0 |
doc |
dev |
MIT |
X | X | | | Python bindings for hictk: read and write .cool and .hic files directly... |
| hicup |
0.9.2 |
|
|
GPLv3 |
X | X | | X | A tool for mapping and performing quality control on Hi-C data |
| hiddendomains |
3.1 |
|
|
GNU |
X | X | | X | hiddenDomains is a suite of programs used to identify significant... |
| hifiadapterfilt |
3.0.0 |
|
dev |
GPL-3.0-or-later |
| | | X | Convert .bam to .fastq and remove reads with remnant PacBio HiFi... |
| hifiasm |
0.24.0 |
doc |
dev |
MIT |
X | X | | | Haplotype-resolved assembler for accurate Hifi reads. |
| hifiasm_meta |
hamtv0.3.2 |
|
|
MIT |
X | X | | | Metagenome assembler for Hifi reads, based on hifiasm. |
| hificnv |
1.0.1 |
|
|
BSD-3-Clause-Clear |
X | | | | Copy number variant caller and depth visualization utility for PacBio HiFi reads |
| hifieval |
0.4.0 |
|
|
MIT |
| | | X | Evaluate long-read error correction mainly with PacBio High-Fidelity... |
| hifihla |
0.3.1 |
|
|
BSD-3-Clause-Clear |
| | | X | An HLA star-calling tool for PacBio HiFi data types |
| hifive |
1.5.7 |
|
|
MIT |
X | X | | | Python library for normalizing and analyzing HiC and 5C data |
| hiline |
0.2.4 |
|
|
MIT |
X | X | | | HiC alignment and classification pipeline. |
| hilinetojuicer |
0.0.2 |
|
|
MIT |
| | | X | Convert HiLine SAM alignments to Juicer format |
| hilive2 |
2.0 |
|
|
BSD-3-Clause |
X | | | | Tool for real-time read alignment of Illumina sequencing data |
| hint |
2.2.8 |
|
|
MIT |
| | | X | HiNT is a computational method for detecting copy number variations and... |
| hiphase |
1.4.5 |
|
|
BSD-3-Clause-Clear |
X | | | | Small and structural variant phasing tool for PacBio HiFi reads |
| hippunfold |
2.0.0 |
|
|
MIT |
| | | X | This tool aims to automatically model the topological folding structure... |
| hisat2 |
2.2.1 |
doc |
dev |
GPL-3.0 |
X | X | | | Graph-based alignment of next generation sequencing reads to a... |
| hisat2-pipeline |
1.0.8 |
|
dev |
GPL-3.0-or-later |
| | | X | A pipeline to automatically run an RNA-seq analysis using... |
| hitac |
2.2.2 |
|
|
BSD-3-Clause |
| | | X | A hierarchical taxonomic classifier for fungal ITS sequences |
| hitea |
0.1.5 |
|
|
MIT |
| | | X | computational tool to identify trasposable element insertions using Hi-C data |
| hits |
0.4.3 |
|
dev |
GPL-3.0-or-later |
X | X | | | Utilities for processing high-throughput sequencing experiments. |
| hivtrace |
1.5.0 |
|
dev |
MIT |
X | X | | X | HIV TRACE is an application that identifies potential transmission... |
| hla-asm |
1.0.1 |
|
|
GPL |
| | | X | find HLA gene exon coordinates in long read-based assemblies and carry... |
| hla-la |
1.0.4 |
|
|
GPL |
X | | | | HLA typing from short and long reads |
| hlafreq |
0.0.5 |
|
dev |
MIT |
| | | X | Download and combine HLA frequency data from multiple studies. |
| hlama |
3.0.1 |
|
|
MIT |
X | | | | Simple matching of HTS samples based on HLA typing |
| hlaprofiler |
1.0.5 |
|
|
Custom |
X | X | | X | HLAProfiler uses k-mer profiles to predict HLA types from paired-end... |
| hmftools-amber |
4.1.1 |
|
|
GPL-3.0-only |
| | | X | Generates a tumor BAF file for use in PURPLE. |
| hmftools-bam-tools |
1.3 |
|
|
GPL-3.0-only |
| | | X | Rapidly process BAMs for various tasks. |
| hmftools-chord |
2.1.0 |
|
|
GPL-3.0-only |
| | | X | Predict HRD using somatic mutations contexts |
| hmftools-cobalt |
2.0 |
|
|
GPL-3.0-only |
| | | X | Calculate read-depth counts and GC ratios to use in PURPLE. |
| hmftools-cuppa |
2.3.2 |
|
|
GPL-3.0-only |
| | | X | Predict tissue of origin for tumor samples from WGTS data. |
| hmftools-esvee |
1.0.2 |
|
|
GPL-3.0-only |
| | | X | Structural variant caller specialised for breakend-breakpoint calling. |
| hmftools-gripss |
2.4 |
|
|
GPL-3.0-only |
| | | X | GRIPSS applies a set of filtering and post processing steps on GRIDSS... |
| hmftools-isofox |
1.7.1 |
|
|
GPL-3.0-only |
| | | X | Isofox is a tool for counting fragment support for identifying and... |
| hmftools-lilac |
1.6 |
|
|
GPL-3.0-only |
| | | X | LILAC is a WGS tool to determine HLA Class I types. |
| hmftools-linx |
2.0.2 |
|
|
GPL-3.0-only |
| | | X | LINX is an annotation, interpretation and visualisation tool for... |
| hmftools-mark-dups |
1.1.7 |
|
|
GPL-3.0-only |
| | | X | Mark read duplicates and form consenus sequences |
| hmftools-neo |
1.2 |
|
|
GPL-3.0-only |
| | | X | Identification of neoepitope and calculation of allele specific... |
| hmftools-orange |
3.7.1 |
|
|
GNU |
| | | X | ORANGE summarizes the key outputs from all algorithms in the Hartwig suite. |
| hmftools-pave |
1.7.1 |
|
|
GPL-3.0-only |
| | | X | PAVE annotates SNV/MNV/INDEL calls with consequence on corresponding... |
| hmftools-peach |
2.0.0 |
|
|
GPL-3.0-only |
| | | X | Infer haplotypes for interpretation in a pharmacogenomic context |
| hmftools-protect |
2.3 |
|
|
GNU |
| | | X | PROTECT determines the clinical evidence applicable for a particular... |
| hmftools-purple |
4.1 |
|
|
GPL-3.0-only |
| | | X | PURPLE is a purity ploidy estimator for tumor samples. |
| hmftools-redux |
1.1 |
|
|
GPL-3.0-only |
| | | X | Post-processing read alignments to control sequencing errors and biases |
| hmftools-rose |
1.3 |
|
|
GNU |
| | | X | ROSE makes an actionability summary of the clinical relevant (for the... |
| hmftools-sage |
4.0 |
|
|
GPL-3.0-only |
| | | X | SAGE is a somatic SNV, MNV and small INDEL caller optimised 100x tumor... |
| hmftools-sigs |
1.2.1 |
|
|
GPL-3.0-only |
| | | X | Fits sample SNV counts to trinucleotide signature definitions. |
| hmftools-sv-prep |
1.2.4 |
|
|
GPL-3.0-only |
| | | X | SV Prep generates a maximally filtered SV BAM file by identifying... |
| hmftools-virus-interpreter |
3.7_beta |
|
|
GPL-3.0-only |
| | | X | Post-process VIRUSBreakend summary results. |
| hmmcopy |
0.1.1 |
|
|
GPL-3 |
X | X | | | C++ based programs for analyzing BAM files and preparing read counts --... |
| hmmer |
3.4 |
|
|
BSD |
X | X | | | Biosequence analysis using profile hidden Markov models |
| hmmer2 |
2.3.2 |
|
|
GPLv2 |
X | X | | | Biosequence analysis using profile hidden Markov models |
| hmmlearn |
20151031 |
|
|
BSD |
X | | | | Hidden Markov Models in Python, with scikit-learn like API |
| hmmratac |
1.2.10 |
|
|
GPLv3 |
| | | X | Peak caller for ATAC-seq data |
| hmnfusion |
1.2.12 |
|
|
MIT |
| | | X | Analysis fusion from DNA genomics |
| hmnillumina |
1.5.1 |
|
|
MIT |
X | | | | A parser for Illumina run |
| hmnqc |
0.5.1 |
|
|
MIT |
| | | X | Compute differents metrics about quality, check identity and coverage... |
| hmnrandomread |
0.10.0 |
|
|
MIT |
X | | | | A sequence-read simulator program for NGS |
| hmntrimmer |
0.6.5 |
|
|
MIT |
X | | | | A trimmer for NGS reads |
| hmtnote |
0.7.2 |
|
|
MIT |
| | | X | Human mitochondrial variants annotation using HmtVar. |
| hocort |
1.2.2 |
|
dev |
MIT |
| | | X | HoCoRT - Host Contamination Removal Tool |
| homer |
5.1 |
|
|
GNU |
X | X | | | Software for motif discovery and next generation sequencing analysis |
| homoeditdistance |
0.0.1 |
|
|
MIT |
| | | X | An implementation of the homo-edit distance algorithm. |
| homopolish |
0.4.1 |
|
|
GNU |
| | | X | Homopolish is a polish tools |
| hopla |
1.2.1 |
|
|
MIT |
| | | X | Hopla enables classic genomic single, duo, trio, etc., analysis, by... |
| hops |
0.35 |
|
|
GPL |
| | | X | Java tool to work with ancient metagenomics |
| hormon |
1.0.0 |
|
|
GPLv2 |
| | | X | A tool for annotation of alpha satellite arrays in centromeres of a... |
| hostile |
2.0.0 |
|
|
MIT |
| | | X | Hostile: accurate host decontamination |
| hotspot3d |
1.8.2 |
|
|
GPLv3 |
X | X | | X | This 3D proximity tool can be used to identify mutation hotspots from... |
| how_are_we_stranded_here |
1.0.1 |
|
|
MIT |
| | | X | Python package for testing strandedness of RNA-Seq fastq files |
| howdesbt |
2.00.15 |
|
|
MIT |
X | X | | | Sequence Bloom Tree, supporting determined/how split filters |
| hpcblast |
1.0.2 |
|
|
MIT |
| | | X | A wrapper for NCBI-BLAST+ suite which provides a simple and efficient... |
| hpsuissero |
1.0.1 |
|
|
MIT |
| | | X | Rapid Haemophilus parasuis serotyping pipeline for Nanopore Data |
| hr2 |
1.04 |
|
|
GPL |
X | X | | | HR2 is a program to calculate elemental compositions for a given mass.... |
| hs-blastn |
0.0.5 |
|
|
GPL-3.0 |
X | | | | hs-blastn, a fast and accurate nucleotide-nucleotide sequences aligner. |
| hsdecipher |
1.1.2 |
|
|
GPL-3.0-or-later |
| | | X | Pipeline for the downstream analysis of highly similar duplicate genes |
| hsdfinder |
1.1.1 |
|
|
MIT |
| | | X | a tool to predict highly similar duplicates (HSDs) in eukaryotes |
| hts-nim-tools |
0.3.11 |
|
|
MIT |
X | | | | useful command-line tools written to show-case hts-nim |
| htsbox |
r346 |
|
|
Unknown |
X | X | | | HTSbox is a fork of early HTSlib. It is a collection of small... |
| htseq |
2.0.5 |
|
|
GPL-3.0-only |
X | X | | | HTSeq is a Python library to facilitate processing and analysis of data... |
| htseq-clip |
2.19.0b0 |
|
|
MIT |
| | | X | htseq-clip: a toolset for the analysis of eCLIP/iCLIP datasets |
| htseqqc |
v1.0 |
doc |
|
MIT |
| | | X | HTSeqQC is an automated quality control analysis tool for a single and... |
| htsinfer |
1.0.0_rc.1 |
|
|
Apache-2.0 |
| | | X | HTSinfer infers metadata from Illumina high throughput sequencing (HTS) data |
| htslib |
1.21 |
doc |
|
MIT |
X | X | | | C library for high-throughput sequencing data formats. |
| htsqualc |
1.1 |
doc |
|
MIT |
| | | X | HTSQualC is an automated quality control analysis tool for a single and... |
| htstream |
1.4.1 |
doc |
dev |
Apache-2.0 |
X | X | | | "HTStream is a quality control and processing pipeline for High... |
| httpretty |
0.8.10 |
|
|
MIT |
X | X | | | HTTP client mock for Python |
| hubward |
0.2.2 |
|
|
BSD |
X | X | | | None |
| hubward-all |
0.2.1 |
|
|
The |
X | | | X | Meta-package for hubward including bedtools and UCSC tools |
| hulk |
1.0.0 |
|
|
MIT |
X | X | | | Histosketching Using Little Kmers |
| humann |
3.9 |
doc |
dev |
MIT |
| | | X | HUMAnN: The HMP Unified Metabolic Analysis Network, version 3 |
| humann2 |
2.8.1 |
|
|
MIT |
X | X | | | HUMAnN2: The HMP Unified Metabolic Analysis Network 2 |
| humid |
1.0.37 |
doc |
|
MIT |
X | X | | | HUMID -- High-performance UMI Deduplicator |
| hurry.filesize |
0.9 |
|
|
ZPL |
X | | | | A simple Python library for human readable file sizes (or anything... |
| hybkit |
0.3.6 |
|
|
GPL-3.0-or-later |
| | | X | Hybkit toolkit and Python3 API chimeric genomic data analysis from... |
| hybpiper |
2.3.2 |
doc |
dev |
GPL-3.0-or-later |
X | X | | X | HybPiper is a suite of Python scripts/modules for targeted sequence capture. |
| hybracter |
0.11.2 |
doc |
dev |
MIT |
| | | X | An automated long-read first bacterial genome assembly pipeline. |
| hybran |
1.8 |
|
dev |
GPLv3 |
| | | X | Comparative prokaryotic genome annotation |
| hydra-multi |
0.5.4 |
|
|
MIT |
X | | | | Hydra detects structural variation breakpoints in both unique and... |
| hylight |
1.0.0 |
|
dev |
MIT |
X | X | | | Strain aware assembly of low coverage metagenomes. |
| hypercluster |
0.1.13 |
doc |
dev |
MIT |
| | | X | A package for automatic clustering hyperparameter optmization |
| hyphy |
2.5.65 |
|
dev |
MIT |
X | X | | | An open-source software package for comparative sequence analysis using... |
| hypo |
1.0.3 |
|
|
GPL-3.0 |
X | | | | Super Fast and Accurate Polisher for Long Read Genome Assemblies. |
| hypro |
0.1 |
|
|
GPL |
| | | X | Extend hypothetical prokka protein annotations using additional... |
| ibdmix |
1.0.1 |
|
|
GPL-3.0 |
X | X | | | ibdmix: estimate introgression by IBD |
| ibdne |
04Sep15.e78 |
|
|
Apache |
X | X | | X | The IBDNe program estimates the historical effective population size of... |
| ibdseq |
r1206 |
|
|
Apache |
X | X | | X | IBDseq is a software program for detecting segments of... |
| ibridges |
1.3.0 |
doc |
dev |
MIT |
| | | X | Package for accessing data and metadata on iRods servers. |
| ice-cream |
1.10 |
|
|
MIT |
| | | X | ICEcream: Integrative and Conjugative Elements Classification and... |
| iced |
0.5.13 |
doc |
dev |
BSD-3-Clause |
X | X | | | The python module iced implements the ICE normalization of hic data. |
| icescreen |
1.3.3 |
doc |
|
AGPL-3.0-or-later |
| | | X | ICEscreen detects and annotates ICEs (Integrative and Conjugative... |
| icfree-ml |
2.9.1 |
|
dev |
MIT |
| | | X | Design of experiments (DoE) and machine learning packages for the iCFree project |
| iclipro |
0.1.1 |
|
|
GPLv3 |
X | X | | X | iCLIPro is a Python package that can be used to control for systematic... |
| icount |
2.0.0 |
|
|
MIT |
X | X | | X | Computational pipeline for analysis of iCLIP data |
| icount-mini |
3.0.1 |
|
|
MIT |
| | | X | Computational pipeline for analysis of iCLIP data |
| icqsol |
0.3.26 |
|
|
MIT |
X | X | | | A collection of utilities for constructing complex geometries from... |
| idba |
1.1.3 |
|
|
GPL2 |
X | X | | | IDBA is a practical iterative De Bruijn Graph De Novo Assembler for... |
| idba_subasm |
1.1.3a2 |
|
|
GPL2 |
X | | | | Fork of IDBA with modifications to perform subassembly for the read... |
| ideas |
1.20 |
|
|
MIT |
X | | | | A method for jointly and quantitatively characterizing multivariate... |
| idemux |
0.1.6 |
|
|
custom |
| | | X | A Lexogen tool for demultiplexing and index error correcting fastq... |
| idemuxcpp |
0.3.0 |
|
|
custom |
X | X | | | A Lexogen tool for demultiplexing and index error correcting fastq... |
| idr |
2.0.4.2 |
|
|
GPLv2 |
X | X | | | The IDR (Irreproducible Discovery Rate) framework is a unified approach... |
| idr-py |
0.4.2 |
doc |
dev |
GPL-2.0+ |
X | X | | X | Helper methods for accessing the Image Data Resource (IDR) |
| ifcnv |
0.2.1 |
|
dev |
GNU |
| | | X | ifCNV: a novel isolation-forest-based package to detect copy number... |
| ifeature |
0.0.6 |
|
|
MIT |
| | | X | A python package for feature extraction and selection from protein and... |
| ig-checkfcs |
1.0.0 |
|
|
BSD |
X | X | | | quick FCS datatype check |
| ig-checkflowtypes |
1.0.0 |
|
|
BSD |
X | X | | | quick flow-related datatype for galaxy checks |
| ig-flowtools |
2.0.2 |
|
|
BSD |
X | X | | X | set of tools for flow cytometry analysis |
| igblast |
1.22.0 |
|
|
Public |
X | X | | | A tool for analyzing immunoglobulin (IG) and T cell receptor (TR) sequences |
| igblast-parser |
0.0.4 |
|
dev |
MIT |
X | X | | | Parser of Igblast results into a csv file |
| igda-script |
1.0.1 |
|
|
GPL2 |
| | | X | The wrapper script of iGDA to detect and phase minor SNVs from... |
| igdiscover |
0.15.1 |
|
|
MIT |
X | X | | X | Analyze antibody repertoires and discover new V genes |
| igfinder |
1.0 |
|
|
MIT |
| | | X | A tool to extract Igh and Igl/Igk gene sequences from assembled transcripts |
| igor_vdj |
1.4.0 |
|
|
GPL3 |
X | | | | IGoR is a C++ software designed to infer V(D)J recombination related... |
| igphyml |
1.1.5 |
|
|
GNU |
X | X | | | IgPhyML is a program designed to build phylogenetic trees and test... |
| igv |
2.19.2 |
|
|
MIT |
X | X | | X | Integrative Genomics Viewer. Fast, efficient, scalable visualization... |
| igv-reports |
1.14.1 |
|
|
MIT |
| | | X | Creates self-contained html pages for visual variant review with IGV (igv.js). |
| igvtools |
2.17.3 |
|
|
MIT |
X | X | | X | Command line tools for IGV |
| illumina-cleanup |
1.0.0 |
|
|
MIT |
X | X | | X | Nextflow pipeline for pre-processing Illumina FASTQ files |
| illumina-interop |
1.3.2 |
|
dev |
GPL-3.0-only |
X | | | | The Illumina InterOp libraries are a set of common routines used for... |
| illumina-utils |
2.13 |
|
|
GPL-3.0-or-later |
| | | X | A library and collection of scripts to work with Illumina paired-end... |
| illuminate |
0.6.3 |
|
|
MIT |
X | X | | | Analytics toolkit for Illumina sequencer metrics. |
| illumiprocessor |
2.10 |
|
|
BSD |
X | X | | X | illumiprocessor is a tool to batch process illumina sequencing reads... |
| im-pipelines |
1.1.6 |
|
|
Apache-2.0 |
| | | X | Components for cheminformatics and computational chemistry from... |
| im2deep |
1.0.2 |
|
dev |
Apache-2.0 |
| | | X | Framework for prediction of collisional cross-section of peptides. |
| ima3 |
1.13 |
|
|
GPL |
X | X | | | IMa3 can be used to solve a fundamental problem in evolutionary... |
| imctools |
2.1.8 |
doc |
dev |
MIT |
| | | X | An Image Mass Cytometry (IMC) file conversion tool that aims to convert... |
| imfusion |
0.3.2 |
|
|
MIT |
X | X | | | IM-Fusion - Tool for identifying transposon insertions and their... |
| immuneml |
3.0.9 |
doc |
dev |
APGL-3.0-only |
X | X | | X | immuneML is a software platform for machine learning analysis of immune... |
| imods |
1.0.4 |
|
|
Copyright |
X | X | | | toolkit to perform Normal Mode Analysis (NMA) in internal coordinates... |
| impg |
0.2.3 |
|
dev |
MIT |
X | X | | | impg: implicit pangenome graphs |
| impute2 |
2.3.2 |
|
|
Academic |
X | X | | | Genotype imputation and haplotype phasing |
| imseq |
1.1.0 |
|
|
GPLv2 |
X | | | | IMSEQ is a fast, PCR and sequencing error aware tool to analyze high... |
| imsindel |
1.0.2 |
|
|
MIT |
| | | X | An accurate intermediate-size indel detection tool incorporating de... |
| indelfixer |
1.1 |
|
|
GNU |
X | X | | X | A sensitive aligner for 454, Illumina and PacBio data, employing a full... |
| infernal |
1.1.5 |
doc |
dev |
BSD-3-Clause |
X | X | | | Infernal is for searching DNA sequence databases for RNA structure and... |
| infinity |
1.4 |
|
|
BSD |
X | X | | | All-in-one infinity value for Python. Can be compared to any object. |
| influx-si-data-manager |
1.0.3 |
|
|
GPL-3.0-or-later |
| | | X | Data manager for handling influx_si inputs on Workflow4Metabolomics... |
| influx_si |
7.2.3 |
doc |
dev |
GPL-2.0-or-later |
| | | X | Metabolic flux and concentration estimation based on stable isotope labeling |
| inforna |
2.1.2 |
|
|
MIT-like |
X | | | | A server for the design of RNA sequences that fold into a given... |
| inheritance |
0.1.5 |
|
|
MIT |
X | X | | X | inheritance models for mendelian diseases |
| inmoose |
0.7.2 |
|
dev |
GPL-3.0-or-later |
X | X | | | InMoose is the Integrated Multi Omic Open Source Environment. It is a... |
| insilicoseq |
2.0.1 |
doc |
dev |
MIT |
| | | X | A sequencing simulator. |
| insilicosv |
0.0.6 |
|
|
MIT |
| | | X | Simulator for complex structural variants |
| inspector |
1.3.1 |
|
|
MIT |
| | | X | Accurate long-read de novo assembly evaluation with Inspector |
| instanovo |
1.0.0 |
|
|
Apache-2.0 |
| | | X | De novo peptide sequencing with InstaNovo |
| instrain |
1.9.0 |
|
|
MIT |
| | | X | Calculation of strain-level metrics |
| insurveyor |
1.1.3 |
|
dev |
GPL-3.0-only |
X | X | | | An insertion caller for Illumina paired-end WGS data. |
| intarna |
3.4.1 |
|
|
MIT |
X | X | | | Efficient RNA-RNA interaction prediction incorporating seeding and... |
| integron_finder |
2.0.5 |
doc |
dev |
GPL-3.0-or-later |
| | | X | Integron Finder aims at detecting integrons in DNA sequences |
| intemap |
1.0 |
|
|
|
X | | | | Integrated metagenomic assembly pipeline for short reads |
| interleafq |
1.1.0 |
|
|
MIT |
| | | X | Interleave and deinterleave FASTQ files |
| intermine |
1.13.0 |
|
|
GNU |
X | X | | X | InterMine WebService client |
| interproscan |
5.59_91.0 |
|
dev |
GPLv3 |
X | | | | InterPro integrates together predictive information about proteins... |
| interval-binning |
1.0.0 |
|
|
MIT |
| | | X | A Python implementation of the interval binning scheme |
| intervals |
0.6.0 |
|
|
BSD |
X | X | | | Python tools for handling intervals (ranges of comparable objects). |
| intervalstats |
1.01 |
|
|
unknown |
X | X | | | None |
| intervaltree_bio |
1.0.1 |
|
|
MIT |
X | X | | X | Interval tree convenience classes for genomic data |
| intervene |
0.6.5 |
|
|
MIT |
X | X | | X | A tool for intersection of multiple gene or genomic region sets and... |
| involucro |
1.1.2 |
|
|
Apache-2.0 |
X | X | | | Build and Deliver Software with Containers |
| ionquant |
1.10.27 |
|
|
Academic |
| | | X | A label free quantification tool |
| iow |
1.0.5 |
doc |
dev |
BSD-3-Clause |
X | X | | | Implementation of Balanced Parentheses |
| ipapy2 |
1.3.0 |
|
|
MIT |
| | | X | Integrated Probabilistic Annotation (IPA) 2.0 - Python implementation |
| iphop |
1.3.3 |
|
|
Modified |
| | | X | Predict host genus from genomes of uncultivated phages. |
| ipk |
0.5.1 |
|
|
MIT |
X | X | | | IPK is a tool for computing phylo-k-mers for a fixed phylogeny. |
| iptkl |
0.6.8 |
doc |
|
MIT |
| | | X | IPTK is a library specialized in the analysis of HLA-peptidomes... |
| ipyrad |
0.9.104 |
|
|
GPL-3.0-only |
| | | X | Interactive assembly and analysis of RAD-seq data sets. |
| ipython-cluster-helper |
0.6.4 |
|
|
MIT |
X | X | | X | Tool to easily start up an IPython cluster on different schedulers |
| iqkm |
1.0 |
|
|
GPL-3.0-only |
| | | X | Identification and quantification of KEGG Modules in metagenomes/genomes |
| iqtree |
2.4.0 |
doc |
dev |
GPL-2.0-or-later |
X | X | | | Efficient phylogenomic software by maximum likelihood. |
| ir |
2.8.0 |
|
|
GPL-2 |
X | X | | | Program for Calculating the Repetitiveness of DNA Sequences |
| irep |
1.1.7 |
|
|
MIT |
X | X | | X | calculate iRep replication rates from metagenome sequencing |
| irescue |
1.1.2 |
doc |
dev |
MIT |
| | | X | A tool to quantify transposable elements expression in scRNA-seq. |
| irf |
3.09 |
|
dev |
AGPL-3.0-or-later |
X | X | | | Inverted Repeats Finder is a program that detects approximate inverted repeats. |
| irfinder |
1.3.1 |
doc |
dev |
MIT |
X | X | | | Intron Retention Finder |
| irida-linker |
1.1.1 |
|
|
Apache-2.0 |
X | X | | X | The NGS Archive Linker is a Perl script used to generate a structure of... |
| irida-sistr-results |
0.6.0 |
doc |
dev |
Apache |
X | X | | X | Exports SISTR results available through IRIDA into a single report. |
| irida-staramr-results |
0.3.1 |
|
|
Apache-2.0 |
| | | X | IRIDA StarAMR Results program enables StarAMR analysis results that... |
| irida-uploader |
0.9.2 |
doc |
dev |
Apache-2.0 |
| | | X | Upload NGS data to IRIDA system |
| irissv |
1.0.5 |
|
|
MIT |
| | | X | Software for refining insertion sequences in structural variant calls |
| irma |
1.2.0 |
|
|
GNU |
| | | X | IRMA: Iterative Refinement Meta-Assembler for the robust assembly,... |
| isa-rwval |
0.10.10 |
|
dev |
CPAL |
| | | X | ISA metadata tracking tools |
| isaac4 |
04.18.11.09 |
|
|
GPL-3.0-only |
X | | | | Ultra-fast whole-genome alignment for Illumina sequencing platforms. |
| isafe |
1.1.1 |
|
|
BSD-3-Clause |
| | | X | A program for identifying a favored mutation in positive selective sweep. |
| isatools |
0.14.2 |
|
dev |
MPL-2.0 |
X | X | | X | Metadata tracking tools help to manage an increasingly diverse set of... |
| iseq |
1.6.0 |
|
dev |
MIT |
| | | X | iSeq is a Bash script that allows you to download sequencing data and... |
| isescan |
1.7.2.3 |
|
|
GNU |
X | X | | | A python pipeline to identify IS (Insertion Sequence) elements in... |
| islandpath |
1.0.6 |
|
|
GNU |
X | X | | X | IslandPath-DIMOB is a standalone software to predict genomic islands in... |
| ismapper |
2.0.2 |
|
|
BSD |
| | | X | A mapping-based tool for identification of the site and orientation of... |
| isocor |
2.2.2 |
doc |
dev |
GPL-3.0-or-later |
| X | | X | A Isotope Correction for mass spectrometry labeling experiments |
| isonclust |
0.0.6.1 |
|
|
GPL-3.0 |
| | | X | De novo clustering of long-read transcriptome reads. |
| isonclust2 |
2.3 |
|
|
MPL2 |
X | X | | | De novo clustering of long transcriptomic reads |
| isoncorrect |
0.1.3.5 |
|
|
GPL-3.0-or-later |
| | | X | De novo error-correction of long-read transcriptome reads. |
| isonform |
0.3.4 |
|
|
GPL-3.0 |
| | | X | De novo construction of isoforms from long-read data |
| isoplot |
1.3.1 |
doc |
dev |
GNU |
| | | X | Generate figures from Isocor output |
| isoquant |
3.6.3 |
doc |
dev |
GPL-2.0-or-later |
| | | X | IsoQuant is a tool for reference-based analysis of long RNA reads, such... |
| isorefiner |
0.1.0 |
|
|
MIT |
| | | X | A refinement tool to identify exon-intron structures of transcript... |
| isoseq |
4.3.0 |
|
|
BSD-3-Clause-Clear |
X | | | | Iso-Seq - Scalable De Novo Isoform Discovery |
| isoseq3 |
4.0.0 |
|
|
BSD-3-Clause-Clear |
X | | | X | Iso-Seq - Scalable De Novo Isoform Discovery |
| isospecpy |
2.2.2 |
|
|
BSD-3-Clause |
X | X | | | Python interface to IsoSpec++ isotopic envelope calculator library |
| ispcr |
33 |
|
|
License |
X | X | | | In silico PCR |
| itero |
1.1.2 |
|
|
BSD |
X | X | | X | A pipeline for iterative, guided contig assembly that integrates... |
| itk |
4.10.1 |
|
|
Apache |
X | X | | | ITK is an open-source, cross-platform system that provides developers... |
| itol-config |
0.1.0 |
doc |
|
MIT |
| | | X | Package to create iTOL config files |
| itolapi |
4.1.5 |
|
|
MIT |
| | | X | API for interacting with itol.embl.de |
| itolparser |
0.2.1 |
|
|
MIT |
| | | X | Small script to produce iTOL colorstrip metadata files from a table |
| itsx |
1.1.3 |
|
|
GNU |
X | X | | X | ITSx is an open source software utility to extract the highly variable... |
| itsxpress |
2.1.4 |
|
dev |
CC0-1.0 |
X | X | | X | ITSxpress: Software to rapidly trim the Internally Transcribed Spacer... |
| iucn_sim |
2.2.0 |
|
|
MIT |
| | | X | Simulate future extinctions and extinction rates for a given set of... |
| iva |
1.0.11 |
|
|
GPLv3 |
X | X | | X | Iterative Virus Assembler |
| ivar |
1.4.4 |
doc |
dev |
GPL-3.0-or-later |
X | X | | | iVar is a computational package that contains functions broadly useful... |
| jacusa2 |
2.0.4 |
|
|
GPL-3.0-or-later |
| | | X | JACUSA2 is a framework for accurate variant assessment, detecting SNVs... |
| jaeger-bio |
1.1.30 |
doc |
dev |
MIT |
| | | X | A quick and precise pipeline for detecting phages in sequence assemblies. |
| jaffa |
2.3 |
|
|
GPL-3.0-or-later |
X | X | | X | JAFFA is a multi-step pipeline that takes either raw RNA-Seq reads, or... |
| jali |
1.3 |
|
|
file |
X | X | | | Alignment method for comparing a protein sequence to a protein family,... |
| jalview |
2.11.4.1 |
|
|
GPL-3.0-only |
X | X | | X | Jalview is a free program for multiple sequence alignment editing,... |
| jamm |
1.0.8.0 |
|
|
GPL |
X | X | | X | JAMM is a peak finder for NGS datasets (ChIP-Seq, ATAC-Seq,... |
| jannovar-cli |
0.36 |
|
|
BSD2 |
X | X | | X | Java tool for performing annotation of VCF files |
| jarvis |
1.1 |
|
|
GPL3 |
X | | | | Efficient lossless compression of genomic sequences |
| jarvis3 |
3.7 |
|
dev |
GPL-3.0-or-later |
X | | | | Improved encoder for genomic sequences. |
| jasmine |
1.1 |
|
|
GPL |
| | | X | Jasmine: a Java pipeline for isomiR characterization in miRNA-Seq Data |
| jasminesv |
1.1.5 |
|
|
MIT |
| | | X | Software for merging structural variants between individuals |
| jass |
2.3 |
|
|
MIT |
| | | X | Computation of joint statistics over sets of GWAS results |
| jass_preprocessing |
2.2 |
|
|
MIT |
| | | X | Harmonizing raw GWAS summary statistic for further analysis with jass |
| java-jdk |
8.0.112 |
|
|
GPL |
X | X | | | The Zulu OpenJDK build. |
| jbrowse |
1.16.11 |
|
|
LGPL |
X | X | | | The JBrowse Genome Browser |
| jbrowse2 |
3.0.5 |
|
|
Apache-2.0 |
| | | X | The JBrowse 2 Genome Browser |
| jcast |
0.3.5 |
|
dev |
MIT |
| | | X | Jcast retrieves splice junction information and translates into amino acids |
| jccirc |
1.0.0 |
doc |
dev |
unknown |
| | | X | circRNA assembler through integrated junction contigs |
| jclusterfunk |
0.0.25 |
|
|
GPL-3.0-only |
| | | X | A command line tool with a bunch of functions for trees |
| jcvi |
1.4.16 |
doc |
dev |
BSD-2-Clause |
X | X | | | Python utility libraries on genome assembly, annotation, and... |
| je-suite |
2.0.RC |
|
|
MIT |
X | X | | X | Je is a suite to handle barcoded fastq files with (or without) Unique... |
| jellyfish |
2.2.10 |
|
dev |
GPL-3.0 |
X | X | | | Jellyfish is a tool for fast, memory-efficient counting of k-mers in... |
| jemalloc |
4.5.0 |
|
|
BSD |
X | X | | | Efficient multithreaded memory allocator |
| jgoslin |
2.2.0 |
|
|
Apache |
| | | X | This project is a parser, validator and normalizer for shorthand lipid... |
| jms-metabolite-services |
0.5.8 |
|
|
MIT |
| | | X | conversion, search of metabolic models and metabolomics data |
| jmztab-m |
1.0.6 |
|
|
Apache |
| | | X | This project is the reference reader, writer and validator... |
| jobtree |
09.04.2017 |
|
|
MIT |
| | | X | Python based pipeline management software for clusters that makes... |
| jolytree |
2.1 |
|
|
GPLv3 |
| | | X | Fast alignment-free phylogenetic reconstruction from genome sequences |
| jpredapi |
1.5.6 |
|
|
MIT |
| | | X | Python library for submitting jobs to JPRED - A Protein Secondary... |
| jq |
1.5 |
|
|
MIT |
X | X | | | None |
| jronn |
7.1.0 |
|
dev |
LGPL-2.1 |
| | | X | JRONN is based on the C implementation of RONN algorithm. |
| json_collect_data_source |
1.0.1 |
|
|
BSD |
X | X | | X | This tool is able to receive multiple datasets (optionally with their... |
| julia-divand |
2.7.9 |
|
|
GPL2 |
X | | | | Performs an n-dimensional variational analysis/gridding of arbitrarily... |
| junit-xml |
1.8 |
|
|
MIT |
X | X | | X | Creates JUnit XML test result documents that can be read by tools such... |
| jupiterplot |
1.1 |
doc |
dev |
GPL-3.0-or-later |
| | | X | Circos Assembly Consistency (Jupiter) plot |
| jupyterngsplugin |
0.0.13a3 |
|
|
PUBLIC-DOMAIN |
| | | X | Jupyter notebook plugin Bioinformatics NGS data analysis |
| justbackoff |
0.4.0 |
|
|
MIT |
X | X | | X | Simple backoff algorithm in Python |
| jvarkit |
2024.08.25 |
|
|
MIT |
| | | X | Java utilities for Bioinformatics. |
| jvarkit-bam2svg |
201904251722 |
|
|
MIT |
X | X | | X | BAM to Scalar Vector Graphics (SVG) |
| jvarkit-bam2wig |
201904251722 |
|
|
MIT |
X | X | | X | Bam to fixedStep Wiggle converter, or BED GRAPH. |
| jvarkit-bamstats04 |
2021.10.13 |
|
|
MIT |
| | | X | Coverage statistics for a BED file. |
| jvarkit-msa2vcf |
201904251722 |
|
|
MIT |
| | | X | Writes a VCF from a multiple sequence alignment (MSA) in CLUSTAW or a... |
| jvarkit-wgscoverageplotter |
20201223 |
|
|
MIT |
| | | X | Whole genome BAM coverage plotter |
| k-slam |
1.0 |
|
|
GPL-3.0 |
X | | | | k-SLAM is a program for alignment based metagenomic analysis of large... |
| k8 |
1.2 |
doc |
dev |
MIT |
X | X | | | Lightweight JavaScript shell based on Google's V8 JavaScript engine. |
| kaiju |
1.10.1 |
|
dev |
GPL-3.0-or-later |
X | X | | | Fast and sensitive taxonomic classification for metagenomics |
| kakscalculator2 |
2.0.1 |
|
|
GPL-3.0-or-later |
X | X | | | KaKs_Calculator2.0 calculates Ka and Ks. |
| kalamari |
5.8.0 |
doc |
dev |
Creative |
X | X | | X | A curated database of completed assemblies with taxonomy IDs |
| kalign2 |
2.04 |
|
|
GPLv2 |
X | X | | | Kalign is a fast and accurate multiple sequence alignment algorithm... |
| kalign3 |
3.4.0 |
|
|
GPL-3.0-only |
X | X | | | Kalign is a fast and accurate multiple sequence alignment algorithm. |
| kallisto |
0.51.1 |
doc |
dev |
BSD-2-Clause |
X | X | | | Quantifying abundances of transcripts from RNA-Seq data, or more... |
| kaptive |
3.0.0b6 |
doc |
dev |
GPL-3.0-or-later |
X | X | | X | Reports information about surface polysaccharide loci for Klebsiella... |
| karect |
1.0 |
doc |
dev |
GPLv2 |
X | | | | Read error correction tool based on multiple alignment. |
| kart |
2.5.6 |
|
|
MIT |
X | X | | | Kart: a divide-and-conquer algorithm for NGS read alignment |
| karyopype |
0.1.6 |
|
|
MIT |
| | | X | Chromosomal visualization in Python. |
| kat |
2.4.2 |
|
|
GPL3 |
X | | | | KAT is a suite of tools that analyse jellyfish hashes or sequence files... |
| kb-python |
0.29.1 |
doc |
dev |
BSD-2-Clause |
| | | X | A wrapper for the kallisto | bustools workflow for single-cell RNA-seq... |
| kbo-cli |
0.1.1 |
doc |
dev |
Dual-licensed |
X | X | | | Command-line interface for the kbo local aligner |
| kcalign |
1.0.2 |
doc |
dev |
AFL-3.0-only |
| | | X | Kalgin-based codon-aware aligner for multiple sequences |
| kcounter |
0.1.1 |
|
|
GPL-3 |
X | X | | | A simple package for counting DNA k-mers in Python. Written in Rust. |
| kegalign-full |
0.1.2.7 |
doc |
dev |
MIT |
| | | X | KegAlign: A Scalable GPU-Based Whole Genome Aligner |
| kegg-pathways-completeness |
1.3.0 |
|
dev |
Apache-2.0 |
| | | X | The tool counts completeness of each KEGG pathway for protein sequences. |
| keggcharter |
1.1.2 |
doc |
dev |
BSD-3-Clause |
| | | X | A tool for representing genomic potential and transcriptomic expression... |
| kerneltree |
0.0.5 |
|
dev |
GPL2 |
X | X | | | Ultrafast interval tree implementation stolen from the kernel, modified... |
| kestrel |
1.0.3 |
|
|
GPL-3.0-or-later |
| | | X | Mapping-free variant caller for short-read Illumina data |
| kfoots |
1.0 |
|
|
GPL-2 |
X | X | | | The package provides methods for fitting multivariate count data with a... |
| kggseq |
1.1 |
|
|
Apache |
| | | X | KGGSeq is a software platform constituted of Bioinformatics and... |
| kgwasflow |
1.3.0 |
doc |
dev |
MIT |
| | | X | kGWASflow is a Snakemake workflow for performing k-mers-based GWAS. |
| khipu-metabolomics |
2.0.2 |
|
|
BSD-3-Clause |
| | | X | Python library for generalized, low-level annotation of MS metabolomics |
| khmer |
3.0.0a3 |
doc |
dev |
BSD-3-License |
X | X | | | khmer k-mer counting library. |
| kid |
0.9.6 |
|
|
MIT |
X | | | X | A simple and pythonic XML template language |
| kin |
3.1.4 |
doc |
dev |
GPL-3.0-only |
| | | X | A tool to estimate pairwise relatedness from ancient DNA, taking in... |
| kinamine_y_shaker |
1.0.0 |
|
|
Apache |
| | | X | Kinamine is a tool to export all phospho-peptides that were discovered... |
| kinex |
1.2.0 |
doc |
dev |
GPL-3.0-only |
| | | X | Kinex infers causal kinases from phosphoproteomics data. |
| king |
2.2.7 |
|
|
GPLv3 |
X | X | | | `Kinship-based INference for Gwas (KING) is a toolset that makes use of... |
| kingfisher |
0.4.1 |
|
|
GPL-3.0-or-later |
| | | X | Download/extract biological FASTA/Q read data and metadata |
| kinship-read |
2.1.1 |
doc |
|
GPL-3.0-only |
| | | X | Relationship Estimation from Ancient DNA version 2 (READv2) |
| kinsimriboswitch |
0.3 |
|
|
GPLv3 |
X | X | | | Pipeline for the simulation of RNA--ligand interaction kinetics as... |
| kipoi |
0.8.6 |
doc |
dev |
MIT |
X | X | | X | Kipoi: model zoo for genomics |
| kipoi-conda |
0.1.6 |
doc |
dev |
MIT |
| | | X | kipoi-conda: conda/pip related functionality used by Kipoi |
| kipoi-utils |
0.7.7 |
doc |
dev |
MIT |
| | | X | kipoi-utils: utils used in various packages related to kipoi |
| kipoi_veff |
0.3.1 |
doc |
|
MIT |
| | | X | kipoi_veff: variant effect prediction plugin for Kipoi |
| kipoiseq |
0.7.1 |
doc |
dev |
MIT |
| | | X | kipoiseq: sequence-based data-laoders for Kipoi |
| kissplice |
2.6.5 |
|
|
CeCILL |
X | X | | | A local transcriptome assembler for SNPs, indels and AS events |
| kitsune |
1.3.5 |
|
dev |
GPL-3.0-only |
| | | X | kitsune |
| kiwidist |
0.3.6 |
|
|
MIT |
X | X | | X | Combining gene-set analysis with network properties |
| kleborate |
3.1.3 |
doc |
dev |
GPL-3.0-or-later |
| | | X | Kleborate: a tool for typing and screening pathogen genome assemblies |
| kma |
1.4.18 |
|
dev |
Apache-2.0 |
X | X | | | KMA is a mapping method designed to map raw reads directly against... |
| kmasker |
1.1.1 |
|
dev |
GPL3 |
X | X | | | A tool for masking and exploring of sequences from plant species. |
| kmc |
3.2.4 |
|
dev |
GPL-3.0-or-later |
X | X | | | Tools for efficient k-mer counting and filtering of reads based on... |
| kmcp |
0.9.4 |
|
|
MIT |
X | X | | | accurate metagenomic profiling of both prokaryotic and viral... |
| kmd_hmdb_api_client |
1.0.1 |
|
|
AGPL-3.0-or-later |
| | | X | The KMD HMDB project API Client |
| kmer-db |
2.2.5 |
|
|
GPL-3 |
X | X | | | Kmer-db is a fast and memory-efficient tool for estimating evolutionary... |
| kmer-jellyfish |
2.3.1 |
doc |
dev |
GPL-3.0-or-later |
X | X | | | Jellyfish is a tool for fast, memory-efficient counting of k-mers in... |
| kmercamel |
2.0.0 |
|
|
MIT |
X | X | | | KmerCamel🐫 - compressing k-mer sets using masked superstrings |
| kmerfinder |
3.0.2 |
|
|
APACHE-2.0 |
| | | X | Prediction of bacterial species using a fast K-mer algorithm. |
| kmergenie |
1.7051 |
|
|
free |
X | X | | | KmerGenie estimates the best k-mer length for genome de novo assembly |
| kmerinshort |
1.0.1 |
|
|
aGPL |
X | X | | | KmerInShort counts kmers from a fasta/fastq file or list of files, and... |
| kmerstream |
1.1 |
|
|
free |
X | X | | | Streaming algorithm for computing kmer statistics for massive genomics datasets |
| kmertools |
0.1.5 |
doc |
dev |
GPL-3.0-only |
X | X | | | kmertools: DNA Vectorisation Tool |
| kmtricks |
1.4.0 |
doc |
dev |
AGPL-3.0 |
X | | | | A k-mer matrix framework |
| kneaddata |
0.12.2 |
doc |
dev |
MIT |
X | X | | X | KneadData is a tool designed to perform quality control on metagenomic... |
| knock-knock |
0.4.2 |
|
|
GPL-3.0-or-later |
| | | X | toolkit for analyzing CRISPR knock-in experiments |
| knot |
1.0.0 |
|
|
|
X | | | | None |
| knot-asm-analysis |
1.3.0 |
|
|
MIT |
| | | X | KNOT: Knowledge Network Overlap exTraction is a tool for the... |
| knotinframe |
2.3.2 |
|
|
GPL-3.0-or-later |
X | X | | | Predicts -1 frameshift sites with simple pseudoknots |
| kobas |
3.0.3 |
|
|
Biopython |
X | X | | X | KEGG Orthology Based Annotation System |
| kodoja |
0.0.10 |
|
|
MIT |
X | X | | X | Kodoja: identifying viruses from plant RNA sequencing data |
| koeken |
0.2.6 |
|
|
MIT |
X | X | | | A Linear Discriminant Analysis (LEfSe) wrapper. |
| kofamscan |
1.3.0 |
|
|
MIT |
| | | X | KofamKOALA assigns K numbers to the user's sequence data by... |
| komb |
1.0 |
|
|
GPL-3.0-or-later |
X | X | | | Characterizing metagenomes using K-Core decomposition |
| konezumiaid |
0.3.6.1 |
|
|
MIT |
| | | X | This is used for automatically designing gRNAs for genome editing by Target-AID. |
| kopt |
0.1.0 |
|
|
MIT |
| | | X | Keras-hyperopt (kopt); Hyper-parameter tuning for Keras using hyperopt. |
| kosudoku |
1.0 |
|
|
Princeton |
| | | X | kosudoku: a suite to rapidly create whole genome knockout collections... |
| kounta |
0.2.3 |
|
|
GPL-3.0 |
| | | X | Generate multi-sample k-mer count matrix |
| koverage |
0.1.11 |
|
|
MIT |
| | | X | Read-coverage statistics pipelines for multiple samples |
| kpal |
2.1.1 |
|
|
MIT |
X | X | | X | Analysis toolkit and programming library for k-mer profiles |
| kpop |
1.1.1 |
|
dev |
GPL-3.0-only |
X | X | | | An assembly-free and scalable method for the comparative analysis of... |
| kraken |
1.1.1 |
|
|
GPLv3 |
X | X | | | Kraken is a system for assigning taxonomic labels to short DNA... |
| kraken-all |
0.10.6_eaf8fb68 |
|
|
GPLv3 |
X | | | | None |
| kraken-biom |
1.2.0 |
|
|
MIT |
X | X | | X | Create BIOM-format tables from Kraken output. |
| kraken-ea |
0.10.5ea.3 |
|
|
GPLv3 |
X | X | | | Kraken is a system for assigning taxonomic labels to short DNA... |
| kraken2 |
2.14 |
doc |
dev |
GPL-3.0-or-later |
X | X | | | Kraken2 is a system for assigning taxonomic labels to short DNA... |
| krakenhll |
0.4.8 |
|
|
GPLv3 |
X | X | | | KrakenHLL metagenomics classification method with unique k-mer counting... |
| krakentools |
1.2 |
|
|
GPL-3.0 |
| | | X | KrakenTools scripts for analysis of Kraken/KrakenUniq/Kraken2/Bracken results |
| krakenuniq |
1.0.4 |
|
|
GPLv3 |
X | X | | | Metagenomics classifier with unique k-mer counting for more specific results |
| krakmeopen |
0.1.5 |
|
|
MIT |
| | | X | A Kraken 2 downstream analysis toolkit. Calculate quality metrics for... |
| krbalancing |
0.0.5 |
|
dev |
GPL-3.0-or-later |
X | X | | | This is a c++ extension for python which computes K.R. balanced matrices. |
| krocus |
1.0.3 |
|
|
GPL-3.0 |
X | X | | X | krocus performs multi-locus sequence typing from uncorrected long reads. |
| krona |
2.8.1 |
|
|
BSD |
X | X | | X | Krona Tools is a set of scripts to create Krona charts from several... |
| kronik |
2.20 |
|
|
Apache |
X | X | | | Utility for processing Hardklor features to find candidate peptides by... |
| kronos |
2.3.0 |
doc |
dev |
MIT |
| | | X | Kronos is a highly flexible Python-based software tool that mainly... |
| kseqpp |
1.1.2 |
|
dev |
MIT |
X | X | | | C++11 re-implementation of kseq by Heng Li |
| ksnp |
1.0.3 |
|
|
GPL3 |
X | X | | | k-mer based haplotype assembly |
| kssd |
2.21 |
|
|
Apache-2.0 |
X | | | | K-mer substring space decomposition |
| ksw |
0.2.3 |
|
|
MIT |
X | X | | | Ksw: (interactive) smith-waterman in C |
| kwip |
0.2.0 |
|
|
GNU |
X | X | | | kWIP implements a de novo, alignment free measure of sample genetic... |
| kyber |
0.6.0d |
|
dev |
MIT |
X | X | | | Tool to create a length-accuracy heatmap from a cram or bam file |
| kyototycoon |
20170410 |
|
|
GNU |
X | | | | a lightweight network server on top of the Kyoto Cabinet key-value... |
| labrat |
0.3.0 |
|
|
MIT |
| | | X | A package to quantify changes in alternative polyadenylation isoform... |
| lace |
1.14.1 |
|
|
GPL |
X | X | | X | Building SuperTranscripts: A linear representation of transcriptome data |
| lamassemble |
1.7.2 |
|
|
MIT |
| | | X | Merge overlapping "long" DNA reads into a consensus sequence |
| lambda |
3.1.0 |
|
|
AGPLv3 |
X | X | | | Lambda is a local aligner optimized for many query sequences and... |
| lamps |
1.0.3 |
|
dev |
GPL-3.0-or-later |
| | | X | Liverpool Annotation of metabolites using Mass Spectrometry |
| lap |
1.1.r186 |
|
|
|
X | | | | De novo genome assembly evaluation |
| lapack |
3.6.0 |
|
|
BSD |
X | | | | None |
| lassaseq |
0.1.0 |
doc |
dev |
GPL-3.0-or-later |
| | | X | Tool for downloading Lassa virus sequences |
| last |
1611 |
doc |
dev |
GPL-3.0-or-later |
X | X | | | LAST finds & aligns related regions of sequences. |
| lastz |
1.04.45 |
|
|
MIT |
X | X | | | LASTZ is a program for aligning DNA sequences, a pairwise aligner. |
| latch |
2.57.2 |
|
|
MIT |
| | | X | The Latch python bioinformatics framework |
| latentstrainanalysis |
0.0.1 |
|
|
MIT |
X | X | | X | Partitioning and analysis methods for large, complex sequence datasets |
| lca |
0.25 |
|
|
GPL-3.0-only |
X | X | | | LCA - Lowest Common Ancestor calculation tool |
| lcfit |
0.5 |
|
|
GPL-3.0 |
X | | | | Likelihood curve fitting by nonlinear least squares. |
| ldblockshow |
1.40 |
|
|
MIT |
X | X | | | a tool for showing linkage disequilibrium heatmaps from variant call... |
| lddt |
2.2 |
|
|
GPL3 |
X | X | | | A superposition-free score that evaluates local distance differences in... |
| ldhelmet |
1.10 |
|
|
GPL3 |
X | X | | | Software program for statistical inference of fine-scale crossover... |
| ldsc |
1.0.1 |
|
|
GPLv3 |
| | | X | ldsc is a tool for estimating heritability and genetic correlation from... |
| learnmsa |
2.0.10 |
|
dev |
MIT |
| | | X | learnMSA: Learning and Aligning large Protein Families |
| leehom |
1.2.15 |
|
|
GPLv3 |
X | | | | Maximum-likelihood adapter trimming and removal |
| lefse |
1.1.2 |
|
|
MIT |
X | X | | X | LDA Effect Size (LEfSe) (Segata et. al 2010) is an algorithm for... |
| legsta |
0.5.1 |
|
|
GPL-3.0 |
| | | X | In silico Legionella pneumophila Sequence Based Typing |
| lemur |
1.0.1 |
|
|
MIT |
| | | X | Lemur is a tool for rapid and accurate taxonomic profiling on long-read... |
| leptonica |
1.73 |
|
|
FreeBSD |
X | | | | Leptonica is a pedagogically-oriented open source site containing... |
| lepwrap |
4.0.1 |
|
|
The |
| | | X | The Snakemake pipeline to use Lep-Map3 to create linkage maps and... |
| leviathan |
1.0.2 |
|
|
AGPL-3.0-or-later |
X | X | | | Linked-reads based structural variant caller with barcode indexing |
| leviosam |
5.2.1 |
|
|
MIT |
X | X | | | lift-over of alignments for variant-aware references |
| leviosam2 |
0.5.0 |
doc |
dev |
MIT |
X | X | | | Fast and accurate coordinate conversion between assemblies. |
| lexicmap |
0.5.0 |
|
|
MIT |
X | X | | | efficient sequence alignment against millions of prokaryotic genomes |
| lexmapr |
0.7.1 |
|
|
GPL-3.0 |
X | X | | X | A Lexicon and Rule-Based Tool for Translating Short Biomedical Specimen... |
| liana |
1.4.0 |
|
|
GPL-3.0-or-later |
| | | X | LIANA+: a one-stop-shop framework for cell-cell communication |
| lib-pod5 |
0.3.15 |
doc |
dev |
MPL-2.0 |
| | | X | Python bindings for the POD5 file format. |
| libarbdb |
6.0.6 |
doc |
dev |
ARB |
X | X | | | ARB 6 Sequence Analysis Suite |
| libbambamc |
0.0.50 |
|
|
GPLv3 |
X | X | | | lightweight C implementation of name collating BAM file input and BAM... |
| libbigwig |
0.4.8 |
|
|
MIT |
X | X | | | A C library for handling bigWig files |
| libcifpp |
7.0.9 |
doc |
dev |
BSD-2-Clause |
X | | | | Library containing code to manipulate mmCIF and PDB files. |
| libdb |
6.1.26 |
|
|
AGPLv3 |
X | X | | | The Berkeley DB embedded database system. |
| libdeflate |
1.2 |
|
|
MIT |
X | X | | | libdeflate is a library for fast, whole-buffer DEFLATE-based... |
| libdivsufsort |
2.0.2 |
|
|
MIT |
X | X | | | A lightweight suffix-sorting library |
| libffi |
3.2.1 |
|
|
https://raw.git |
| X | | | A Portable Foreign Function Interface Library |
| libgab |
1.0.5 |
|
|
GPL |
X | | | | Several C++ subroutines useful for bioinformatics |
| libgenome |
1.3.1 |
|
|
GPL-2.0 |
X | X | | | A C++ development library designed to make common operations on DNA and... |
| libgff |
2.0.0 |
|
dev |
MIT |
X | X | | | A simple "libraryfication" of the GFF/GTF parsing code that is... |
| libgtextutils |
0.7 |
|
|
AGPL |
X | X | | | Gordon Text utils Library |
| libidn |
7.45.0 |
|
|
LGPLv3 |
X | X | | | Library for internationalized domain name support |
| libis |
0.1.6 |
|
|
MIT |
| | | X | Low input Bisulfite sequencing alignment |
| libis_moabs |
0.0.7 |
|
|
MIT |
| | | X | Low input Bisulfite sequencing alignment |
| libmaus2 |
2.0.813 |
|
dev |
GPL-3.0-or-later |
X | | | | Collection of data structures and algorithms for NGS data. |
| libmems |
1.6.0 |
|
|
GPL-2.0 |
X | | | | libMems is a freely available software development library to support... |
| libmuscle |
3.7 |
|
|
GPLv2 |
X | X | | | libMuscle header files. |
| libopenms |
3.3.0 |
|
|
BSD |
X | X | | | OpenMS is an open-source software C++ library for LC-MS data management... |
| libsbml |
5.20.4 |
|
|
LGPL |
X | X | | | LibSBML is a free, open-source programming library to help you read,... |
| libsequence |
1.9.8 |
|
|
GNU |
X | X | | | A C++ class library for evolutionary genetics. |
| libshorah |
1.99.4 |
|
|
GPLv3 |
X | X | | | libshorah - Short Reads Assembly into Haplotypes |
| libssw |
1.2.5 |
doc |
dev |
MIT |
X | X | | | An SIMD Smith-Waterman C/C++/Python/Java Library for Use in Genomic... |
| libstatgen |
1.0.15 |
|
dev |
GPL3 |
X | X | | | Useful set of classes for creating statistical genetic programs. |
| libsvm |
3.16 |
|
|
|
X | | | | None |
| liftoff |
1.6.3 |
|
dev |
GPL-3 |
| | | X | An accurate GFF3/GTF lift over pipeline |
| liftofftools |
0.4.4 |
|
|
GPL-3.0-only |
| | | X | A tool for comparing annotations across genome assemblies |
| liftover |
1.3.2 |
|
dev |
MIT |
X | X | | | A Python package for converting point coordinates between genome... |
| lightassembler |
1.0 |
|
|
GPL |
X | X | | | Lightweight assembly algorithm designed to be executed on a desktop... |
| lighter |
1.1.3 |
doc |
dev |
GPL-3.0-or-later |
X | X | | | Lighter is a kmer-based error correction method for whole genome... |
| lightning |
0.2.dev0 |
|
|
Unknown |
X | X | | | lightning is a library for large-scale linear classification,... |
| lightstringgraph |
0.4.0 |
|
|
GPL-3 |
X | | | | LightStringGraphs (LSG) is an external memory string graph construction tool. |
| lima |
2.13.0 |
|
|
BSD-3-Clause-Clear |
X | | | | lima - The PacBio Barcode Demultiplexer |
| limix |
0.7.12 |
|
|
BSD |
X | X | | | None |
| linearfold |
1.0.1.dev20220829 |
|
|
custom |
X | | | | Linear-Time Prediction for RNA Secondary Structures |
| linearpartition |
1.0.1.dev20240123 |
|
|
custom |
X | | | | Linear-Time Approximation of RNA Folding Partition Function and Base... |
| linkage2allegro |
2017.3 |
|
|
GPL3 |
X | X | | X | Converts between the output linkage formats of Merlin, Simwalk,... |
| linkedsv |
0.1.0 |
|
dev |
MIT |
X | X | | | A novel structural variant caller for 10X Genomics (linked-read) sequencing data |
| links |
2.0.1 |
|
|
GPLv3 |
X | X | | | Long Interval Nucleotide K-mer Scaffolder |
| linkstats |
0.1.3 |
|
|
MIT |
X | X | | | Collect and process statistics from aligned linked-reads. |
| liqa |
1.3.4 |
doc |
dev |
MIT |
| | | X | A statistical tool to quantify isoform-specific expression using... |
| liquorice |
0.5.6 |
|
|
GPL-3.0 |
| | | X | A tool for bias correction and quantification of changes in coverage... |
| lisa2 |
2.3.2 |
|
|
MIT |
| | | X | Lisa: inferring transcriptional regulators through integrative modeling... |
| lissero |
0.4.9 |
doc |
dev |
GPL-3.0 |
| | | X | In silico serotyping of Listeria monocytogenes |
| liv_utils |
0.0.1 |
|
|
MIT |
| | | X | Liverpool University Basic Tools |
| livekraken |
1.0 |
|
|
GPLv3 |
X | X | | | LiveKraken is a real-time metagenomic classifier for Illumina sequencing data. |
| lja |
0.2 |
|
|
BSD-3-Clause |
X | | | | La Jolla Assembler(LJA) - tool for genome assembly from PacBio HiFI... |
| lmas |
2.0.8 |
|
dev |
GPL-3 |
| | | X | LMAS - Last (Meta)Genomic Assembler Standing |
| localhgt |
1.0.1 |
|
|
MIT |
X | X | | | An ultrafast horizontal gene transfer detection method from large... |
| locarna |
2.0.1 |
|
|
GPL |
X | X | | | Multiple alignment of RNAs |
| locidex |
0.3.0 |
|
dev |
Apache-2.0 |
| | | X | Locidex: Common search engine for similarity based typing applications. |
| locityper |
0.18.0 |
|
dev |
MIT |
X | X | | | Targeted genotyper for complex polymorphic loci from short and long read WGS. |
| locus_processing |
0.0.4 |
|
|
MIT |
| | | X | Tools for working with locus definition files |
| lodei |
1.0.0 |
|
|
GPL-3.0-or-later |
| | | X | Analyze differentially edited A-to-I regions in two sets of RNA-seq samples. |
| lofreq |
2.1.5 |
doc |
dev |
MIT |
X | X | | | A fast and sensitive variant-caller for inferring SNVs and indels from... |
| log4cpp |
1.1 |
|
|
Lesser |
X | X | | | Log4cpp is library of C++ classes for flexible logging to files,... |
| logbook |
1.4.3 |
|
|
BSD |
X | X | | | A logging replacement for Python |
| logol |
1.7.8 |
|
|
Affero |
X | | | | Logol is a pattern matching grammar language and a set of tools to... |
| logomaker |
0.8 |
|
|
MIT |
| | | X | Package for making Sequence Logos |
| lohhla |
20171108 |
|
|
UNKNOWN |
X | X | | X | A computational tool to evaluate HLA loss using next-generation sequencing data. |
| lollipop |
0.5.2 |
|
|
GNU |
| | | X | A tool for Deconvolution for Wastewater Genomics |
| longbow |
2.3.0 |
|
|
GPL-3.0-or-later |
| | | X | A Python program for nanopore sequencing basecalling configuration prediction |
| longcallr_nn |
0.0.2 |
|
dev |
MIT |
| | | X | longcallR_nn is a variant caller specifically designed for long-read... |
| longestrunsubsequence |
1.0.1 |
|
|
MIT |
| | | X | Implementation of a solver for the Longest Run Subsequence Problem.... |
| longgf |
0.1.2 |
|
|
GPL3 |
X | X | | | A fast tool to detect gene fusion from long-read RNA-seq data. |
| longphase |
1.7.3 |
|
dev |
GPL-3.0-only |
X | | | | LongPhase is an ultra-fast program for simultaneously co-phasing SNPs,... |
| longqc |
1.2.0c |
|
|
MIT |
| | | X | LongQC is a tool for the data quality control of the PacBio and ONT long reads |
| longreadsum |
1.3.1 |
doc |
dev |
MIT |
X | X | | | Long read sequencing data quality control tool |
| longshot |
1.0.0 |
doc |
dev |
MIT |
X | X | | | Diploid SNV caller for error-prone reads. |
| longstitch |
1.0.5 |
doc |
dev |
GPL-3.0-or-later |
| | | X | A genome assembly correction and scaffolding pipeline using long reads. |
| loompy |
2.0.16 |
|
|
BSD-2-Clause |
X | X | | X | Work with .loom files for single-cell RNA-seq data |
| lorax |
0.3.9 |
|
|
BSD-3-Clause |
X | X | | | A long-read analysis toolbox for cancer genomics |
| lordec |
0.9 |
|
|
CeCILL |
X | X | | | A hybrid error correction program for long, PacBio reads |
| lordfast |
0.0.10 |
|
|
GPL-3.0 |
X | X | | | Sensitive and Fast Alignment Search Tool for Long Read sequencing Data |
| lorikeet |
20 |
|
|
GPL-3 |
X | X | | X | Tool for digital spoligotyping of MTB strains from Illumina read data |
| lorikeet-genome |
0.8.2 |
doc |
|
GPL3 |
X | | | | Metagenomic Variant Calling & Diversity Analysis |
| lorma |
0.4 |
|
|
GNU |
X | | | | LoRMA is a tool for correcting sequencing errors in long reads. |
| lotus2 |
2.34.1 |
|
dev |
GPL-3.0-or-later |
| | | X | LotuS2 is a lightweight complete 16S/18S/ITS pipeline |
| lovis4u |
0.1.1.2 |
|
|
BSD-3-Clause |
| | | X | Loci Visualisation Tool. |
| lra |
1.3.7.2 |
|
|
USC-RL |
X | | | | Long read aligner for sequences and contigs |
| lrez |
2.2.4 |
|
|
AGPL-3.0-or-later |
X | X | | | Standalone tool and library allowing to work with barcoded linked-reads |
| lrge |
0.1.3 |
|
|
MIT |
X | X | | | Genome size estimation from long read overlaps |
| lrphase |
1.1.2 |
|
|
MIT |
| | | X | Phasing individual long reads using known haplotype information. |
| lrsim |
1.0 |
|
|
MIT |
X | | | | Simulator for 10X Genomics Linked Reads |
| lrtk |
2.0 |
|
|
MIT |
| | | X | This is a unified and versatile ToolKit for analyzing Linked-Read... |
| lrzip |
0.651 |
|
|
GPLv2 |
X | X | | | Long Range ZIP or Lzma RZIP. This is a compression program optimised... |
| ls-gkm |
0.0.1 |
|
|
GPL3 |
X | X | | | gkm-SVM, a sequence-based method for predicting regulatory DNA... |
| lsabgc |
1.1.2 |
|
dev |
BSD-3-Clause |
| | | X | lsaBGC-Pan - refined workflow for pan-BGC-omic evolutionary investigations. |
| lsc |
2.0 |
|
|
Apache |
X | X | | X | LSC is a long read error correction tool that offers fast correction... |
| lsd |
2.2.3 |
|
|
Apache |
X | X | | X | The LAPPS Grid Services DSL (LSD). Used to invoke LAPPS web services... |
| ltr_finder |
1.07 |
|
dev |
MIT |
X | X | | | LTR_Finder is an efficient program for finding full-length LTR... |
| ltr_finder_parallel |
1.1 |
doc |
dev |
MIT |
| | | X | Perl wrapper to parallelize ltr_finder |
| ltr_harvest_parallel |
1.1 |
doc |
dev |
MIT |
| | | X | Perl wrapper for parallel execution of LTR_harvest |
| ltr_retriever |
3.0.1 |
|
dev |
GPL-3.0-or-later |
| | | X | Sensitive and accurate identification of LTR retrotransposons |
| luciphor2 |
2020_04_03 |
|
|
Apache-2.0 |
| | | X | Luciphor2 performs PTM-site localization on MS/MS data |
| lukasa |
0.15.0 |
|
|
GPL-3.0 |
| | | X | Fast and accurate mapping of proteins against eukaryotic genomes |
| lumpy-sv |
0.3.1 |
|
|
MIT |
X | X | | X | a general probabilistic framework for structural variant discovery |
| lumpy-sv-minimal |
0.3.1 |
|
|
MIT |
X | | | | A general probabilistic framework for structural variant discovery.... |
| lusstr |
0.10 |
|
dev |
BSD-3-Clause |
| | | X | Tool for converting NGS sequence data of forensic STR loci to various... |
| lyner |
0.4.3 |
|
dev |
MIT |
| | | X | A chaining toolbox for working with dataframes |
| lz-ani |
1.2.3 |
|
|
GPL-3.0-or-later |
X | X | | | Fast and accurate tool for calculating Average Nucleotide Identity... |
| lz4-bin |
131 |
|
|
BSD |
X | X | | | Extremely Fast Compression Application |
| m-party |
0.2.2 |
doc |
dev |
MIT |
| | | X | Mining Protein dAtasets foR Targeted EnzYmes |
| m6anet |
2.1.0 |
|
|
MIT |
| | | X | m6anet is a python package for detection of m6a modifications from... |
| ma |
2.0.2 |
|
|
MIT |
X | | | | MA - The Modular Aligner |
| maaslin |
0.05 |
|
|
Custom |
X | X | | X | MaAsLin is a multivariate statistical framework that finds associations... |
| maaslin2 |
1.16.0 |
|
|
Custom |
| | | X | MaAsLin2 is comprehensive R package for efficiently determining... |
| maast |
1.0.8 |
|
|
MIT |
X | X | | | Microbial agile accurate SNP Typer |
| macaron |
1.0 |
|
|
LGPL-3 |
| | | X | Multi-bAse Codon-Associated variant Re-annotatiON |
| mace |
1.2 |
|
|
GPL3 |
X | X | | | Model Based Analysis for ChIP-exo data |
| machina |
1.2 |
|
|
BSD-3 |
X | X | | | Metastatic And Clonal History INtegrative Analysis |
| macrel |
1.5.0 |
|
dev |
MIT |
X | X | | X | A pipeline for AMP (antimicrobial peptide) prediction |
| macs |
1.4.3 |
|
|
Artistic |
| | | X | Model Based Analysis for ChIP-Seq data |
| macs2 |
2.2.9.1 |
doc |
dev |
BSD-3-Clause |
X | X | | | Model Based Analysis for ChIP-Seq data |
| macs3 |
3.0.3 |
doc |
dev |
BSD-3-Clause |
X | X | | | Model Based Analysis for ChIP-Seq data. |
| macse |
2.07 |
|
|
CeCILL |
| | | X | MACSE: Multiple Alignment of Coding SEquences Accounting for... |
| macsyfinder |
2.1.4 |
doc |
|
GPL-3.0-or-later |
| | | X | MacSyFinder: Detection of macromolecular systems in protein datasets... |
| maegatk |
0.2.0 |
doc |
dev |
MIT |
| | | X | Mitochondrial Alteration Enrichment and Genome Analysis Toolkit. |
| maelstrom-core |
0.1.1 |
|
|
MIT |
X | | | | Rust utilities for NGS data processing. |
| maf2synteny |
1.2 |
|
dev |
BSD |
X | X | | | A tool that postprocesses whole genome alignment (for two or more... |
| mafft |
7.525 |
|
|
BSD |
X | X | | | Multiple alignment program for amino acid or nucleotide sequences based... |
| magcluster |
0.2.5 |
|
|
GPL-2.0-or-later |
| | | X | Magnetosome gene cluster identification, annotation and visualization tool |
| mage-tab-merger |
0.0.4 |
doc |
dev |
MIT |
| | | X | Utility scripts to merge SDRFs, condensed SDRFs and IDFs (MAGE-Tab) for... |
| mageck |
0.5.9.5 |
|
|
BSD |
X | X | | | MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout), an... |
| mageck-vispr |
0.5.6 |
|
|
MIT |
X | X | | X | MAGeCK-VISPR is a comprehensive quality control, analysis and... |
| magetab-curation-scripts |
1.1.0 |
|
|
Apache |
| | | X | Perl-based scripts for ArrayExpress and Expression Atlas curation of... |
| magic-impute |
3.0.0 |
doc |
dev |
GPL-2.0 |
| | | X | Markov Affinity-based Graph Imputation of Cells |
| magicblast |
1.7.0 |
|
|
Public |
X | X | | | NCBI BLAST next generation read mapper |
| magneto |
1.3 |
doc |
dev |
GPL-3.0-only |
| | | X | MAGNETO is an automated snakemake workflow dedicated to MAG... |
| magphi |
2.0.2 |
doc |
dev |
MIT |
| | | X | A bioinformatics tool allowing for examnination and extraction of... |
| magpurify |
2.1.2 |
|
|
GPL-3 |
X | X | | X | Identify and remove incorrectly binned contigs from... |
| magus-msa |
0.2.0 |
doc |
dev |
MIT |
| | | X | Multiple Sequence Alignment using Graph Clustering |
| make_prg |
0.5.0 |
|
|
MIT |
| | | X | A tool to create and update PRGs from a set of Multiple Sequence Alignments. |
| makehub |
1.0.8 |
doc |
dev |
GPL-3.0-or-later |
| | | X | MakeHub is a command line tool for the fully automatic generation of of... |
| maker |
3.01.03 |
|
|
GPL3 |
X | X | | X | MAKER is a portable and easily configurable genome annotation pipeline. |
| malder |
1.0.1e83d4e |
|
|
Custom |
X | X | | | MALDER is a version of ALDER (http://groups.csail.mit.edu/cb/alder/)... |
| malt |
0.62 |
|
|
GPLv3 |
| | | X | A tool for mapping metagenomic data |
| malva |
2.0.0 |
|
|
GPL-3.0-or-later |
X | | | | genotyping by Mapping-free ALternate-allele detection of known VAriants |
| mammal |
1.1.1 |
|
|
GNU |
X | X | | | Accelerated Estimation of Frequency Classes in Site-heterogeneous... |
| mamotif |
1.1.0 |
|
|
BSD |
X | X | | X | An integrative toolkit for detecting cell type-specific regulators |
| mango |
0.0.5 |
doc |
dev |
Apache |
| | | X | A scalable genomic visualization tool |
| manorm |
1.3.0 |
|
|
BSD |
X | X | | X | A robust model for quantitative comparison of ChIP-Seq data sets. |
| manormfast |
0.1.2 |
|
|
GNU |
X | X | | | MAnorm version, Fast but more memory |
| manta |
1.6.0 |
|
|
GPL-3.0-only |
X | X | | | Structural variant and indel caller for mapped sequencing data |
| mantis |
0.2 |
|
|
BSD-3-Clause |
X | | | | Mantis: A Fast, Small, and Exact Large-Scale Sequence-Search Index |
| mantis-msi |
1.0.5 |
|
|
GPL-3 |
X | X | | X | MANTIS is a program developed for detecting microsatellite instability... |
| mantis-msi2 |
2.0.0 |
|
|
GPL-3 |
X | X | | | MANTIS2 is a program developed for detecting microsatellite instability... |
| mantis_pfa |
1.5.5 |
|
dev |
MIT |
X | X | | | Consensus-driven protein function annotation tool |
| mapad |
0.43.0 |
|
|
MIT |
X | X | | | An aDNA aware short-read mapper |
| mapcaller |
0.9.9.41 |
|
|
MIT |
X | X | | | MapCaller: combined short-read mapper and variant caller |
| mapdamage2 |
2.2.2 |
|
|
MIT |
X | X | | X | mapDamage: tracking and quantifying damage patterns in ancient DNA... |
| mapdia |
3.1.0 |
|
|
file |
X | X | | | Performs essential data preprocessing, including novel retention... |
| mapgl |
1.3.1 |
|
|
MIT |
| | | X | Prediction of lineage-specific gain and loss of sequence elements using... |
| mapping-iterative-assembler |
1.0 |
|
|
Artistic-2.0 |
X | X | | | Consensus calling or `reference assisted assembly`, chiefly of ancient... |
| mappy |
2.28 |
|
|
MIT |
X | X | | | Minimap2 Python binding |
| mapsembler2 |
2.2.4 |
|
|
GNU |
X | X | | | Targeted assembly software |
| mapseq |
2.1.1 |
|
|
dual-licensed |
X | X | | | Open source metagenomic 16S/18S read classifier enabling comparative... |
| mapsplice |
2.2.1 |
|
|
Custom |
X | | | | MapSplice is a software for mapping RNA-seq data to reference genome... |
| mapula |
2.1.2 |
doc |
dev |
Mozilla |
| | | X | Calculation of alignment statistics |
| marge |
1.0 |
|
|
MIT |
X | X | | X | Model-based Analysis of Regulation of Gene Expression |
| mark-nonconverted-reads |
1.2 |
|
|
AGPL-3.0 |
| | | X | A simple filter to mark potential nonconverted reads from methylation... |
| marker-magu |
0.4.0 |
|
dev |
MIT |
| | | X | Marker-MAGu: Trans-Kingdom Marker Gene Pipeline for Taxonomic Profiling... |
| markermag |
1.1.28 |
|
|
AGPL-3.0 |
| | | X | linking MAGs with 16S rRNA marker genes |
| markov_clustering |
0.0.6 |
|
|
MIT |
| | | X | This module implements the MCL algorithm in python. |
| mars |
1.2.4 |
|
|
MIT |
| | | X | Multiple Alignment-based Refinement of SVs (MARS) |
| marti |
0.9.22 |
doc |
|
MIT |
| | | X | Metagenomic Analysis in Real Time |
| marvd2 |
0.11.9 |
doc |
|
GPL-3.0-only |
| | | X | Metagenomic Archaeal Virus Detector 2 |
| marvel |
0.2 |
|
|
GPL3 |
| | | X | MARVEL: Metagenomic Analyses and Retrieval of Viral Elements |
| mash |
2.3 |
doc |
dev |
https://github. |
X | X | | | Fast sequence distance estimator that uses MinHash. |
| mashmap |
3.1.3 |
doc |
dev |
Custom |
X | X | | | A fast approximate aligner for long DNA sequences. |
| mashpit |
0.9.10 |
|
dev |
GPL-2.0-or-later |
| | | X | Sketch-based surveillance platform. |
| mashtree |
1.4.6 |
doc |
dev |
GPL-3.0-or-later |
X | X | | | Create a tree using Mash distances. |
| maskrc-svg |
0.5 |
|
|
GPL-3.0 |
| | | X | Masks recombinant regions in an alignment based on ClonalFrameML or... |
| mason |
2.0.9 |
|
|
https://github. |
X | X | | | Mason is a collection of tools for the simulation of biological sequences. |
| mass2chem |
0.5.0 |
|
|
BSD-Protection |
| | | X | Common utilities for interpreting mass spectrometry data |
| massdash |
0.1.0 |
|
dev |
BSD-3-Clause |
| | | X | MassDash is a streamlined DIA mass spec visualization, analysis,... |
| massiveqc |
0.1.2 |
|
|
MIT |
| | | X | Tools for QC massive RNA-seq samples |
| masurca |
4.1.2 |
doc |
dev |
GPL-3.0-only |
X | | | | MaSuRCA (Maryland Super-Read Celera Assembler) genome assembly... |
| matam |
1.6.1 |
|
|
AGPL-3.0 |
X | | | | MATAM is a software dedicated to the fast and accurate targeted... |
| matchms |
0.28.2 |
doc |
dev |
Apache-2.0 |
| | | X | Python library for fuzzy comparison of mass spectrum data and other... |
| matchmsextras |
0.4.2 |
|
|
Apache-2.0 |
| | | X | Additional network analysis functions for matchms |
| matchtigs |
2.1.9 |
|
dev |
MIT |
X | X | | X | "Different algorithms for computing small and minimum plain text... |
| mathstats |
0.2.6.5 |
|
|
GPLv3 |
X | X | | X | Statistical functions, goodness-of-fit tests and special and special... |
| matlock |
20181227 |
|
|
GNU |
X | X | | | Simple tools for working with Hi-C data |
| mauve |
2.4.0.snapshot |
|
dev |
GPL-2.0 |
X | | | X | Mauve is a system for constructing multiple genome alignments in the... |
| mauvealigner |
1.2.0 |
|
dev |
GPL-2.0 |
X | | | | The mauveAligner and progressiveMauve command-line tools for generating... |
| mavenn |
1.1.0 |
doc |
dev |
MIT |
| | | X | MAVE-NN: genotype-phenotype maps from multiplex assays of variant effect. |
| mavis |
2.2.6 |
doc |
|
Non-commercial |
| | | X | A Structural Variant Post-Processing Package |
| mavis-config |
1.2.2 |
|
|
GPL-3.0-or-later |
| | | X | Config validation for running MAVIS via Snakemake |
| mawk |
1.3.4 |
|
|
Copyright |
X | X | | | mawk is an interpreter for the AWK Programming Language. |
| maxbin2 |
2.2.7 |
|
|
BSD |
X | X | | | MaxBin is software for binning assembled metagenomic sequences based on... |
| maxentpy |
0.02 |
|
|
MIT |
X | X | | | maxentpy is a python wrapper for MaxEntScan to calculate splice site strength. |
| maxentscan |
0_2004.04.21 |
|
|
unknown |
X | | | X | MaxEntScan is based on the approach for modeling the sequences of short... |
| maxit |
11.200 |
doc |
|
RCSB |
X | X | | | MAXIT assists in the processing and curation of macromolecular structure data. |
| maxquant |
2.0.3.0 |
|
|
http://www.coxd |
X | | | X | MaxQuant is a quantitative proteomics software package designed for... |
| mbg |
1.0.16 |
|
|
MIT |
X | X | | | Minimizer based sparse de Bruijn graph constructor |
| mbgc |
2.0.1 |
|
dev |
GPL-3.0-or-later |
X | X | | | A tool for compressing collection of genomes in FASTA format. |
| mbuffer |
20160228 |
|
|
GPLv3 |
X | | | | mbuffer is a tool for buffering data streams with a large set of unique features |
| mccortex |
1.0 |
|
|
MIT |
X | X | | | De novo genome assembly and multisample variant calling |
| mcl |
22.282 |
doc |
dev |
GPL-3.0-only |
X | X | | | MCL - a cluster algorithm for graphs. |
| mcroni |
1.0.4 |
|
|
MIT |
| | | X | mcr-1 analysis |
| mcross |
0.9.5 |
|
|
MIT |
| | | X | The script to detect RNA-protein cross linking sites |
| mcscanx |
1.0.0 |
|
dev |
BSD-2-Clause |
X | X | | | Multiple Collinearity Scan toolkit X version |
| md-cogent |
8.0.0 |
|
|
BSD-3-Clause-Clear |
| | | X | COding GENome reconstruction Tool using transcript sequences |
| mdasim |
2.1.1 |
|
|
GPL-3.0 |
X | | | | This is MDAsim 2+, a tool to simulate whole genome amplification of a... |
| mdmcleaner |
0.8.7 |
|
|
GPL-3.0 |
| | | X | A pipeline for the assessment, classification and refinement of... |
| mdust |
2006.10.17 |
|
|
The |
X | X | | | mdust from DFCI Gene Indices Software Tools. |
| me-pcr |
1.0.6 |
|
|
Public |
X | X | | | Multithreaded Electronic PCR (in-silico PCR) based on NCBI e-PCR. |
| mea |
0.6.4 |
|
|
GPLv3 |
X | | | | Mea was developed as part of the lab class "Bioinformatik von RNA-... |
| medaka |
2.0.1 |
doc |
dev |
MPL-2.0 |
X | X | | | A tool to create consensus sequences and variant calls from nanopore... |
| medicc2 |
1.1.2 |
|
dev |
GPL-3.0-or-later |
X | X | | | Whole-genome doubling-aware copy number phylogenies for cancer evolution |
| medpy |
0.4.0 |
|
|
GNU |
X | X | | X | Medical image processing in Python |
| medusa |
1.6 |
|
|
GPL |
| | | X | A draft genome scaffolder that uses multiple reference genomes in a... |
| medusa-data-fusion |
0.1 |
|
|
GPLv3 |
X | X | | X | Medusa is an approach to detect size-k modules of objects that, taken... |
| megadepth |
1.2.0 |
|
|
MIT |
X | X | | | Megadepth is an efficient tool for extracting coverage related... |
| megagta |
0.1_alpha |
|
|
GNU |
X | | | | HMM-guided metagenomic gene-targeted assembler using iterative de Bruijn graphs |
| megahit |
1.2.9 |
|
|
GPL-3.0 |
X | X | | | MEGAHIT: An ultra-fast single-node solution for large and complex... |
| megalodon |
2.5.0 |
doc |
dev |
Oxford |
X | X | | | Nanopore modified base and sequence variant detection. |
| megan |
6.25.10 |
|
|
GPL |
X | | | | A tool for studying the taxonomic content of a set of DNA reads |
| megapath |
2 |
|
|
BSD-3-Clause |
X | | | | MegaPath: sensitive and rapid pathogen detection using metagenomic NGS... |
| megapath-nano |
2 |
|
|
BSD-3-Clause |
X | | | X | MegaPath-Nano: Accurate Compositional Analysis and Drug-level... |
| megatron |
0.1a |
|
dev |
BSD-3 |
| | | X | MEGATRON - MEGA TRajectories of clONes |
| mehari |
0.28.1 |
|
dev |
MIT |
X | | | | VEP-like tool for sequence ontology and HGVS annotation of VCF files... |
| melon |
0.2.5 |
|
|
MIT |
| | | X | Melon: metagenomic long-read-based taxonomic identification and... |
| melt |
1.0.3 |
|
|
GNU |
X | X | | X | A nucleotide melt temp calculator |
| meme |
5.5.7 |
doc |
|
Custom |
X | X | | | Motif-based sequence analysis tools. |
| memopair |
0.1.6 |
|
|
MIT |
X | X | | | A package for identifying methylated motif pairs |
| memote |
0.17.0 |
|
|
Apache-2.0 |
| | | X | the genome-scale metabolic model test suite |
| mendelscan |
1.2.2 |
|
|
Unknown |
X | X | | X | Analyze exome data for Mendelian disorders. |
| meneco |
1.5.2 |
|
|
GPLv3+ |
X | X | | | Metabolic Network Completion. Compute minimal completions to your draft... |
| menetools |
2.0.6 |
|
|
GPLv3+ |
X | X | | X | Python 3 Metabolic Network Topology Tools |
| meningotype |
0.8.5 |
|
|
GPL-3.0 |
| | | X | In silico serotyping and finetyping (porA and fetA) of Neisseria meningitidis |
| mentalist |
0.2.4 |
|
|
MIT |
X | | | | The MLST pipeline developed by the PathOGiST research group. |
| meraculous |
2.2.6 |
|
|
GPLv3 |
X | | | | Meraculous is a whole genome assembler for Next Generation Sequencing... |
| mercat |
0.2 |
|
|
BSD |
X | X | | X | Mercat: a versatile counter and diversity estimator for data base... |
| mercat2 |
1.4.1 |
|
|
BSD-3-Clause |
| | | X | versatile k-mer counter and diversity estimator for database... |
| merfin |
1.0 |
|
|
Apache-2.0 |
X | X | | | Improved variant filtering and polishing via k-mer validation. |
| merfishtools |
1.5.0 |
|
|
MIT |
X | | | | MERFISHtools implement a Bayesian framework for accurately predicting... |
| merge-gbk-records |
0.2.0 |
|
|
Apache-2.0 |
| | | X | Turn multiple GenBank records (either in multiple files or a single... |
| mergenotcombined |
1.0 |
|
|
GPL-3.0 |
X | | | | Merge Forward and reverse reads from fastq files |
| mergevcf |
1.0.1 |
|
|
MIT |
X | X | | X | Python package and routines for merging VCF files |
| merlin |
1.1.2 |
|
|
OpenSource |
X | X | | | MERLIN uses sparse trees to represent gene flow in pedigrees and is a... |
| merqury |
1.3 |
|
|
PUBLIC |
| | | X | Evaluate genome assemblies with k-mers and more. |
| merquryfk |
1.1.1 |
|
|
https://github. |
X | X | | | MerquryFK replaces meryl with the FastK k-mer counter suite to... |
| meryl |
2013 |
doc |
dev |
GPL |
X | X | | | meryl is a multi-threaded, multi-process, out-of-core k-mer counter |
| mess |
0.10.0 |
doc |
dev |
MIT |
| | | X | Snakemake pipeline for simulating shotgun metagenomic samples |
| met4j |
2.0.1 |
|
|
CeCILL-2.1 |
| | | X | Met4J is an open-source Java library dedicated to the structural... |
| meta-apo |
1.1 |
|
|
GPL3 |
X | X | | | Meta-Apo improves accuracy of 16S-amplicon-based prediction of... |
| meta-neuro |
1.0.1 |
doc |
dev |
BSD-3-Clause |
X | X | | | Medial Tractography Analysis (MeTA) |
| meta-sparse |
0.1.12 |
|
|
GNU |
X | X | | | SPARSE indexes reference genomes in public databases into hierarchical... |
| meta_eukaryome_detect |
0.1.1 |
doc |
dev |
MIT |
| | | X | Pathogen, Parasite, Eukaryote and Virus detection in metagenomes. |
| metabat2 |
2.17 |
|
|
BSD-3-Clause-LBNL |
X | X | | | Metagenome binning |
| metabinkit |
0.2.3 |
doc |
dev |
GPL-3 |
X | | | | Set of programs to perform taxonomic binning. |
| metabinner |
1.4.4 |
|
|
BSD |
| | | X | Ensemble binning method to recover individual genomes from complex... |
| metabolabpy |
0.9.68 |
doc |
dev |
GPL-3.0-or-later |
| | | X | Python package to process 1D and 2D NMR spectroscopic data for... |
| metabolights-utils |
1.4.2 |
|
|
Apache-2.0 |
| | | X | MetaboLights open metabolomics data repository command line interface... |
| metabuli |
1.1.0 |
|
|
GPLv3 |
X | X | | | Metabuli: specific and sensitive metagenomic classification via joint... |
| metacache |
2.5.0 |
|
|
GPL-3.0-or-later |
X | | | | MetaCache is a classification system for mapping genomic sequences... |
| metacerberus |
1.4.0 |
|
|
BSD-3-Clause |
| | | X | Versatile Functional Ontology Assignments for Metagenomes via Hidden... |
| metacerberus-lite |
1.4.0 |
|
|
BSD-3-Clause |
| | | X | MetaCerberus with reduced dependencies: Versatile Functional Ontology... |
| metacherchant |
0.1.0 |
|
|
MIT |
X | X | | X | genomic environment analysis tool |
| metachip |
1.10.13 |
|
|
GPL3+ |
| | | X | HGT detection pipeline |
| metaclassifier |
1.0.1 |
doc |
dev |
GNU |
| | | X | MetaClassifier is an integrated pipeline for classifying and... |
| metaclock |
1.0.0 |
|
|
A-GPL |
| | | X | A python package for facilitating strain-level phylogenetic and... |
| metacluster |
5.1 |
|
|
GPLv2 |
X | | | | MetaCluster5.1 is a new software for binning short pair-end reads |
| metacoag |
1.2.2 |
doc |
dev |
GPL-3.0-or-later |
X | X | | X | MetaCoAG: Binning Metagenomic Contigs via Composition, Coverage and... |
| metacortex |
0.5.1 |
|
|
GPL-3.0-or-later |
X | | | | MetaCortex is an assembler for metagenomic, or environmental sequence data. |
| metadmg |
0.4 |
|
|
GPLv3, |
X | X | | | metaDMG-cpp: fast and efficient method for estimating mutation and... |
| metaeuk |
7.bba0d80 |
|
|
GPL-3 |
X | X | | | MetaEuk - sensitive, high-throughput gene discovery and annotation for... |
| metafun |
0.1.1 |
|
|
MIT |
| | | X | Custom package for metafun workflow management |
| metafx |
1.1.0 |
|
|
The |
| | | X | MetaFX (METAgenomic Feature eXtraction) is a library for feature... |
| metagem |
1.0.5 |
|
|
MIT |
| | | X | Generate context specific genome-scale metabolic models and predict... |
| metagene_annotator |
1.0 |
|
|
The |
X | X | | | MetaGeneAnnotator is a gene-finding program for prokaryote and phage |
| metagenome-atlas |
2.19.0 |
doc |
dev |
BSD-3-Clause |
X | | | X | ATLAS - Three commands to start analysing your metagenome data |
| metagraph |
0.3.6 |
doc |
dev |
MIT |
X | X | | | Ultra Scalable Framework for DNA Search, Alignment, Assembly |
| metalign |
0.12.5 |
doc |
dev |
MIT |
| | | X | Metalign: efficient alignment-based metagenomic profiling via... |
| metamaps |
0.1.98102e9 |
|
|
Public |
X | X | | | MetaMaps is a tool for long-read metagenomic analysis |
| metamate |
0.4.3 |
|
|
GPL-3.0 |
| | | X | metaMATE: your metabarcoding friend! |
| metamdbg |
1.1 |
doc |
dev |
MIT |
X | X | | | MetaMDBG: a lightweight assembler for long and accurate metagenomics reads. |
| metameta |
1.2.0 |
|
|
The |
X | | | X | MetaMeta - pipeline for integrating metagenome analysis tools to... |
| metametamerge |
1.1 |
|
|
The |
X | X | | X | Merging module of the MetaMeta Pipeline |
| metamlst |
1.2.3 |
|
|
MIT |
| | | X | A computational pipeline for MLST typing from metagenomic data |
| metamobilepicker |
0.7.3 |
doc |
|
MIT |
| | | X | MetaMobilePicker: identification of MGEs and ARGs based in metagenomic samples |
| metanovo |
1.9.4 |
|
|
MIT |
X | | | | Produce targeted databases for mass spectrometry analysis. |
| metaomestats |
0.4 |
|
|
MIT |
| | | X | Scripts for calculating statistics from FASTA sequences |
| metaphlan |
4.1.1 |
doc |
dev |
MIT |
| | | X | Metagenomic Phylogenetic Analysis |
| metaphlan2 |
2.96.1 |
|
|
MIT |
X | X | | X | Metagenomic Phylogenetic Analysis |
| metaphor |
1.7.14 |
doc |
dev |
MIT |
| | | X | Metaphor - Metagenomic Pipeline for Short Reads |
| metaphyler |
1.25 |
|
|
Artistic |
X | | | | Estimating Bacterial Composition from Metagenomic Sequences |
| metapi |
3.0.0 |
|
|
GPL-3.0-only |
| | | X | A general metagenomics data mining system focus on robust microbiome research |
| metaplatanus |
1.3.1 |
|
|
GPL-3.0 |
X | | | | MetaPlatanus: A hybrid metagenome assembler |
| metaplex |
1.1.0 |
|
|
BSD-3-Clause |
| X | | X | Read Processing and Quality Control Toolkit for Dual-Indexed Metabarcoding |
| metapop |
1.0.2 |
|
|
GPL-2.0 |
| | | X | A pipeline for the macro- and micro-diversity analyses and... |
| metaprob |
2 |
|
|
copyright |
X | | | | assembly-assisted tool for un-supervised metagenomic binning |
| metaprokka |
1.15.0 |
|
dev |
GPL-3.0-only |
| | | X | A fork of Prokka using Prodigal-GV for phage annotation and... |
| metaquant |
0.1.2 |
|
dev |
Apache |
X | X | | X | Quantitative microbiome analysis |
| metaquantome |
2.0.2 |
|
dev |
Apache |
| | | X | Quantitative metaproteomics analysis of taxonomy and function. |
| metaseq |
0.5.6 |
|
|
MIT |
X | X | | | Framework for integrated analysis and plotting of ChIP/RIP/RNA/*-seq data. |
| metaseq-all |
0.5.6 |
|
|
The |
X | X | | X | Meta-package for metaseq including bedtools and UCSC tools |
| metasnek |
0.0.8 |
|
|
MIT |
| | | X | Misc functions for metagenomics pipelines |
| metasnv |
2.0.4 |
|
|
GPLv3 |
X | X | | | SNV calling software |
| metasv |
0.5.4 |
|
|
MIT |
X | X | | | An accurate and integrative structural-variant caller for next... |
| metator |
1.3.7 |
doc |
dev |
GPL-3.0-or-later |
X | X | | | Metagenomic binning based on Hi-C data. |
| metatree |
0.0.1 |
|
|
GNU |
| | | X | Visualisation of polyphyletic groups between phylogenetic trees to a... |
| metav |
1.0.6 |
|
dev |
GPL-3.0-or-later |
| | | X | Rapid detection and classification of viruses in metagenomics sequencing. |
| metavelvet |
1.2.02 |
|
|
GNU |
X | | | | MetaVelvet : An extension of Velvet assembler to de novo metagenome... |
| metavelvet-annois |
0.2.01 |
|
|
GNU |
X | | | X | Metavelvet AnnoIS - an extra package for metavelvet for versions < 1.2.01 |
| metavelvet-sl |
1.0 |
|
|
|
X | | | | MetaVelvet-SL : An extension of Velvet assembler to de novo metagenomic... |
| metavelvet-sl-feature-extraction |
1.0 |
|
|
|
X | X | | | Perl libraries that do feature extraction for metavelvet-sl |
| metavelvet-sl-pipeline |
1.0 |
|
|
|
X | | | | Perl libraries that run the full pipeline for metavelvet-sl |
| metawatt |
3.5.3 |
|
|
AFL |
X | | | X | MetaWatt is a metagenomic binning tool |
| metawrap |
1.2 |
|
|
MIT |
X | | | X | MetaWRAP is a pipeline for genome-resolved metagenomic data analysis |
| metawrap-mg |
1.3.0 |
|
|
MIT |
| | | X | MetaWRAP is a pipeline for genome-resolved metagenomic data analysis |
| metaxa |
2.2.3 |
|
|
GPL-3.0 |
X | X | | X | Improved Identification and Taxonomic Classification of Small and Large... |
| metdatamodel |
0.6.0 |
|
|
BSD-3-Clause |
| | | X | Data models for metabolomics |
| meteor |
2.0.18 |
|
dev |
GPL-3.0-or-later |
| | | X | Meteor is a plateform for quantitative metagenomics profiling of... |
| metfrag |
2.4.5 |
|
|
GNU |
X | X | | X | MetFrag is a freely available software for the annotation of high... |
| methbat |
0.14.0 |
|
|
BSD-3-Clause-Clear |
X | | | | A battery of methylation tools for PacBio HiFi reads |
| methphaser |
0.0.3 |
|
|
MIT |
| | | X | MethPhaser: methylation-based haplotype phasing of human genomes |
| methpipe |
5.0.1 |
|
|
GPL-3 |
X | X | | | A pipeline for analyzing DNA methylation data from bisulfite sequencing. |
| methplotlib |
0.21.2 |
|
|
MIT |
| | | X | Plot methylation data obtained from nanopolish |
| methylartist |
1.3.1 |
|
|
MIT |
| | | X | Tools for parsing and plotting nanopore methylation data |
| methyldackel |
0.6.1 |
|
|
MIT |
X | X | | | A (mostly) universal methylation extractor for BS-seq experiments.... |
| methylextract |
1.9.1 |
|
|
GNU |
X | X | | X | High-Quality methylation maps and SNV calling from whole genome... |
| methylmap |
0.5.11 |
|
|
MIT |
| | | X | Plotting tool for population-scale nucleotide modifications |
| methylpy |
1.4.7 |
doc |
|
Apache-2.0 |
X | X | | | Bisulfite sequencing data processing and differential methylation analysis |
| metilene |
0.2.8 |
|
|
GPLv2 |
X | X | | | Fast and sensitive detection of differential DNA methylation |
| mfold |
3.6 |
|
|
Custom |
X | X | | | Mfold web server for nucleic acid folding and hybridization prediction. |
| mfqe |
0.5.0 |
|
|
GPL3 |
X | | | | mfqe is a tool for quickly seperating fasta and fastq files |
| mg-toolkit |
0.10.4 |
|
dev |
Apache-2.0 |
| | | X | Metagenomics toolkit. |
| mgatk |
0.7.0 |
doc |
|
MIT |
| | | X | Mitochondrial genome analysis toolkit. |
| mgca |
0.0.0 |
doc |
dev |
GPLv3 |
| | | X | Microbial genome component and annotation pipeline |
| mgcod |
1.0.2 |
|
|
GPL-3 |
| | | X | Recognition of genetic codes (incl. multiple genetic codes in phage... |
| mgcplotter |
1.0.1 |
|
|
GPL-3.0 |
| | | X | Microbial Genome Circular plotting tool using Circos |
| mge-cluster |
1.1.0 |
|
|
MIT |
| | | X | A classification framework for mobile genetic elements (MGEs) |
| mgems |
1.3.3 |
|
dev |
MIT |
X | X | | | mGEMS - sequencing data binning based on probabilistic classification |
| mgf-formatter |
1.0.0 |
|
|
Eclipse |
X | X | | X | Tools for convert peak lists into MGF files formatted for particular... |
| mgikit |
1.0.0 |
|
dev |
AFL-3.0 |
X | X | | | mgikit is a collection of tools used to demultiplex fastq files and... |
| mgkit |
0.5.8 |
|
|
GPL-2.0-or-later |
X | X | | | Metagenomics Framework |
| mglex |
0.2.1 |
|
|
GPL-3.0 |
X | X | | X | MGLEX - MetaGenome Likelihood EXtractor |
| mgltools |
1.5.7 |
|
|
OTHER |
X | X | | | MGLTools is an program for visualization and analisys of molecular structures. |
| mgnify-pipelines-toolkit |
1.0.0 |
|
dev |
Apache-2.0 |
| | | X | Collection of scripts and tools for MGnify pipelines. |
| mgs-canopy |
1.0 |
|
|
GPL3 |
X | | | | Canopy clustering algorithm |
| mhap |
2.1.3 |
|
|
Apache-2.0 |
X | X | | X | MHAP: MinHash Alignment Protocol. A tool for finding overlaps of... |
| mhc-annotation |
0.1.1 |
|
|
MIT |
| | | X | Tools to annotate haplotypes of MHC with gene and transcript information |
| mhcflurry |
2.1.4 |
doc |
|
Apache-2.0 |
| | | X | MHC Binding Predictor |
| mhcgnomes |
1.8.6 |
|
|
Apache |
| | | X | Python library for parsing MHC nomenclature in the wild |
| mhcnames |
0.4.8 |
|
|
Apache |
| | | X | Python library for MHC nomenclature parsing |
| mhcnuggets |
2.4.1 |
|
|
Apache |
X | X | | X | MHCnuggets: Neoantigen peptide MHC binding prediction for class I and II |
| mhg |
1.1.0 |
|
|
MIT |
| | | X | MHG is an annotation-free graph-based tool to merge and partition... |
| micall-lite |
0.1rc5 |
|
|
GNU |
X | X | | | A bioinformatic pipeline for mapping of FASTQ data to a set of... |
| micom |
0.37.0 |
|
|
Apache-2.0 |
| | | X | Microbial community modeling based on cobrapy. |
| micomplete |
1.1.1 |
doc |
dev |
GPL-3.0-or-later |
| | | X | Quality control of assembled genomes |
| micro_razers |
1.0.6 |
|
|
GPLv3 |
X | | | | MicroRazerS - Rapid Alignment of Small RNA Reads |
| microbeannotator |
2.0.5 |
|
|
Artistic |
| | | X | A user friendly microbe genome annotation tool |
| microbecensus |
1.1.1 |
|
|
GNU |
X | X | | X | A command-line tool for estimating average genome size from shotgun... |
| microhapdb |
0.11 |
|
dev |
BSD |
| | | X | Portable database of microhaplotype marker and allele frequency data. |
| microhapulator |
0.8.4 |
|
dev |
BSD-3-Clause |
| | | X | Tools for empirical microhaplotype calling, forensic interpretation,... |
| microphaser |
0.8.0 |
|
|
MIT |
X | | | | Phasing small tumor DNA sequences for mutated neopeptide generation... |
| micropita |
1.1.0 |
|
|
MIT |
X | X | | X | microPITA is a computational tool enabling sample selection in... |
| microview |
0.11.0 |
|
|
BSD-3-Clause |
X | X | | | Generate reports from taxonomic classification data |
| midas |
1.3.2 |
|
|
GPL-3.0 |
X | | | X | An integrated pipeline for estimating strain-level genomic variation... |
| midsv |
0.11.1 |
|
|
MIT |
| | | X | Python module to convert SAM to MIDSV format. |
| miga |
1.0.0 |
|
dev |
LGPL-3.0 |
X | X | | | Python package to optimize mutual information between two multiple... |
| migmap |
1.0.3 |
|
|
Apache-2.0 |
X | X | | X | A wrapper for IgBlast V-(D)-J mapping tool designed to facilitate... |
| migraine |
0.6.0 |
|
|
CeCILL |
X | X | | | Implements coalescent algorithms for maximum likelihood analysis of... |
| migrate-n |
3.6.11 |
|
|
MIT |
X | | | | Population Genetics - Panmixia and Migration detection |
| miidl |
0.0.5 |
|
|
MIT |
| | | X | A Python package for microbial biomarkers identification powered by... |
| mikado |
2.3.4 |
doc |
dev |
LGPL-3.0-or-later |
X | X | | | A Python3 annotation program to select the best gene model in each locus |
| mikrokondo-tools |
0.0.1rc0 |
|
dev |
Apache-2.0 |
| | | X | A collection of utilities to make using the mikrokondo pipeline easier |
| milonga |
1.0.3 |
|
|
BSD-3-Clause |
| | | X | MiLongA - A snakemake workflow for Microbial Long-read Assembly |
| mimeo |
1.1.2 |
|
dev |
MIT |
X | X | | X | Scan genomes for internally repeated sequences, elements which are... |
| mimodd |
0.1.9 |
|
|
GPL3 |
X | X | | | Tools for Mutation Identification in Model Organism Genomes |
| mimseq |
1.3.8 |
|
|
GPL-3.0-only |
| | | X | Modification-induced misincorporation tRNA sequencing. |
| mimsi |
0.4.5 |
|
|
GNU |
| | | X | A Deep Mulitple Instance Learning Classifier for Microsatellite Instability |
| minced |
0.4.2 |
|
|
GPL-3.0 |
X | X | | X | MinCED - Mining CRISPRs in Environmental Datasets |
| mindagap |
0.0.2 |
doc |
|
BSD |
| | | X | Takes a single panorama image and fills the empty grid lines with... |
| mindthegap |
2.3.0 |
|
|
AGPL-3.0-or-later |
X | X | | | MindTheGap performs detection and assembly of DNA insertion variants in... |
| minepy |
1.2.3 |
|
|
GNU |
X | X | | | minepy - Maximal Information-based Nonparametric Exploration |
| mini3di |
0.2.1 |
|
|
BSD-3-Clause |
| | | X | A NumPy port of the foldseek code for encoding protein structures to 3di. |
| minia |
3.2.6 |
|
|
file |
X | X | | | Minia is a short-read assembler based on a de Bruijn graph, capable of... |
| minialign |
0.5.3 |
|
|
MIT |
X | X | | | Fast and accurate alignment tool for PacBio and Nanopore long reads. |
| miniasm |
0.3 |
doc |
dev |
MIT |
X | X | | | Ultrafast de novo assembly for long noisy reads (though having no... |
| minibusco |
0.2.1 |
|
dev |
Apache |
| | | X | minibusco: a faster and more accurate reimplementation of BUSCO |
| minigraph |
0.21 |
doc |
dev |
MIT |
X | X | | | Proof-of-concept seq-to-graph mapper and graph generator |
| minimac4 |
4.1.6 |
|
|
GPL-3.0-or-later |
X | X | | | Computationally efficient genotype imputation |
| minimap |
0.2 |
|
|
MIT |
X | X | | | Experimental tool to find approximate mapping positions between long sequences |
| minimap2 |
2.28 |
doc |
dev |
MIT |
X | X | | | A versatile pairwise aligner for genomic and spliced nucleotide sequences. |
| minimap2-coverage |
1.2.0c |
|
|
MIT |
X | | | | A versatile pairwise aligner for genomic and spliced nucleotide... |
| minimizers |
0.1.2 |
|
dev |
MIT |
| | | X | Minimizers extraction from fasta files. |
| minimock |
1.2.8 |
|
|
MIT |
X | X | | | The simplest possible mock library |
| minipolish |
0.1.3 |
|
|
GPLv3 |
| | | X | A tool for Racon polishing of miniasm assemblies |
| miniprot |
0.14 |
|
|
MIT |
X | X | | | Miniprot aligns a protein sequence against a genome with affine gap... |
| miniprot-boundary-scorer |
1.0.0 |
|
dev |
Artistic-1.0 |
X | X | | | Miniprot boundary scorer parses introns, starts, stops and exons from... |
| minirmd |
1.1 |
|
|
GPL-3.0-only |
X | X | | | Remove duplicate and near-duplicate reads |
| minnow |
1.2 |
|
|
GPLv3 |
X | X | | | A principled framework for rapid simulation of dscRNA-seq data at the read level |
| minorseq |
1.12.0 |
|
|
BSD-3-Clause-Clear |
X | | | | Minor Variant Calling and Phasing Tools |
| mintie |
0.4.3 |
|
|
MIT |
| | | X | Method for Identifying Novel Transcripts and Isoforms using Equivalence... |
| mintmap |
1.0 |
|
|
open |
X | X | | X | Generate tRF profiles from short RNA-Seq datasets |
| minute |
0.10.1 |
doc |
dev |
MIT |
| | | X | MINUTE-ChIP data analysis workflow |
| minvar |
2.2.2 |
|
|
Custom |
X | X | | X | A tool to detect minority variants in HIV-1 and HCV populations |
| minys |
1.1 |
|
|
file |
X | X | | | MinYS allows targeted assembly of bacterial genomes using a... |
| mir-prefer |
0.24 |
|
|
GPL |
X | X | | X | microRNA PREdiction From small RNA-seq data |
| mira |
4.9.6 |
|
|
GNU |
X | | | | MIRA is a whole genome shotgun and EST sequence assembler for Sanger,... |
| mira-moods |
1.9.4.2 |
|
|
MIT |
X | X | | | MOODS: Motif Occurrence Detection Suite |
| mira-multiome |
2.1.1 |
|
|
BSD-3-Clause-LBNL |
| | | X | Single-cell multiomics data analysis |
| miranda |
3.3a |
|
|
GPLv2 |
X | X | | | An algorithm for finding genomic targets for microRNAs |
| mirdeep-p2 |
1.1.4 |
|
|
GNU |
| | | X | A fast and accurate tool for analyzing the miRNA transcriptome in plants |
| mirdeep2 |
2.0.1.3 |
|
|
academic |
X | X | | X | A completely overhauled tool which discovers microRNA genes by... |
| mirfix |
2.1.1 |
|
|
GPL-3.0 |
| | | X | MIRfix automatically curates miRNA datasets by improving alignments of... |
| mirge |
2.0.6 |
|
|
MIT |
X | X | | X | comprehensive analysis of miRNA sequencing data |
| mirge-build |
0.0.1 |
doc |
dev |
MIT |
| | | X | miRge-build: Building libraries of small RNA sequencing Data |
| mirge3 |
0.1.4 |
doc |
dev |
MIT |
| | | X | Comprehensive analysis of small RNA sequencing Data |
| mirmachine |
0.2.13 |
doc |
dev |
MIT |
| | | X | A command line to tool detect miRNA homologs in genome sequences. |
| mirnature |
1.1 |
|
|
GPL-3.0 |
| | | X | MiRNAture improves on ideas from MIRfix and integrates it with homology... |
| mirscore |
0.3.2 |
|
|
MIT |
| | | X | miRScore: A rapid and precise microRNA validation tool |
| mirtop |
0.4.28 |
doc |
dev |
MIT |
X | X | | X | Small RNA-seq annotation. |
| mirtrace |
1.0.1 |
|
|
GPL-2.0 |
| | | X | miRTrace is a new quality control and taxonomic tracing tool developed... |
| miru-hero |
0.10.0 |
|
|
GPL-3.0-or-later |
| | | X | Compute MIRU and Spoligotype from a M. tuberculosis genome |
| misopy |
0.5.4 |
|
|
GPL2 |
X | X | | | Mixture of Isoforms model (MISO) for isoform quantitation using RNA-Seq |
| mitgard |
1.1 |
doc |
|
GPL-3.0-or-later |
| | | X | Mitochondrial Genome Assembly from RNA-seq Data. |
| mitobim |
1.9.1 |
|
|
MIT |
| | | X | mitochondrial baiting and iterative mapping |
| mitofinder |
1.4.1 |
|
|
MIT |
X | X | | | Mitofinder is a pipeline to assemble mitochondrial genomes and annotate... |
| mitorsaw |
0.1.1 |
|
|
Pacific |
X | | | | A tool for mitochondrial analysis for HiFi sequencing data |
| mitos |
2.1.9 |
|
dev |
MIT |
| | | X | MITOS is a tool for the annotation of metazoan mitochondrial genomes. |
| mitosalt |
1.1.1 |
|
|
MIT-0 |
| | | X | MitoSAlt is a pipeline to identify large deletions and duplications in... |
| mitoz |
3.6 |
|
|
GPLv3 |
| | | X | MitoZ: A toolkit for assembly, annotation, and visualization of animal... |
| mity |
1.1.0 |
|
|
MIT |
| | | X | Mity is a bioinformatic analysis pipeline designed to call... |
| mixem |
0.1.4 |
|
|
MIT |
| | | X | Expectation-Maximization (EM) algorithm for fitting mixtures of... |
| mkdesigner |
0.5.1 |
|
dev |
MIT |
| | | X | Genome-wide design of markers for PCR-based genotyping from NGS data. |
| mlgenotype |
0.1.12 |
doc |
dev |
MIT |
| | | X | A package with utilities for training random forest classifiers to... |
| mlpy |
3.5.0 |
doc |
dev |
GPL3 |
X | | | | mlpy is a Python module for Machine Learning built on top of... |
| mlrho |
2.9 |
|
|
file |
X | X | | | Takes as input a file with assembled reads from a single diploid... |
| mlst |
2.23.0 |
|
|
GPL-2.0 |
X | X | | X | Scan contig files against PubMLST typing schemes |
| mlst-cge |
2.0.9 |
|
|
APACHE-2.0 |
| | | X | Multi Locus Sequence Typing (MLST) determine the ST from an assembled... |
| mlstdb |
0.1.3 |
|
dev |
MIT |
| | | X | A Python package to update and manage the MLST database for the MLST tool. |
| mm2plus |
1.0 |
|
|
MIT |
X | | | | Fast long-read mapper and whole-genome aligner (accelerated version of minimap2) |
| mmannot |
1.1 |
|
|
GPL3/LGPL3 |
X | X | | | mmannot annotates reads, or quantifies the features. mmmannot takes... |
| mmft |
0.2.1 |
|
|
MIT |
X | X | | | Max's minimal fasta toolkit |
| mmlong2 |
1.1.0 |
|
|
GPL-3.0-only |
| | | X | An all-in-one genome-centric metagenomics workflow using long reads |
| mmlong2-lite |
1.1.0 |
|
|
GPL-3.0-only |
| | | X | Lightweight workflow for microbial genome recovery using either... |
| mmquant |
1.0.9 |
|
|
GPL3/LGPL3 |
X | X | | | RNA-Seq quantification tool, with special handling on multi-mapping reads. |
| mmseqs2 |
17.b804f |
|
|
MIT |
X | X | | | MMseqs2: ultra fast and sensitive sequence search and clustering suite |
| mmseqs2-server |
8.c4b9644 |
|
|
GPLv3 |
X | X | | | Server for MMseqs2, Foldseek and ColabFold |
| mmtf-python |
1.0.2 |
|
|
MIT |
X | X | | | A decoding libary for the PDB mmtf format |
| mmult |
0.0.0.2 |
|
|
MIT |
X | X | | | Multiple sample analysis from large-scale WGBS data |
| mmvc |
1.0.2 |
|
|
MIT |
X | | | | Call variants based on a Bayesian multinomial mixture model. |
| mnnpy |
0.1.9.5 |
|
|
BSD-3-Clause |
X | X | | | Mutual nearest neighbors correction in python. |
| moabs |
1.3.9.6 |
|
|
MIT |
X | X | | | Methylation analysis on Bisulfite-Sequencing reads |
| mob_suite |
3.1.9 |
doc |
dev |
Apache-2.0 |
X | X | | X | MOB-suite is a set of tools for finding, typing and reconstruction of... |
| mobidic-mpa |
1.3.0 |
|
dev |
MIT |
| | | X | MPA: MoBiDiC Prioritization Algorithm |
| mobster |
0.2.4.1 |
|
|
GPL3 |
X | X | | X | NGS tool for detecting MEI and gene retrotransposition events in WGS... |
| moca |
0.4.3 |
|
|
ISC |
X | X | | X | Tool for motif conservation analysis |
| mockinbird |
1.0.0a1 |
doc |
dev |
GPL-3.0-or-later |
X | X | | | A fully automatic and reproducible PAR-CLIP analysis pipeline |
| modeltest-ng |
0.1.7 |
doc |
dev |
GPL-3.0 |
X | X | | | ModelTest-NG is a tool for selecting the best-fit model of evolution... |
| modlamp |
4.3.0 |
doc |
|
BSD |
| | | X | python package for in silico peptide design and QSAR studies |
| modle |
1.1.0 |
doc |
dev |
MIT |
X | X | | | High-performance stochastic modeling of DNA loop extrusion interactions |
| mofapy |
1.2 |
|
|
LGPL |
| | | X | Multi-Omics Factor Analysis |
| mofapy2 |
0.7.2 |
|
|
LGPL |
| | | X | Multi-Omics Factor Analysis |
| moff |
2.0.3 |
|
|
Apache |
X | X | | X | moFF is an OS independent tool designed to extract apex MS1 intensity... |
| mokapot |
0.10.0 |
doc |
dev |
Apache-2.0 |
| | | X | Fast and flexible semi-supervised learning for peptide detection |
| molpopgen-analysis |
0.8.8 |
|
|
GNU |
X | X | | | Deprecated and no longer maintained programs for the (pre-NGS-era)... |
| moments |
1.3.1 |
doc |
dev |
MIT |
X | X | | | Evolutionary inference using SFS and LD statistics. |
| moni |
0.2.2 |
|
|
MIT |
X | | | | A Pangenomics Index for Finding MEMs |
| monocle3-cli |
0.0.9 |
|
dev |
Apache-2.0 |
X | X | | X | A set of wrappers for individual components of the monocle3 package.... |
| monopogen |
1.6.0 |
|
|
GPL-3.0-or-later |
| | | X | Monopogen is an analysis package for SNV calling from single-cell... |
| monovar |
0.0.1 |
|
|
MIT |
X | X | | X | single cell joint genotyper |
| monsda |
1.2.8 |
doc |
|
GPL-3.0-or-later |
| | | X | MONSDA, Modular Organizer of Nextflow and Snakemake driven HTS Data Analysis |
| moods |
1.9.4.2 |
doc |
dev |
GPL-3.0-or-later |
X | X | | | MOODS: Motif Occurrence Detection Suite |
| moreutils |
0.5.7 |
|
|
GPLv2 |
X | | | | None |
| morpheus |
290 |
doc |
dev |
MIT |
X | | | | mass spectrometry–based proteomics database search algorithm |
| mosaic |
0.3.1 |
|
|
MIT |
| X | | | mosaic: counts Strand-seq reads and classifies strand states of each... |
| mosaicatcher |
0.3.1 |
|
|
MIT |
X | X | | | mosaicatcher: counts Strand-seq reads and classifies strand states of... |
| mosaik |
2.2.26 |
|
|
GPL |
X | X | | | MOSAIK is a stable, sensitive and open-source program for mapping... |
| mosca |
2.3.0 |
doc |
dev |
GPL-3.0-or-later |
| | | X | MOSCA - Meta-Omics Software for Community Analysis |
| mosdepth |
0.3.10 |
doc |
dev |
MIT |
X | X | | X | Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing. |
| moss |
0.1.1 |
|
|
MIT |
X | | | | A multi-sample somatic SNV caller |
| mothur |
1.48.0 |
|
dev |
GPL-3.0 |
X | X | | | This project seeks to develop a single piece of open-source, expandable... |
| motifraptor |
0.3.0 |
|
|
Partners |
X | X | | | Motif-centric analysis on GWAS data |
| motifscan |
1.3.0 |
|
|
BSD |
X | X | | | A package for motif discovery and motif enrichment analysis |
| motulizer |
0.3.2 |
doc |
dev |
GNU |
| | | X | making OTUs from genomes, and stats on them. and even core-genomes |
| motus |
3.1.0 |
|
dev |
GPL-3.0 |
X | X | | X | Marker gene-based OTU (mOTU) profiling |
| mp-est |
3.0.0 |
doc |
dev |
GNU |
X | X | | | Maximum Pseudo-likelihood Estimation of Species Trees |
| mp3treesim |
1.0.6 |
|
|
MIT |
| | | X | Triplet-based similarity score for fully multi-labeled trees with... |
| mpa-portable |
2.0.0 |
|
|
Apache |
X | | | X | MPA Portable is a light-weight and stand-alone software for the... |
| mpa-server |
3.4 |
|
|
Apache |
| | | X | Independent platform for interpretation of proteomics identification results |
| mpra-data-access-portal |
0.1.10 |
|
|
MIT |
| | | X | Saturation mutagenesis MPRA data access portal. |
| mqc |
1.10 |
|
|
GNU |
X | X | | | qualtiy control tool to assess the mapping quality of a ribosome... |
| mquad |
0.1.8b |
doc |
dev |
Apache-2.0 |
| | | X | MQuad: Mixture Model for Mitochondrial Mutation detection in... |
| mrbayes |
3.2.7 |
doc |
dev |
GPL-3.0-or-later |
X | X | | | Bayesian Inference of Phylogeny |
| mreps |
2.6.01 |
|
|
GNU |
X | X | | | mreps is a flexible and efficient software for identifying serial... |
| mrsfast |
3.4.2 |
|
|
BSD |
X | X | | | mrsFAST - micro-read substitution-only Fast Alignment Search Tool. |
| mrtrix3 |
3.0.4 |
doc |
dev |
MPL-2.0 |
X | | | | A set of tools to perform various advanced diffusion MRI analyses,... |
| ms |
2014_03_04 |
|
|
Unknown |
X | | | | None |
| ms-entropy |
1.3.4 |
doc |
dev |
Apache-2.0 |
X | X | | | This package provides a Python implementation of calculating spectral... |
| ms2deepscore |
2.5.1 |
|
dev |
Apache-2.0 |
| | | X | Deep learning similarity measure for comparing MS/MS spectra with... |
| ms2pip |
4.1.0 |
doc |
dev |
Apache-2.0 |
X | X | | | MS²PIP: MS² Peak Intensity Prediction |
| ms2query |
1.5.3 |
|
|
Apache-2.0 |
| | | X | Reliable and fast MS/MS spectral based analogue search |
| ms2rescore |
3.1.4 |
doc |
dev |
Apache-2.0 |
| | | X | Modular and user-friendly platform for AI-assisted rescoring of peptide... |
| ms2rescore-rs |
0.4.1 |
|
|
Apache-2.0 |
X | X | | | Rust functionality for the MS²Rescore package |
| msa4u |
0.4.0 |
|
|
WTFPL |
| | | X | A simple visualisation tool for Multiple Sequence Alignment. |
| msaboot |
0.1.2 |
|
|
Apache |
X | X | | X | Generate bootstrapping replicates for multiple sequence alignment data. |
| msaconverter |
0.0.4 |
|
|
GNU |
| | | X | To convert multiple alignment alignments (MSA) into different formats |
| msalign2 |
1.0 |
|
|
GPL3 |
X | | | | Aligns 2 CE-MS or LC-MS datasets using accurate mass information. |
| msamtools |
1.1.3 |
|
|
MIT |
X | X | | | microbiome-related extension to samtools |
| msaprobs |
0.9.7 |
|
|
GPL3 |
X | X | | | MSAProbs is a well-established state-of-the-art multiple sequence... |
| mseqtools |
0.9.1 |
|
|
MIT |
X | X | | | fastq/fasta file manipulation toolkit |
| msfragger |
4.1 |
|
|
Academic |
| | | X | Ultrafast, comprehensive peptide identification for mass... |
| msgf_plus |
2024.03.26 |
|
|
https://github. |
X | X | | X | MS-GF+ is a MS/MS database search tool |
| msi |
0.3.7 |
doc |
dev |
GPL-3 |
| | | X | Metabarcoding sequences identification - from nanopore reads to taxa tables. |
| msisensor |
0.5 |
|
dev |
MIT |
X | | | | MSIsensor is a C++ program to detect replication slippage variants at... |
| msisensor-pro |
1.3.0 |
doc |
dev |
Custom |
X | X | | | Microsatellite Instability (MSI) detection using high-throughput... |
| msisensor-rna |
0.1.6 |
|
dev |
Community-Spec-1.0 |
| | | X | MSIsensor-RNA: Microsatellite instability detection using RNA sequencing data. |
| msisensor2 |
0.1 |
|
|
GPL3 |
X | | | | MSIsensor2 is a novel algorithm based machine learning, featuring a... |
| msmc2 |
2.1.4 |
|
|
GPL |
| | | X | This program implements MSMC2, a method to infer population size... |
| msmetaenhancer |
0.4.0 |
doc |
dev |
MIT |
| | | X | MSMetaEnhancer is a Python tool that adds more annotations (e.g.... |
| msms |
2.6.1 |
|
|
Free |
X | X | | | MSMS is a program written in the C programming language to compute... |
| msoma |
0.1.0 |
doc |
dev |
MIT |
| | | X | mSOMA: Somatic Mutation Detection using a betabinomial null model |
| msp2db |
0.0.9 |
|
|
GNU |
| | | X | Python package to create an SQLite database from a collection of MSP... |
| msprime |
0.4.0 |
|
|
GNU |
X | X | | | A fast and accurate coalescent simulator. |
| msproteomicstools |
0.11.0 |
|
|
BSD |
X | X | | | msproteomicstools is a Python library that can be used in LC-MS/MS... |
| msstitch |
3.17 |
|
dev |
MIT |
X | X | | X | MS proteomics post processing utilities. |
| mstmap |
1 |
|
|
GPL3 |
X | X | | | Accurate construction of genetic maps (Wu et al., PLoS Genetics,... |
| msweep |
2.2.1 |
|
|
MIT |
X | X | | | mSWEEP - bacterial community composition estimation from pseudoalignments |
| mtb-snp-it |
1.1 |
|
|
MIT |
| | | X | SNP-IT: Whole genome SNP based identification of members of the... |
| mtbseq |
1.1.0 |
|
|
GPLv3 |
X | | | X | Pipeline for WGS analysis of M. tuberculosis |
| mtglink |
2.4.1 |
|
|
file |
| | | X | MTG-link is a local assembly tool for linked-read data |
| mtgrasp |
1.1.8 |
|
|
GPL-3.0 |
| | | X | reference-grade de novo animal mitochondrial genome assembly and standardization |
| mtm-align |
20220104 |
|
|
Unknown |
X | | | | Align multiple protein structures |
| mtnucratio |
0.7.1 |
|
|
GPLv3 |
| | | X | A small tool to determine MT to Nuclear ratios for NGS data. |
| mtsv |
1.0.6 |
|
|
MIT |
X | | | | MTSv is a suite of metagenomic binning and analysis tools. |
| mtsv-tools |
2.0.2 |
|
|
MIT |
X | | | | mtsv_tools contains core tools for alignment-based metagenomic binning |
| muat |
0.1.5 |
|
|
Apache-2.0 |
| | | X | A package for Mutation Attention Tool |
| mudskipper |
0.1.0 |
|
|
BSD |
X | X | | | mudskipper is a tool for converting genomic BAM/SAM files to... |
| mugsy |
1.2.3 |
|
|
Artistic |
X | | | X | Mugsy is a multiple whole genome aligner. |
| multigps |
0.74 |
|
|
MIT |
X | | | | MultiGPS is a framework for analyzing collections of multi-condition... |
| multiqc |
1.27.1 |
doc |
dev |
GPL-3.0-or-later |
X | X | | X | Create aggregate bioinformatics analysis reports across many samples and tools. |
| multiqc-bcbio |
0.2.9 |
|
|
GPL3 |
X | X | | X | MultiQC plugin for bcbio report visualization. |
| multiqc_sav |
0.0.3 |
|
|
GPL3 |
| | | X | MultiQC plugin to visualize Illumina SAV plots |
| multirnafold |
2.1 |
|
|
GPL-2.0-or-later |
X | X | | | RNA/DNA secondary structure prediction for one, two, or many interacting strands |
| multisub |
1.0.0 |
|
|
GPL3 |
| | | X | multiSub is a command-line tool to prepare and/or submit a SARS-CoV-2... |
| multitax |
1.3.1 |
|
|
MIT |
| | | X | Python package to obtain, parse and explore biological taxonomies |
| multivcfanalyzer |
0.85.2 |
|
|
GPL |
| | | X | MultiVCFAnalyzer is a VCF file post-processing tool tailored for aDNA.... |
| multivelo |
0.1.3 |
|
|
BSD-3-Clause |
| | | X | Multi-omic extension of single-cell RNA velocity |
| multixrank |
0.3 |
|
|
MIT |
| | | X | MultiXrank - heterogeneous MULTIlayer eXploration by RANdom walK with... |
| multiz |
11.2 |
|
|
MIT |
X | X | | | DNA multiple sequence aligner from Penn State's Miller lab. |
| mumemto |
1.2.1 |
|
|
GPL-3.0-only |
X | X | | | Finding maximal unique matches across pangenomes |
| mummer |
3.23 |
|
|
The |
X | X | | | MUMmer is a system for rapidly aligning entire genomes |
| mummer2circos |
1.4.2 |
|
dev |
MIT |
| | | X | Circular bacterial genome plots based on BLAST or NUCMER/PROMER alignments |
| mummer4 |
4.0.1 |
doc |
dev |
Artistic |
X | X | | | MUMmer is a system for rapidly aligning entire genomes. |
| munkres |
1.0.7 |
|
|
Apache |
X | X | | X | munkres algorithm for the Assignment Problem |
| mupbwt |
0.1.2 |
|
|
GPL-3.0-or-later |
X | | | | A light pbwt-based index |
| muscle |
5.3 |
|
|
GPL-3.0-only |
X | X | | | Multiple sequence and structure alignment with top benchmark scores... |
| muse |
2.1.2 |
doc |
dev |
GPL-2.0-or-later |
X | X | | | An accurate and ultra-fast somatic point mutation calling tool for... |
| muset |
0.5.1 |
|
dev |
GPL-3.0-or-later |
X | | | | A pipeline for building an abundance unitig matrix from FASTA/FASTQ files |
| music |
1.0.0 |
|
|
academic |
X | X | | | MUltiScale enrIchment Calling for ChIP-Seq Datasets |
| music-deconvolution |
0.1.1 |
|
|
GPL |
| | | X | Multi-subject single cell deconvolution |
| musicc |
1.0.4 |
|
|
BSD |
X | X | | X | MUSICC: A marker genes based framework for metagenomic normalization... |
| mustang |
3.2.4 |
doc |
|
file |
X | X | | | Mustang is a program that implements an algorithm for structural... |
| mutalyzer_hgvs_parser |
0.3.7 |
doc |
dev |
MIT |
| | | X | Mutalyzer HGVS variant description parser |
| mutamr |
0.0.1 |
|
dev |
GPL-3.0-or-later |
| | | X | Stripped down tool for generation of annotated vcf from paired-end... |
| mutmap |
2.3.9 |
|
dev |
GPL-3.0-or-later |
| | | X | MutMap: pipeline to identify causative mutations responsible for a phenotype. |
| mutscan |
1.14.0 |
|
|
MIT |
X | X | | | Detect and visualize target mutations by scanning FastQ files directly |
| mutyper |
1.0.2 |
doc |
|
MIT |
X | X | | | A Python package and command line utility for annotating the local... |
| mvicuna |
1.0 |
|
|
https://www.bro |
X | X | | | M-Vicuna is a modularized version of VICUNA, a de novo assembly program... |
| mview |
1.68 |
doc |
dev |
GPL-2.0-or-later |
| | | X | MView extracts and reformats the results of a sequence database search... |
| mvip |
1.1.5 |
|
|
GNU |
| | | X | MVP v.1.0, a user-friendly pipeline written in Python and providing a... |
| mvirs |
1.1.1 |
doc |
dev |
GNU |
| | | X | mVIRs: Localisation of inducible prophages using NGS data |
| mvp |
0.4.3 |
|
|
GPLv3+ |
X | X | | X | detect creation/destruction of sequence motifs as a result of mutations |
| mwga-utils |
0.1.6 |
|
|
GPL3 |
X | X | | | Collection of utilities for processing Multispecies Whole Genome Alignments |
| mycotools |
0.32.11 |
doc |
dev |
BSD-3-Clause |
| | | X | Comparative genomics automation and standardization software. |
| mydbfinder |
1.0.5 |
|
|
APACHE-2.0 |
| | | X | MyDbFinder identifies genes from your own database in total or partial... |
| mygene |
3.2.2 |
|
|
BSD |
X | X | | X | Python Client for MyGene.Info services. |
| mykatlas |
0.6.1 |
|
|
MIT |
X | | | | Assists in discoveries of antibiotic-resistance with mykrobe |
| mykrobe |
0.13.0 |
|
|
MIT |
X | X | | | Antibiotic resistance prediction in minutes |
| myriad |
0.1.4 |
|
|
MIT |
X | X | | | Simple distributed computing. |
| mysql-connector-c |
6.1.6 |
|
|
LGPL |
X | X | | | MySQL Connector/C, the C interface for communicating with MySQL servers. |
| mysqlclient |
1.3.10 |
|
|
GNU |
X | X | | | Python interface to MySQL |
| mzmine |
3.9.0 |
|
|
MIT |
| | | X | Integrative analysis of multimodal mass spectrometry data |
| mzml2isa |
1.1.1 |
|
|
GNU |
X | X | | X | mzml2isa - mzML to ISA-tab parsing tool |
| mzpaf |
0.2.0b0 |
doc |
dev |
CC-BY-1.0 |
| | | X | HUPO-PSI Peptide peak annotation format |
| mzspeclib |
1.0.3 |
doc |
dev |
Apache-2.0 |
| | | X | HUPO-PSI Spectral library format |
| mztosqlite |
2.1.1 |
|
|
GPL, |
X | X | | X | Convert proteomics data files into a SQLite database. |
| n50 |
1.7.0 |
doc |
dev |
mit |
| | | X | calculate N50 from FASTA/FASTQ files, producing both machine and human... |
| naf |
1.3.0 |
|
|
zlib |
X | X | | | Compressed binary file format for DNA/RNA/protein sequence data |
| nafcodec |
0.3.1 |
doc |
dev |
MIT |
X | X | | | PyO3 bindings and Python interface to nafcodec, an encoder/decoder for... |
| naibr-plus |
0.5.3 |
|
|
MIT |
| | | X | Identify novel adjacencies created by structural variations using... |
| naltorfs |
0.1.2 |
|
|
MIT |
| | | X | Nested Alternate Open Reading Frames (nAlt-ORFs) |
| namfinder |
0.1.3 |
|
|
MIT |
X | X | | | Finds Non-overlapping Approximate Matches (NAMs) between query and... |
| nanoblaster |
0.16 |
|
|
MIT |
X | X | | | Basic Local Alignment and Search Tool for Oxford Nanopore Long Sequences |
| nanocall |
v0.7.4 |
|
|
MIT |
X | | | | An Oxford Nanopore Basecaller |
| nanocaller |
3.6.1 |
|
|
MIT |
| | | X | NanoCaller for accurate detection of SNPs and indels in... |
| nanocomp |
1.24.2 |
|
|
MIT |
X | X | | X | Comparing runs of Oxford Nanopore sequencing data and alignments |
| nanocompore |
1.0.4 |
|
|
GNU |
| | | X | Nanocompore identifies raw signal changes between two conditions dRNA-Seq data. |
| nanocount |
1.0.0.post6 |
doc |
|
MIT |
| | | X | Transcript abundance estimation from Nanopore *direct-RNA sequencing* datasets |
| nanofilt |
2.8.0 |
|
|
MIT |
X | X | | X | Filtering and trimming of Oxford Nanopore Sequencing data |
| nanoget |
1.19.3 |
|
|
GPL-3.0-only |
X | X | | X | Functions to extract information from Oxford Nanopore sequencing data... |
| nanoinsight |
0.0.3 |
|
|
GPL-3.0-or-later |
| | | X | Repeat annotation tool for insertions called by NanoVar |
| nanolyse |
1.2.1 |
|
|
MIT |
X | X | | X | Removing lambda DNA control reads from fastq dataset |
| nanomath |
1.4.0 |
|
dev |
GPL-3.0-or-later |
X | X | | X | A few simple math function for other Oxford Nanopore processing scripts |
| nanometa-live |
0.4.3 |
doc |
|
GPL-3.0-or-later |
| | | X | Workflow and GUI for real-time species classification and pathogen... |
| nanomod |
0.2.2 |
|
|
GPL3 |
| | | X | A computational method for Nanopore signal analysis and modification detection. |
| nanomonsv |
0.7.2 |
|
|
GPL-3.0 |
| | | X | Python tools for detecting structural variation from nanopore sequence data |
| nanomotif |
0.5.6 |
doc |
dev |
MIT |
| | | X | Identifying methlyation motifs in nanopore data |
| nanonet |
2.0.0 |
|
|
MPL-2.0 |
X | | | | Nanonet provides recurrent neural network basecalling for Oxford... |
| nanopack |
1.1.1 |
|
dev |
GPL-3.0-only |
| | | X | A meta package for several long read processing and analysis tools. |
| nanoplexer |
0.1.2 |
|
|
MIT |
X | | | | Tool for demultiplexing Nanopore barcode sequence data |
| nanoplot |
1.44.1 |
|
|
MIT |
X | X | | X | Plotting suite for long read sequencing data and alignments |
| nanoplotter |
1.10.0 |
|
|
GPL-3.0 |
X | X | | X | Plotting functions of Oxford Nanopore sequencing data for NanoPack |
| nanopolish |
0.14.0 |
|
|
MIT |
X | X | | | Signal-level algorithms for MinION data. |
| nanopolishcomp |
0.6.12 |
|
|
MIT |
| | | X | NanopolishComp is a Python3 package for downstream analyses of... |
| nanopore_simulation |
0.3 |
|
|
MPL-2.0 |
X | X | | X | Nanopore SimulatION is a tool for simulating an Oxfornd Nanopore... |
| nanoq |
0.10.0 |
|
|
MIT |
X | X | | | Ultra-fast quality control and summary reports for nanopore reads |
| nanoqc |
0.10.0 |
|
dev |
GPL-3.0-or-later |
X | X | | X | Create fastQC-like plots for Oxford Nanopore sequencing data. |
| nanoraw |
0.5 |
|
|
Other |
X | X | | X | Analysis of nanopore sequencing data. |
| nanosim |
3.2.3 |
|
dev |
GPL-3.0-only |
X | X | | X | NanoSim is a fast and scalable read simulator for Nanopore sequencing data. |
| nanosim-h |
1.1.0.4 |
|
|
GPLv3 |
X | X | | X | NanoSim-H is a simulator of Oxford Nanopore reads that captures the... |
| nanosimh |
v1.0.1.8 |
|
|
GPL |
X | X | | | NanoSimH is a fork of NanoSim (https://github.com/bcgsc/NanoSim), a... |
| nanosplit |
0.1.4 |
|
|
MIT |
X | X | | | Perform splitting of Oxford Nanopore sequencing data in a fail and pass dataset. |
| nanospring |
0.2 |
|
|
MIT |
X | | | | NanoSpring is a compression tool for nanopore reads in Fastq files |
| nanostat |
1.6.0 |
|
|
MIT |
X | X | | X | Calculate statistics for Oxford Nanopore sequencing data and alignments |
| nanosv |
1.2.4 |
|
|
MIT |
X | X | | X | Structural variation detection tool for Oxford Nanopore data. |
| nanovar |
1.8.3 |
|
|
GPL-3.0-or-later |
X | | | X | Structural variant caller using low-depth long reads |
| narfmap |
1.4.2 |
|
|
GPL-3 |
X | | | | NARFMAP is a fork of the Dragen mapper/aligner Open Source Software. |
| nasm |
2.11.08 |
|
|
Simplified |
X | | | | None |
| nasp |
1.2.1 |
|
|
Academic |
X | X | | | NASP: an accurate, rapid method for the identification of SNPs in WGS... |
| nbitk |
0.5.0 |
doc |
|
Apache-2.0 |
| | | X | nbitk: Naturalis BioInformatics ToolKit |
| ncbi-acc-download |
0.2.8 |
|
|
Apache |
| | | X | Download files from NCBI Entrez by accession. |
| ncbi-amr |
1.04 |
|
|
Public |
X | X | | | AMRFinder find acquired antimicrobial resistance genes in protein or... |
| ncbi-amrfinderplus |
4.0.19 |
doc |
dev |
Public |
X | X | | | AMRFinderPlus finds antimicrobial resistance and other genes in protein... |
| ncbi-datasets-pylib |
16.6.1 |
doc |
dev |
Unlicense |
| | | X | Easily gather data from across NCBI databases |
| ncbi-fcs-gx |
0.5.4 |
|
|
NCBI-PD |
X | | | | The NCBI Foreign Contamination Screen. Genomic cross-species aligner,... |
| ncbi-genome-download |
0.3.3 |
|
|
Apache |
X | X | | X | Download genome files from the NCBI FTP server. |
| ncbi-ngs-sdk |
3.0.1 |
|
|
Public |
X | X | | | NGS is a new, domain-specific API for accessing reads, alignments and... |
| ncbi-stxtyper |
1.0.40 |
doc |
|
Public |
X | X | | | StxTyper identifies and types Stx operons from assembled genomic sequence. |
| ncbi-util-legacy |
6.1 |
|
|
Public |
X | | | | NCBI software development toolkit |
| ncbi-vdb |
3.2.0 |
doc |
dev |
Public |
X | X | | | SRA tools database engine. |
| ncbi-vdb-py |
3.2.0 |
|
dev |
Public |
| | | X | SRA tools database engine (Python bindings). |
| ncbimeta |
0.8.3 |
|
|
MIT |
| | | X | Efficient and comprehensive metadata acquisition from the NCBI... |
| ncbitax2lin |
2.3.2 |
|
|
MIT |
| | | X | NCBItax2lin |
| ncbitk |
1.0a17 |
|
|
MIT |
| | | X | A tool kit for accessing NCBI's GenBank |
| ncfp |
0.2.0 |
doc |
dev |
MIT |
X | X | | X | A program/module to find nt sequences that code for aa sequences |
| ncls |
0.0.68 |
|
|
BSD |
X | X | | | Fast overlap datastructure. |
| ncrf |
1.01.02 |
|
|
MIT |
X | X | | | Noise-Cancelling Repeat Finder, Uncovering tandem repeats in... |
| nda-tools |
0.3.0 |
|
|
MIT |
| | | X | Python package for interacting with NDA web services. |
| ndex-python |
3.0.11.23 |
|
|
BSD |
X | X | | X | NDEx Python includes a client and a data model. |
| ndex2 |
3.10.0 |
doc |
dev |
BSD-3-Clause |
| | | X | Nice CX Python includes a client and a data model. |
| neat |
4.2.8 |
|
|
BSD-3-Clause |
| | | X | Toolset for generating synthethic FASTQ, VCF and BAM files. |
| neatms |
0.7 |
doc |
|
MIT |
| | | X | NeatMS is an open source python package for untargeted LCMS deep... |
| nebulizer |
0.7.1 |
doc |
dev |
AFL-3.0 |
| | | X | Command-line utilities to help with managing users, data libraries and... |
| necat |
0.0.1_update20 |
doc |
dev |
Unknown |
X | X | | | NECAT is an error correction and de-novo assembly tool for Nanopore... |
| nedbit-features-calculator |
1.2 |
|
|
MIT |
X | X | | | Network diffusion and biology-informed topological features |
| nedrex |
0.1.4 |
|
|
MIT |
| | | X | A Python library for interfacing with the NeDRex API |
| needle |
1.0.1 |
|
|
BSD-3-Clause |
X | | | | Needle: A fast and space-efficient pre-filter for the quantification of... |
| needletail |
0.6.3 |
|
dev |
MIT |
X | X | | | Fast FASTX parsing in Python |
| neffy |
0.1.1 |
doc |
|
GPL-3.0-only |
X | X | | | A Python interface of NEFFy C++ tool: NEFF Calculator and MSA File Converter |
| neffy-cli |
0.1.1 |
doc |
dev |
GPL-3.0-only |
X | X | | | NEFF calculator and MSA file converter |
| negative_training_sampler |
0.3.1 |
|
|
MIT |
| | | X | Generates negative samples with the same GC distribution as the... |
| nemo |
2.3.51 |
|
|
GPLv2 |
X | X | | | Individual-based forward-time genetics simulation software |
| nemo-age |
0.30.0 |
|
|
GPL-3 |
X | X | | | In Nemo-age, it is possible to model genetic and phenotypic evolution... |
| neodisambiguate |
1.1.0 |
doc |
|
MIT |
| | | X | Disambiguate reads that were mapped to multiple references. |
| neofox |
1.2.2 |
doc |
|
GPL-3.0-or-later |
| | | X | Annotation of mutated peptide sequences (mps) with published or novel... |
| neoloop |
0.4.3.post2 |
|
dev |
https://github. |
| | | X | Predict neo-loops induced by structural variations |
| neptune |
1.2.5 |
|
|
Apache |
X | X | | X | Neptune: Genomic Signature Discovery |
| neptune-signature |
2.0.0 |
|
dev |
Apache-2.0 |
| | | X | Neptune: Genomic Signature Discovery |
| nerpa |
1.0.0 |
doc |
dev |
Dual-licensed |
X | X | | | A tool for discovering biosynthetic gene clusters of nonribosomal peptides |
| nest |
2.14.0 |
|
|
GPL |
X | | | | NEST is a simulator for spiking neural network models. |
| netcdf-c_mpich |
4.9.2 |
|
|
MIT |
X | | | | NetCDF-C - netCDF interface for C |
| netcdf-fortran_mpich |
4.6.1 |
|
|
MIT |
X | | | | NetCDF-Fortran - netCDF interface for Fortran |
| netcdf-metadata-info |
1.1.6 |
|
|
GNU |
X | X | | | Metadata information from netcdf file for Galaxy use. |
| netifaces |
0.10.4 |
|
|
MIT |
X | X | | | None |
| netreg |
1.8.0 |
doc |
|
GPL3 |
X | X | | | netReg fits linear regression models using network-penalization. |
| netsyn |
0.1.2 |
|
|
CeCiLL |
| | | X | NetSyn is a tool to detect conserved genomic contexts (i.e. synteny... |
| networkxgmml |
0.1.6 |
|
|
UNKNOWN |
X | X | | X | XGMML parser for networkx |
| neurodocker |
0.5.0 |
|
|
Apache-2.0 |
X | X | | X | Neurodocker is a command-line program that generates custom Dockerfiles... |
| newick_utils |
1.6 |
|
|
BSD |
X | X | | | The Newick Utilities are a suite of Unix shell tools for processing... |
| newt |
0.52.18 |
|
|
GPL |
X | | | | None |
| nextalign |
2.14.0 |
doc |
dev |
MIT |
X | X | | | Viral genome alignment |
| nextclade |
3.10.2 |
doc |
dev |
MIT |
X | X | | | Viral genome alignment, mutation calling, clade assignment, quality... |
| nextclade2 |
2.14.0 |
doc |
dev |
MIT |
X | X | | | Viral genome alignment, mutation calling, clade assignment, quality... |
| nextclade_js |
0.14.4 |
|
|
MIT |
X | X | | | SARS-CoV-2 genome clade assignment, mutation calling, and sequence... |
| nextdenovo |
2.5.2 |
doc |
dev |
GPL-3.0-or-later |
X | X | | | String graph-based de novo assembler for long reads (CLR, HiFi and ONT) |
| nextflow |
24.10.5 |
|
|
Apache-2.0 |
X | X | | X | A DSL for data-driven computational pipelines http://nextflow.io |
| nextgenmap |
0.5.5 |
|
|
MIT |
X | X | | | NextGenMap is a flexible highly sensitive short read mapping tool that... |
| nextpolish |
1.4.1 |
doc |
dev |
GPL-3.0-or-later |
X | X | | | Fast and accurately polish the genome generated by noisy long reads |
| nextpolish2 |
0.2.1 |
doc |
dev |
GBPL |
X | X | | | Repeat-aware polishing genomes assembled using HiFi long reads. |
| nextstrain |
20200304 |
doc |
dev |
The |
| | | X | Nextstrain toolchain (meta-package) |
| nextstrain-cli |
8.5.4 |
doc |
dev |
MIT |
| | | X | The Nextstrain command-line interface (CLI) |
| nf-core |
3.2.0 |
doc |
dev |
MIT |
| | | X | Python package with helper tools for the nf-core community. |
| nf-test |
0.9.2 |
|
|
MIT |
| | | X | nf-test is a simple test framework for Nextflow pipelines. |
| ngless |
1.5.0 |
|
|
MIT |
X | X | | | A tool for short-read processing with a focus on metagenomics |
| nglview |
1.1.7 |
doc |
dev |
MIT |
X | X | | X | An IPython widget to interactively view molecular structures and... |
| ngmaster |
1.0.0 |
doc |
dev |
GNU |
| | | X | In silico multi-antigen sequence typing for Neisseria gonorrhoeae... |
| ngmerge |
0.3 |
|
|
MIT |
X | X | | | Merging paired-end reads and removing sequencing adapters. |
| ngmlr |
0.2.7 |
|
|
MIT |
X | X | | | ngmlr is a long-read mapper designed to align PacBio or Oxford Nanopore... |
| ngs-bits |
2025_01 |
|
|
MIT |
X | X | | | Short-read sequencing tools |
| ngs-chew |
0.9.4 |
|
|
MIT |
| | | X | Simple QC and sanity checking of germline NGS data |
| ngs-disambiguate |
2018.05.03 |
|
|
MIT |
X | | | | Disambiguation algorithm for reads aligned to human and mouse genomes... |
| ngs-sdk |
1.2.2 |
|
|
Public |
X | | | | None |
| ngs-smap |
5.0.1 |
|
|
GPL-3.0-or-later |
| | | X | SMAP is an analysis tool for stack-based NGS read mapping |
| ngs-tools |
1.8.6 |
doc |
dev |
MIT |
| | | X | Reusable tools for working with next-generation sequencing (NGS) data |
| ngs_te_mapper2 |
1.0.2 |
|
|
BSD |
| | | X | A program to identify transposable element insertions using next... |
| ngscheckmate |
1.0.1 |
doc |
dev |
MIT |
X | X | | X | Software package for identifying next generation sequencing (NGS) data... |
| ngsderive |
4.0.0 |
doc |
dev |
MIT |
| | | X | Backwards derive attributes from NGS data |
| ngsep |
4.0.1 |
|
|
GPL-3 |
| | | X | NGSEP - Next Generation Sequencing Experience Platform |
| ngseqbasic |
2.0.1 |
|
|
GPL-3.0 |
X | | | | Basic ChIP/DNaseI/ATAC analysis - from FASTQ to visualisation of... |
| ngshmmalign |
0.1.1 |
|
|
GNU |
X | X | | | ngshmmalign is a profile HMM aligner for NGS reads designed... |
| ngsindex |
0.1.7 |
|
|
MIT |
| | | X | Utilities for working with NGS index formats. |
| ngslca |
1.0.5 |
|
|
GPLv3, |
X | X | | | ngsLCA: fast and flexible taxonomic classification of DNA reads aligned... |
| ngsngs |
0.9.2 |
|
|
GPLv3, |
X | X | | | NGSNGS: Next Generation Simulator for Next Generation Sequencing data |
| ngsplotdb-ngsplotdb-hg19 |
3.00 |
|
|
GPL-2.0 |
X | X | | | HG19 genome database for NGSplot |
| ngsutils |
0.5.9 |
|
|
BSD |
X | X | | | Tools for next-generation sequencing analysis http://ngsutils.org |
| niemads |
1.0.16 |
|
|
GNU |
| | | X | NiemaDS: Non-standard data structures for Python 2 and 3 |
| niemagraphgen |
1.0.6 |
|
dev |
GPL-3.0-or-later |
X | X | | | Niema's C++ implementations of graph generators |
| nii2dcm |
0.1.2 |
|
dev |
BSD-3 |
| | | X | nii2dcm: NIfTI to DICOM creation with Python |
| nim-falcon |
3.0.2 |
|
|
MIT |
X | X | | | Nim-based executables used by Falcon assembly workflow |
| nimnexus |
0.1.1 |
|
|
MIT |
X | | | | command-line tools for processing ChIP-nexus data |
| ninja-nj |
1.00 |
doc |
dev |
MIT |
X | X | | | Nearly Infinite Neighbor Joining Application |
| nlstradamus |
1.8 |
|
|
GNU |
X | X | | | NLStradamus: a simple Hidden Markov Model for nuclear localization... |
| nmrglue |
0.9 |
|
|
BSD-3-Clause |
X | X | | | A module for working with NMR data in Python |
| nmrml2isa |
0.3.3 |
|
|
GPL-3.0-or-later |
X | X | | X | nmrml2isa - nmrML to ISA-Tab parsing tool |
| nmrpro |
20161019 |
|
|
MIT |
X | X | | X | NMRPro reads and processes different types of NMR spectra. |
| noah-cli |
0.2.0 |
|
dev |
MIT |
| | | X | a project management tool for reproducible, portable, and streamlined... |
| nohuman |
0.3.0 |
|
|
MIT |
X | X | | | Remove human reads from a sequencing run |
| noise2read |
0.3.0 |
|
|
MIT |
| | | X | Turn noise to read |
| nolb |
1.9 |
|
|
All |
X | X | | | NOn-Linear rigid Block NMA approach (NOLB) is a conceptually simple and... |
| nonpareil |
3.5.5 |
|
dev |
Artistic |
X | X | | | Estimate average coverage and create curves for metagenomic datasets |
| nopilesum |
1.1.2 |
|
|
MIT |
X | X | | | nopilesum is a D program that functions as an alternative to... |
| nordic |
2.6.0 |
doc |
dev |
MIT |
X | X | | | NORDic: a Network-Oriented package for the Repurposing of Drugs |
| noresm |
2.0.2 |
doc |
|
BSD |
X | | | | The Norwegian Earth System Model (NorESM) is a coupled climate model... |
| norns |
0.1.6 |
|
|
MIT |
X | X | | X | Simple yaml-based config module |
| nose-capturestderr |
1.2 |
|
|
GPL |
X | X | | | Nose plugin for capturing stderr. |
| notramp |
1.1.9 |
doc |
|
BSD-2 |
| | | X | Super-fast Normalization and Trimming for Amplicon Sequencing Data... |
| novae |
0.2.2 |
|
|
BSD-3-Clause |
| | | X | Graph-based foundation model for spatial transcriptomics data |
| novasplice |
0.0.4 |
|
|
MIT |
| | | X | NovaSplice is a python tool to predict novel intronic splice sites from... |
| novoalign |
4.03.04 |
|
|
Commercial |
X | X | | | Powerful tool designed for mapping of short reads onto a reference... |
| novobreak |
1.1.3rc |
|
|
MIT |
X | X | | | local assembly for breakpoint detection in cancer genomes |
| novoplasty |
4.3.5 |
|
|
Other |
X | X | | X | The organelle assembler and heteroplasmy caller |
| np-likeness-scorer |
2.1 |
|
|
|
X | X | | | Calculates Natural Product(NP)-likeness of a molecule, i.e. the... |
| npinv |
1.24 |
|
|
MIT |
| | | X | an accurate tool for detecting and genotyping inversion using multiple... |
| npstructures |
0.2.19 |
|
|
MIT |
| | | X | Simple data structures that augments the numpy library |
| npyscreen |
4.10.5 |
|
|
BSD |
X | X | | X | Writing user interfaces without all that ugly mucking about in hyperspace |
| nrpys |
0.1.1 |
|
|
AGPL-3.0-or-later |
X | X | | X | Python language bindings for nrps-rs substrate specificity predictor. |
| nseg |
1.0.1 |
|
dev |
Public |
X | X | | | nseg identifies and masks regions of low complexity in nucleic acid sequences. |
| nspdk |
9.2 |
|
|
GNUv3 |
X | | | | Neighborhood Subgraph Pairwise Distance Kernel (NSPDK). |
| ntcard |
1.2.2 |
|
|
MIT |
X | X | | | Estimating k-mer coverage histogram of genomics data |
| ntedit |
2.1.1 |
doc |
dev |
GPL-3.0-or-later |
X | X | | | Ultrafast, lightweight, scalable genome assembly polishing, and SNV... |
| nthits |
1.0.3 |
|
|
MIT |
X | X | | | ntHits is a tool for efficiently counting and filtering k-mers based on... |
| ntjoin |
1.1.5 |
|
|
GPL-3.0 |
X | X | | X | Genome assembly scaffolder using minimizer graphs |
| ntlink |
1.3.11 |
|
|
GPL-3.0 |
X | X | | X | Genome assembly scaffolder using long reads and minimizers |
| ntm-profiler |
0.6.0 |
|
|
GPL-3.0-or-later |
| | | X | Profiling tool for NTM to detect species and resistance from WGS data |
| ntroot |
1.1.6 |
|
|
GPL-3.0 |
X | X | | X | Ancestry inference from genomic data |
| ntsm |
1.2.1 |
doc |
dev |
MIT |
X | X | | | ntsm - Nucleotide Sequence/Sample Matcher |
| ntstat |
1.0.1 |
|
|
GPL-3.0-or-later |
X | X | | | a toolkit for statistical analysis of k-mer frequency and depth |
| ntsynt |
1.0.2 |
|
|
GPL-3.0 |
X | X | | | Detecting multi-genome synteny blocks using minimizer graph mapping |
| nucamino |
0.1.3 |
|
|
MIT |
X | X | | | A nucleotide to amino acid alignment program optimized for virus gene sequences |
| nucdiff |
2.0.3 |
|
|
MPL-2.0 |
X | X | | X | NucDiff locates and categorizes differences between two closely related... |
| nucleoatac |
0.3.4 |
doc |
|
MIT |
X | X | | X | Python package for calling nucleosomes using ATAC-Seq data. Also... |
| nucleosome_prediction |
3.0 |
|
|
LGPLv2 |
X | | | | This tool allows you to submit a genomic sequence and to recieve a... |
| nudup |
2.3.3 |
|
|
GNU |
X | X | | X | Marks/removes duplicate molecules based on the molecular tagging... |
| nullarbor |
2.0.20191013 |
|
|
GPL2 |
X | | | X | Reads to report pipeline for bacterial isolate NGS data |
| numkit |
1.2.2 |
doc |
dev |
Modified |
| | | X | Numerical first aid kit (with numpy/scipy). |
| nvc |
0.0.4 |
|
|
GNU |
X | X | | X | The Naive Variant Caller |
| nwalign3 |
0.1.2 |
|
|
BSD |
X | X | | | Updated version of nwalign with Python 3.x compatibility. |
| nxtrim |
0.4.3 |
doc |
dev |
BSD-2-Clause |
X | X | | | Software to remove Nextera Mate Pair adapters and categorise reads... |
| oakvar |
2.12.10 |
doc |
dev |
AGPL-3.0-or-later |
| | | X | OakVar - Genomic Variant Analysis Platform |
| oarfish |
0.7.2 |
|
|
BSD-3-Clause |
X | X | | | oarfish is a tool for fast, accurate and versatile transcript... |
| oases |
0.2.09 |
|
|
GPL-3.0-or-later |
X | X | | | De novo transcriptome assembler for short reads |
| oatk |
1.0 |
|
|
MIT |
X | X | | | Oatk: an organelle genome assembly toolkit |
| oauth2client |
1.5.2 |
|
|
Apache |
X | X | | | client library for OAuth 2.0 |
| obitools |
1.2.13 |
|
|
CeCILL-V2 |
X | X | | | The OBITools package is a set of programs specifically designed for... |
| obonet |
1.1.0 |
doc |
dev |
BSD-2-Clause-Patent |
| | | X | Parse OBO formatted ontologies into networkx |
| occultercut |
1.1 |
|
|
GPL-3.0-or-later |
X | | | | A package for measuring the local GC-content bias in genomes and fungal species |
| ococo |
0.1.2.7 |
|
|
MIT |
X | X | | | Ococo, the first online consensus caller. |
| ocrad |
0.21 |
|
|
GPL |
X | X | | | Ocrad is an optical character recognition program. |
| octopus |
0.7.4 |
|
|
MIT |
X | X | | | Octopus is a mapping-based variant caller that implements several... |
| octopusv |
0.1.0 |
|
|
MIT |
| | | X | OctopusV: Advanced Structural Variant Analysis Toolkit |
| odamnet |
1.1.0 |
|
dev |
MIT |
| | | X | Study molecular relationships between chemicals and rare diseases |
| odgi |
0.9.0 |
doc |
dev |
MIT |
X | | | | An optimized dynamic genome/graph implementation. |
| odose |
1.0 |
|
|
MIT |
X | X | | | Ortholog Direction of Selection Engine. |
| ogdf |
201207 |
|
|
GPLv3 |
X | X | | | The Open Graph Drawing Framework is a self-contained C++ class library... |
| olga |
1.2.4 |
|
|
GPL-3.0-only |
| | | X | OLGA (Optimized Likelihood estimate of immunoGlobulin Amino-acid... |
| oligoarrayaux |
3.8.1 |
|
|
ACADEMIC |
X | X | | | OligoArrayAux is a subset of the UNAFold package for use with OligoArray. |
| oligomap |
1.0.1 |
|
|
GNU |
X | X | | | Oligomap is a program for fast identification of nearly-perfect matches... |
| oligotyping |
2.1 |
|
|
GNU |
X | X | | | The oligotyping and minimum entropy decomposition (MED) pipeline for... |
| olivar |
1.3.0 |
|
dev |
GPL-3.0-or-later |
| | | X | Olivar PCR tiling design |
| omamer |
2.1.0 |
|
|
LGPL-3.0 |
| | | X | OMAmer - tree-driven and alignment-free protein assignment to sub-families |
| omark |
0.3.1 |
|
|
LGPL-3.0 |
| | | X | OMArk - Proteome quality assesment based on OMAmer placements |
| omb_mpich |
7.5 |
|
|
BSD-3-Clause |
X | | | | OSU Micro Benchmarks |
| omero-py |
5.11.1 |
|
|
GPL-2.0-only |
| | | X | Client library offering helper methods to access an OMERO server. |
| omssa |
2.1.9 |
|
|
Public |
X | X | | | Open Mass Spectrometry Search Algorithm (OMSSA) |
| oncocnv |
7.0 |
|
|
GNU |
| | | X | a package to detect copy number changes in Deep Sequencing data |
| oncofuse |
1.1.1 |
|
|
Apache |
X | X | | X | Predicting oncogenic potential of gene fusions |
| oncogemini |
1.0.0 |
|
|
MIT |
| | | X | OncoGEMINI is an adaptation of GEMINI intended for the improved... |
| oncopipe |
1.0.12 |
doc |
|
MIT |
| | | X | Functions for running Snakemake modules |
| oncotator |
1.9.9.0 |
doc |
|
Custom |
X | | | X | Oncotator is a tool for annotating human genomic point mutations and... |
| onehot2seq |
0.0.2 |
|
|
MIT |
| | | X | Decode a one-hot numpy array to biological sequences |
| ont-fast5-api |
4.1.3 |
|
|
MPL-2.0 |
X | X | | X | Oxford Nanopore Technologies fast5 API software |
| ont-modkit |
0.4.3 |
doc |
dev |
Oxford |
X | X | | | A bioinformatics tool for working with modified bases in Oxford... |
| ont-tombo |
1.5.1 |
|
|
mpl-2.0 |
X | X | | | Detection of modified bases from raw nanopore sequencing data. |
| ont_vbz_hdf_plugin |
1.0.12 |
|
|
MPL-2 |
X | X | | | VBZ compression plugin for nanopore signal data |
| ontime |
0.3.1 |
|
|
MIT |
X | X | | | Extract subsets of ONT (Nanopore) reads based on time |
| onto2nx |
0.1.1 |
doc |
|
GPL |
X | X | | X | A package for parsing ontologies in the OWL and OBO format into NetworkX graphs |
| ope |
0.8 |
|
|
MIT |
| | | X | Tools for gnu-parallel with FASTA input and parsers for some common formats. |
| open-cravat |
2.11.1 |
doc |
dev |
MIT |
| | | X | OpenCRAVAT - variant analysis toolkit |
| openbabel |
2.3.90dev7d621d9 |
|
|
GPLv2 |
X | X | | | A chemical toolbox designed to speak the many languages of chemical data |
| opencontactcli |
1.1 |
|
|
https://github. |
X | X | | | Static contact mapping algorithm to identify potential peptide... |
| openduck |
0.1.2 |
|
|
Apache |
| | | X | Open source library for dynamic undocking (DUck) |
| openmg |
0.1 |
|
|
GNU |
X | X | | X | Exhaustive generation of chemical structures |
| openms |
3.3.0 |
|
|
BSD |
X | X | | | OpenMS is an open-source software C++ library for LC-MS data management... |
| openms-thirdparty |
3.3.0 |
|
|
BSD |
X | X | | | OpenMS is an open-source software C++ library for LC-MS data management... |
| openms-tools |
2.4.0 |
|
|
BSD |
X | X | | | OpenMS is an open-source software C++ library for LC-MS data management... |
| openpyxl |
2.4.0 |
|
|
MIT |
X | X | | | A Python library to read/write Excel 2010 xlsx/xlsm files |
| openslide |
3.4.1 |
|
|
GNU |
X | X | | | OpenSlide is a C library that provides a simple interface to read... |
| openslide-python |
1.1.1 |
|
|
GNU |
X | X | | | Python interface to OpenSlide |
| opentargets |
3.1.16 |
|
|
Apache |
| | | X | Client for Open Targets REST API at targetvalidation.org |
| opentargets-urlzsource |
1.0.0 |
|
|
Apache |
| | | X | File and url handling |
| opentargets-validator |
1.0.0 |
|
|
Apache, |
| | | X | Evidence validation at targetvalidation.org |
| opfi |
0.1.2 |
|
|
MIT |
| | | X | A package for discovery, annotation, and analysis of gene clusters in... |
| opsin |
2.4.0 |
|
|
Artistic |
X | X | | X | OPSIN is a Java(1.6+) library for IUPAC name-to-structure conversion... |
| optbuild |
0.2.1 |
|
|
GNU |
X | X | | X | build command lines for external programs |
| opticlust |
0.4.1 |
doc |
|
GPL-3.0-or-later |
| | | X | Single cell clustering and recommendations at a glance. |
| optilcms |
1.1.0 |
doc |
dev |
MIT |
| | | X | Pipeline for processing LC-MS raw data with optimized parameters. |
| optimir |
1.2 |
|
|
GPL-3 |
| | | X | Integrating genetic variations in miRNA alignment |
| optitype |
1.3.5 |
|
|
BSD |
X | | | X | Precision HLA typing from next-generation sequencing data |
| optplus |
0.2 |
|
|
UNKNOWN |
X | X | | X | additional options for optparse |
| orfanage |
1.2.0 |
|
|
GPL-3.0-or-later |
X | X | | | Ultra-efficient and sensitive method to search for ORFs in spliced... |
| orfipy |
0.0.4 |
|
|
MIT |
X | X | | | orfipy: fast and flexible search for open reading frames in fasta sequences |
| orfm |
1.3 |
|
|
LGPL-3.0 |
X | X | | | OrfM is a simple and not slow ORF caller |
| orfquant |
1.1.0 |
|
|
GPL-3 |
| | | X | SaTAnn is a method that annotates and quantifies translation at the... |
| orientagraph |
1.1 |
|
|
GPL3 |
X | X | | | OrientAGraph enables Maximum Likelihood Network Orientation (MNLO), as... |
| orientationpy |
0.2.0.4 |
doc |
dev |
GNU |
| | | X | OrientationPy is the pythonic successor to the well-loved OrientationJ... |
| orna |
2.0 |
|
|
MIT |
X | X | | | In silico read normalization |
| orsum |
1.8.0 |
|
|
MIT |
| | | X | A tool to filter long lists of enriched terms resulting from one or... |
| orthanq |
1.9.1 |
|
dev |
MIT |
X | X | | | Uncertainty aware HLA typing and general haplotype quantification. |
| orthodb |
0.9.1 |
doc |
dev |
GPL3 |
| | | X | Interface to OrthoDB REST API. |
| orthofinder |
3.0.1b1 |
|
|
GPLv3 |
X | X | | X | Accurate inference of orthogroups, orthologues, gene trees and rooted... |
| orthofisher |
1.1.1 |
doc |
|
MIT |
| | | X | Orthofisher is a broadly applicable tool for automated gene... |
| orthoflow |
0.3.4 |
doc |
dev |
Apache-2.0 |
| | | X | Orthoflow is a workflow for phylogenetic inference of genome-scale... |
| orthologer |
3.5.0 |
doc |
dev |
GPL3 |
X | X | | | Establish orthology among fasta files. |
| orthomcl |
2.0.9 |
|
|
EuPathDB |
X | X | | X | Ortholog groups of protein sequences |
| osra |
2.1.0 |
|
|
Simplified |
X | | | | OSRA is a utility designed to convert graphical representations of... |
| ostir |
1.1.2 |
doc |
dev |
GPL-3.0-or-later |
| | | X | Open Source Transcription Initiation Rates |
| ourotools |
0.2.8 |
doc |
dev |
MIT |
| | | X | A comprehensive toolkit for quality control and analysis of single-cell... |
| outrigger |
1.1.1 |
|
|
BSD |
X | X | | X | Outrigger detects *de novo* exons and quantifies their percent spliced-in |
| p7zip |
15.09 |
|
|
LGPLv2 |
X | | | | p7zip is a quick port of 7z.exe and 7za.exe (command line version of... |
| pacbio_falcon |
052016 |
|
|
Standard |
X | X | | | A set of tools for fast aligning long reads for consensus and assembly |
| pacini_typing |
1.6.4 |
|
dev |
AGPL-3.0 |
| | | X | YAML-based bacterial genotyping application |
| pacu_snp |
0.0.7 |
|
dev |
GPL-3.0-or-later |
| | | X | PACU is a workflow for whole genome sequencing based phylogeny of... |
| paf2chain |
0.1.1 |
|
dev |
MIT |
X | X | | | convert PAF format to CHAIN format |
| pafpy |
0.2.0 |
doc |
|
Unlicense |
| | | X | A lightweight library for working with PAF (Pairwise mApping Format) files |
| pairix |
0.3.9 |
|
dev |
MIT |
X | X | | | 2D indexing on bgzipped text files of paired genomic coordinates |
| pairsnp |
0.3.1 |
|
|
MIT |
X | X | | | pairsnp calculates pairwise SNP distance matrices from multiple... |
| pairtools |
1.1.3 |
doc |
dev |
MIT |
X | X | | | CLI tools to process mapped Hi-C data. |
| pal2nal |
14.1 |
|
|
GPLv2.0 |
| | | X | robust conversion of protein sequence alignments into the corresponding... |
| pal_finder |
0.02.04 |
|
|
GPLv3 |
X | X | | X | Find microsatellite repeat elements from sequencing reads and design... |
| paladin |
1.4.6 |
|
dev |
MIT |
X | X | | | Protein Alignment and Detection Interface |
| palantir |
1.3.6 |
doc |
dev |
GPL-2.0-only |
| | | X | Palantir for modeling continuous cell state and cell fate choices in... |
| palikiss |
1.1.0 |
|
|
GPL-3.0-or-later |
X | X | | | pAliKiss predicts RNA secondary structures for fixed RNA multiple... |
| paml |
4.10.7 |
|
|
GNU |
X | X | | | A package of programs for phylogenetic analyses of DNA or protein... |
| pan-plaster |
1.2.1 |
|
|
MIT |
| | | X | Plaster is a program for quick linear pangenome construction. |
| panacota |
1.4.0 |
doc |
dev |
GNU |
| | | X | Large scale comparative genomics tools: annotate genomes, do pangenome,... |
| panacus |
0.3.3 |
|
dev |
MIT |
X | X | | | panacus is a tool for computing counting statistics for GFA files. |
| panaroo |
1.5.2 |
doc |
dev |
MIT |
| | | X | panaroo - an updated pipeline for pangenome investigation |
| pancake |
1.1.2 |
|
|
MIT |
X | X | | X | A Data Structure for Pangenomes -- Identification of Singletons and... |
| pandaseq |
2.11 |
|
|
GPL3 |
X | X | | | PANDASEQ is a program to align Illumina reads, optionally with PCR... |
| pandora |
0.9.2 |
|
|
MIT |
X | | | | Pan-genome inference and genotyping with long noisy or short accurate reads |
| panfeed |
1.7.0 |
|
dev |
Apache-2.0 |
| | | X | Compute gene-cluster specific k-mers over a pangenome |
| pango-collapse |
0.8.2 |
|
|
GPL-3.0-or-later |
| | | X | Collapse Pango sublineages up to user defined parent lineages. |
| pango-designation |
1.32 |
|
dev |
CC-BY-NC-4.0 |
| | | X | Repository for suggesting new lineages that should be added to the... |
| pango_aliasor |
0.3.0 |
|
|
MIT |
| | | X | Pango lineage aliasing and dealiasing |
| pangolearn |
2022.03.22 |
|
|
GPL-3.0 |
| | | X | Store of the trained model for pangolin to access. |
| pangolin |
4.3.1 |
|
|
GPL-3.0-only |
| | | X | Phylogenetic Assignment of Named Global Outbreak LINeages |
| pangolin-data |
1.32 |
|
|
GPL-3.0-only |
| | | X | Repository for storing latest model, protobuf, designation hash and... |
| pangu |
0.2.8 |
|
|
BSD-3-Clause-Clear |
| | | X | CYP2D6 PGx caller for PacBio HiFi Data |
| pangwes |
0.3.0_alpha |
|
|
MIT |
X | X | | | Performing pangenome-spanning epistasis and co-selection analysis via... |
| panisa |
0.1.7 |
|
dev |
GPL-3.0-or-later |
| | | X | panISa is a software to search insertion sequence (IS) on resequencing... |
| panoct |
3.23 |
|
|
GPL-3.0 |
X | X | | | PanOCT, Pan-genome Ortholog Clustering Tool, is a program for... |
| panoptes-ui |
0.2.3 |
|
|
MIT |
| | | X | panoptes: monitor computational workflows in real time |
| panpasco |
1.0.1 |
|
|
MIT |
| | | X | Pipeline for pangenome mapping and pairwise SNP distance |
| panphlan |
3.1 |
|
dev |
MIT |
X | | | X | PanPhlAn is a strain-level metagenomic profiling tool for identifying... |
| panta |
1.0.1 |
|
|
MIT |
| | | X | PanTA - pan-genome pipeline |
| pantax |
1.0.2 |
|
|
GPL-3.0-or-later |
X | | | | Strain-level taxonomic classification of metagenomic data using pangenome graphs |
| pantools |
4.3.3 |
doc |
dev |
GPL-3.0-only |
X | X | | X | PanTools is a pangenomic toolkit for comparative analysis of large... |
| panx |
1.6.0 |
|
|
GNU |
X | X | | | Microbial pan-genome analysis and exploration tool |
| papaa |
0.1.9 |
|
|
BSD-3-Clause |
| | | X | PAPAA tools to measure mutation specific pathway acitvity in TCGA... |
| paplot |
0.5.6 |
|
|
MIT |
| | | X | Automatic generation of cancer genome interactive report. |
| paraclu |
10 |
|
|
GPL-3.0-or-later |
X | X | | | Paraclu finds clusters in data attached to sequences. |
| parafly |
r2013_01_21 |
|
|
The |
X | X | | | Given a file containing a list of unix commands, multithreading is used... |
| paragone |
1.1.3 |
doc |
|
GPL-3.0-or-later |
X | X | | | Identify ortholog groups from a set of paralog sequences from multiple taxa. |
| paragraph |
2.3 |
|
|
Apache |
X | | | | Graph realignment tools for structural variants |
| parallel |
20170422 |
|
|
GPLv3 |
X | X | | | GNU parallel is a shell tool for executing jobs in parallel using one... |
| parallel-fastq-dump |
0.6.7 |
|
|
MIT |
X | X | | X | parallel fastq-dump wrapper |
| parallel-meta-suite |
1.0 |
|
|
GPL3 |
X | | | | Parallel-META-Suite is an interactive software package for rapid and... |
| parallel-virfinder |
0.3.1 |
|
|
Apache |
| | | X | parallel-virfinder, split virfinder execution in chuncks |
| paralyzer |
1.5 |
|
|
PARalyzer |
X | X | | X | We developed the PARalyzer algorithm to generate a high resolution map... |
| paraphase |
3.2.1 |
|
|
BSD-3-Clause-Clear |
| | | X | HiFi-based caller for highly homologous genes |
| parasail-python |
1.3.4 |
|
dev |
BSD-3-Clause |
X | X | | | Python bindings for the parasail C library containing implementations... |
| parascopy |
1.17.4 |
|
dev |
MIT |
X | X | | X | Calling paralog-specific copy number and sequence variants in... |
| paraview |
5.2.0 |
|
|
BSD |
X | | | | ParaView is an open-source, multi-platform data analysis and... |
| pardre |
2.2.5 |
|
|
GPL-3.0-only |
X | X | | | ParDRe is a parallel tool to remove duplicate reads. |
| parebrick |
0.5.7 |
|
dev |
MIT |
| | | X | A bioinf tool for finding genome rearrangements in bacterial genomes. |
| parent-map |
1.1.2 |
|
|
GNU |
| | | X | Analyze parental contributions to evolved or engineered protein or DNA sequences |
| pargenes |
1.2.0 |
|
|
GNU |
X | | | | A massively parallel tool for model selection and tree inference on... |
| parm |
0.0.7 |
|
|
https://github. |
| | | X | promoter activity regulatory model |
| parnas |
0.1.6 |
|
|
MIT |
| | | X | Representative taxon sampling from phylogenetic trees |
| parse-vcf |
0.2.8 |
|
|
MIT |
| | | X | Variant Call Format parser and convenience methods |
| parse_mito_blast |
1.0.2 |
|
|
BSD |
| | | X | Filtering blast out from querying assembly against mitochondrial database. |
| parsnp |
2.1.3 |
doc |
dev |
custom; |
X | X | | | Parsnp is a command-line-tool for efficient microbial core genome... |
| pasa |
2.5.3 |
doc |
dev |
BSD-3-Clause |
X | X | | | PASA, acronym for Program to Assemble Spliced Alignments (and... |
| pash |
3.0.6.2 |
|
|
Unknown |
X | | | | A versatile software package for read mapping and integrative analysis... |
| pass |
0.3.1 |
doc |
|
GPL-3.0-only |
| | | X | Proteome Assembler with Short Sequence peptides |
| pasta |
1.9.2 |
|
|
GPL-3.0-or-later |
X | X | | | An implementation of the PASTA (Practical Alignment using Sate and... |
| paste-bio |
1.4.0 |
|
dev |
BSD |
| | | X | A computational method to align and integrate spatial transcriptomics... |
| pastml |
1.9.50 |
doc |
dev |
GPL-3.0-or-later |
| | | X | Ancestral character reconstruction and visualisation for rooted... |
| pastrami |
0.9.6 |
|
|
CC |
| | | X | Pastrami is a novel, scalable computational algorithm for rapid human... |
| pasty |
2.2.1 |
|
|
Apache-2.0 |
| | | X | A tool easily taken advantage of for in silico serogrouping of... |
| patchify |
0.2.3 |
|
|
MIT |
| | | X | A library that helps you split image into small, overlappable patches,... |
| pathogen-embed |
3.1.0 |
|
|
MIT |
| | | X | Create reduced dimension embeddings for pathogen sequences |
| pathogen-profiler |
4.8.0 |
|
|
GPL3 |
| | | X | Library giving access to classes and functions to create a profiling... |
| pathogentrack |
0.2.3 |
|
|
MIT |
| | | X | A pipeline to identify pathogenic microorganisms from scRNA-seq raw data |
| pathogist |
0.3.6 |
|
|
GPL-3.0 |
| | | X | Calibrated multi-criterion genomic analysis for public health microbiology |
| patholive |
1.0 |
|
|
BSD |
| | | X | A real-time pathogen diagnostics tool for metagenomic Illumina sequencing data. |
| pathoscope |
2.0.7 |
|
|
GPLv3 |
X | X | | X | Species identification and strain attribution with unassembled sequencing data |
| pathphynder |
1.2.3 |
|
|
MIT |
| | | X | A workflow for ancient DNA placement into reference phylogenies. |
| pathracer |
3.16.0.dev |
|
|
GPLv2 |
X | X | | | PathRacer is a tool for alignment of profile HMM against assembly graph. |
| pathwaymatcher |
1.9.1 |
|
|
Apache |
X | X | | X | PathwayMatcher is a software tool writen in Java to search for pathways... |
| pauda |
1.0.1 |
|
|
GPL |
X | | | | PAUDA is a new approach toward the problem of comparing DNA reads... |
| pauvre |
0.1924 |
|
|
GNU |
X | X | | X | Tools for plotting Oxford Nanopore and other long-read data. |
| pavfinder |
1.8.5 |
|
|
GPL-3.0 |
| | | X | PAVFinder is a Python package that detects structural variants from de... |
| pb-assembly |
0.0.8 |
|
|
BSD |
X | | | X | Meta-package for Falcon/Unzip tool-suite (originally by Jason Chin) |
| pb-cpg-tools |
3.0.0 |
|
|
Pacific |
X | | | | Collection of tools for the analysis of CpG data |
| pb-dazzler |
0.0.1 |
|
|
Custom |
X | X | | | The Dresden Assembler suite -- Pacific Biosciences forks |
| pb-falcon |
2.2.4 |
|
|
BSD |
X | | | | FALCON/Unzip tool-suite (originally by Jason Chin) |
| pb-falcon-phase |
0.1.0 |
|
|
BSD |
X | | | | Non-python parts of falcon-phase (Pacific Biosciences) |
| pb-falconc |
1.15.0 |
|
|
BSD |
X | X | | | C utilities for PacBio assembly (pbipa etc.) |
| pbaa |
1.2.0 |
|
|
BSD-3-Clause-Clear |
X | | | X | PacBio tool to cluster HiFi reads and generate high quality consensus sequences |
| pbalign |
0.3.2 |
|
|
BSD-3-Clause-Clear |
X | X | | X | Python wrapper for producing PBBAM valid alignments |
| pbbam |
2.4.0 |
|
|
BSD-3-Clause-Clear |
X | X | | | PacBio BAM C++ library |
| pbccs |
6.4.0 |
|
|
BSD-3-Clause-Clear |
X | | | X | pbccs - Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads) |
| pbcommand |
2.1.1 |
|
|
BSD-3-Clause-Clear |
X | X | | X | Library for generating the CLI of various PacBio tools |
| pbcopper |
2.3.0 |
|
|
BSD-3-Clause-Clear |
X | X | | | Core C++ library for data structures, algorithms, and utilities |
| pbcore |
2.1.2 |
|
|
BSD-3-Clause-Clear |
X | X | | X | A Python library for reading and writing PacBio data files |
| pbcoretools |
0.8.1 |
|
|
BSD-3-Clause-Clear |
X | X | | X | CLI tools and add-ons for PacBio's core APIs |
| pbdagcon |
0.1 |
|
|
BSD-3-Clause-Clear |
X | | | | A sequence consensus algorithm implementation based on using directed... |
| pbfusion |
0.5.1 |
|
|
BSD-3-Clause-Clear |
| | | X | Fusion gene detection tool for PacBio Iso-Seq data |
| pbgcpp |
2.0.2 |
|
|
BSD-3-Clause-Clear |
X | | | X | pbgcpp - GenomicConsensus in C++ |
| pbgzip |
2016.08.04 |
|
|
MIT/Expat |
X | X | | | Parallel Block GZIP |
| pbh5tools |
0.8.0 |
|
|
BSD-3-Clause |
X | X | | | A swiss-army knife for interrogating PacBio® HDF5 files (cmp.h5, bas.h5). |
| pbhoover |
1.1.0 |
|
|
GPLv3 |
X | X | | X | Variant caller for legacy and low coverage Pacific Biosciences'... |
| pbiotools |
4.0.2 |
|
|
MIT |
| | | X | Miscellaneous bioinformatics and other supporting utilities for Python 3 |
| pbipa |
1.8.0 |
|
|
BSD |
X | | | | Improved Phased Assembly |
| pbjasmine |
2.4.0 |
|
|
BSD-3-Clause-Clear |
X | | | | jasmine |
| pblaa |
2.4.2 |
|
|
BSD-3-Clause-Clear |
X | | | X | PacBio tool to deconvolute mixtures of alleles and loci into phased... |
| pblat |
2.5.1 |
|
dev |
OTHER |
X | X | | | blat with multi-threads support |
| pbmarkdup |
1.2.0 |
|
|
BSD-3-Clause-Clear |
X | | | | pbmarkdup - Mark duplicate reads from PacBio sequencing of an amplified library |
| pbmm2 |
1.17.0 |
|
|
BSD-3-Clause-Clear |
X | X | | | A minimap2 frontend for PacBio native data formats |
| pbpigeon |
1.4.0 |
|
|
BSD-3-Clause-Clear |
X | | | X | PacBio transcript toolkit |
| pbptyper |
2.0.0 |
|
|
MIT |
| | | X | In silico Penicillin Binding Protein (PBP) typer for Streptococcus... |
| pbsim |
1.0.3 |
|
|
GPLv2 |
X | X | | | PBSIM simulates PacBio reads |
| pbsim2 |
2.0.1 |
|
|
GPL-2.0 |
X | X | | | PBSIM2: a simulator for long read sequencers with a novel generative... |
| pbsim3 |
3.0.5 |
|
|
GPL-2.0-only |
X | X | | | A simulator for all types of Pacific Biosciences (PacBio) and Oxford... |
| pbskera |
1.4.0 |
|
|
BSD-3-Clause-Clear |
| | | X | PacBio tool to split concatenated read designs |
| pbstarphase |
1.3.1 |
|
|
BSD-3-Clause-Clear |
X | | | | A phase-aware pharmacogenomic diplotyper for PacBio sequencing data |
| pbsv |
2.11.0 |
|
|
BSD-3-Clause-Clear |
X | | | X | pbsv - PacBio structural variant (SV) calling and analysis tools |
| pbtk |
3.5.0 |
|
|
BSD-3-Clause-Clear |
X | | | | pbtk - PacBio BAM toolkit |
| pbwt |
3.0 |
|
|
Apache-2.0 |
X | X | | | Positional Burrows-Wheeler Transform - methods for storing and... |
| pcaone |
0.4.8 |
doc |
dev |
GPL-3.0-only |
X | X | | | PCAone - Principal Component Analysis All in One |
| pcasuite |
1.0.0 |
|
|
Apache |
X | X | | | PCAzip compresses a trajectory, recentering the snapshots using a... |
| pcst-fast |
1.0.10 |
|
|
MIT |
X | X | | | A fast implementation of the Goemans-Williamson scheme for the PCST... |
| pdb2fasta |
1.0 |
|
dev |
GPL-2-only |
X | X | | | Convert PDB structures to FASTA sequences. |
| pdbx |
1.0.0 |
doc |
dev |
GPL-3.0-or-later |
X | X | | | pdbx is a parser module in python for structures of the protein data... |
| pdfkit |
0.6.1 |
|
|
MIT |
X | | | | Wkhtmltopdf python wrapper to convert html to pdf using the webkit... |
| pdivas |
1.2.0 |
|
|
MIT |
| | | X | PDIVAS: Pathogenicity predictor of Deep-Intronic Variants causing... |
| peakachu |
0.2.0 |
|
|
ISCL |
X | X | | | Peak calling tool for CLIP-seq data. |
| peakhood |
0.3 |
|
|
MIT |
| | | X | Individual site context extraction for CLIP-Seq peak regions |
| peakranger |
1.18 |
|
|
Artistic |
X | | | | PeakRanger is a multi-purporse software suite for analyzing... |
| peaks2utr |
1.4.1 |
|
|
GPL-3.0-or-later |
| | | X | A robust, parallelized Python CLI for annotating three_prime_UTR |
| peaksql |
0.0.4 |
doc |
dev |
MIT |
| | | X | Dynamic machine learning database for genomics. |
| peakzilla |
1.0 |
|
|
GPLv2 |
X | X | | X | Peakzilla identifies sites of enrichment and transcription factor... |
| pear |
0.9.6 |
|
|
Creative |
X | X | | | paired-end read merger |
| pecat |
0.0.3 |
|
|
BSD-2-Clause |
X | | | | A phased error correction and assembly tool |
| ped_parser |
1.6.6 |
|
|
BSD |
X | | | X | A ped file parser. |
| pedagree |
0.0.11 |
|
|
MIT |
X | | | | pleasingly pythonic pedigree manipulation |
| peddy |
0.4.8 |
|
|
MIT |
X | X | | X | genotype :: ped correspondence check, ancestry check, sex check.... |
| pedesigner |
0.2.0 |
|
|
GPL-3.0-only |
| | | X | A tool for prime-editing guideRNA (pegRNA) design |
| peekseq |
0.0.1 |
doc |
|
GPL-3.0 |
| | | X | De novo protein-coding potential calculator using a k-mer approach |
| peer |
1.3 |
|
|
GPL-2.0-or-later |
X | X | | | A collection of Bayesian approaches to infer hidden determinants and... |
| peewee |
2.8.0 |
|
|
MIT |
X | X | | | a little orm |
| pegas |
1.0.4 |
doc |
dev |
GPL-2.0-or-later |
| | | X | PeGAS is a Snakemake pipeline for genome analysis |
| pegasusio |
0.9.1 |
doc |
|
BSD-3-Clause |
X | X | | | PegasusIO is the IO package for Pegasus. |
| pegasuspy |
1.10.1 |
doc |
dev |
BSD-3-Clause |
X | X | | | An efficient Python analysis tool which scales to transcriptomes of... |
| peglit |
1.1.0 |
|
|
BSD-3-Clause |
| | | X | Automatically identifies non-interfering nucleotide linkers between a... |
| pegs |
0.6.6 |
doc |
dev |
BSD-3-Clause |
| | | X | Peak-set Enrichment of Gene-Sets (PEGS) |
| peka |
1.0.2 |
|
dev |
GPL-3.0-or-later |
| | | X | Analysis of kmers located around locations of interest |
| pepgenome |
1.1.beta |
|
|
Apache-2.0 |
| | | X | A java tool to map peptide and peptidoform evideces to ENSEMBL Genome... |
| pepnovo |
20101117 |
|
|
BSD |
X | X | | | PepNovo serves as a high throughput de novo peptide sequencing tool for... |
| pepquery |
2.0.2 |
|
|
GPL-3 |
| | | X | PepQuery is a peptide-centric search engine for novel peptide... |
| pepr |
1.1.24 |
|
|
GNU |
X | X | | X | Peak-calling and Prioritization pipeline for replicated ChIP-Seq data |
| pepsirf |
1.6.0 |
|
|
GPL-3.0-Only |
X | X | | | Peptide-based Serological Immune Response Framework |
| peptide-shaker |
3.0.11 |
doc |
dev |
Apache-2.0 |
X | X | | X | Independent platform for interpretation of proteomics identification results. |
| peptides |
0.3.4 |
|
|
MIT |
| | | X | Physicochemical properties, indices and descriptors for amino-acid sequences. |
| perbase |
0.10.2 |
doc |
dev |
MIT |
X | X | | X | Per-base metrics on BAM/CRAM files. |
| percolator |
3.7.1 |
doc |
dev |
Apache-2.0 |
X | | | | Semi-supervised learning for peptide identification from shotgun... |
| peregrine-2021 |
0.4.13 |
|
|
CC |
X | X | | | A genome assembler designed for long-reads that have good enough accuracy |
| perl-aceperl |
1.92 |
|
|
unknown |
X | X | | | Object-Oriented Access to ACEDB Databases |
| perl-acme-damn |
0.08 |
|
|
perl_5 |
X | X | | | 'Unbless' Perl objects. |
| perl-algorithm-cluster |
1.59 |
|
|
unknown |
X | X | | | Perl interface to the C Clustering Library |
| perl-algorithm-dependency |
1.112 |
|
|
perl_5 |
X | X | | X | Base class for implementing various dependency trees |
| perl-algorithm-diff |
1.1903 |
|
|
unknown |
X | X | | X | Compute intelligent differences between two files / lists but use the... |
| perl-algorithm-munkres |
0.08 |
|
|
unknown |
X | X | | X | Munkres.pm |
| perl-aliased |
0.34 |
|
|
perl_5 |
X | X | | X | Use shorter versions of class names. |
| perl-alien-build |
2.84 |
|
|
perl_5 |
X | X | | | Build external dependencies for use in CPAN |
| perl-alien-libxml2 |
0.17 |
|
|
perl_5 |
X | X | | | Install the C libxml2 library on your system |
| perl-apache-test |
1.43 |
|
|
unknown |
X | X | | X | Special Tests Sequence Failure Finder |
| perl-app-cpanminus |
1.7044 |
|
|
perl_5 |
X | X | | | get, unpack, build and install modules from CPAN |
| perl-appconfig |
1.71 |
|
|
perl_5 |
X | X | | X | AppConfig is a bundle of Perl5 modules for reading configuration files... |
| perl-archive-extract |
0.88 |
|
|
perl_5 |
X | X | | X | Generic archive extracting mechanism |
| perl-archive-tar |
2.40 |
|
|
perl_5 |
X | X | | X | Manipulates TAR archives |
| perl-archive-tar-wrapper |
0.33 |
|
|
gpl_3 |
X | X | | X | API wrapper around the 'tar' utility |
| perl-archive-zip |
1.68 |
|
|
perl_5 |
X | X | | X | Provide an interface to ZIP archive files. |
| perl-array-compare |
3.0.1 |
|
|
perl_5 |
X | X | | X | Perl extension for comparing arrays. |
| perl-array-set |
0.063 |
|
|
perl_5 |
X | X | | X | Perform set operations on arrays |
| perl-array-utils |
0.5 |
|
|
unknown |
X | X | | X | small utils for array manipulation |
| perl-atlas-modules |
0.3.1 |
|
|
Apache |
X | X | | | A package exporting in-house perl functions and classes used in the... |
| perl-attribute-handlers |
0.96 |
|
|
perl_5 |
X | X | | X | Simpler definition of attribute handlers |
| perl-authen-sasl-saslprep |
1.100 |
|
|
perl_5 |
X | X | | X | A Stringprep Profile for User Names and Passwords (RFC 4013) |
| perl-autodie |
2.36 |
|
|
perl_5 |
X | X | | X | Replace functions with ones that succeed or die with lexical scope |
| perl-autoloader |
5.74 |
|
|
perl_5 |
X | X | | X | load subroutines only on demand |
| perl-b |
1.48 |
|
|
perl_5 |
X | X | | X | The Perl Compiler Backend |
| perl-b-debug |
1.26 |
|
|
perl_5 |
X | X | | X | print debug info about ops |
| perl-b-hooks-endofscope |
0.26 |
|
|
perl_5 |
X | X | | | Execute code after a scope finished compilation |
| perl-base |
2.23 |
|
|
unknown |
X | X | | X | compile-time class fields |
| perl-bignum |
0.66 |
|
|
perl_5 |
X | X | | X | Transparent BigNumber support for Perl |
| perl-bio-asn1-entrezgene |
1.73 |
|
|
perl_5 |
X | X | | X | Regular expression-based Perl Parser for NCBI Entrez Gene |
| perl-bio-automatedannotation |
2021.01.04.08. |
|
|
open_source |
X | X | | X | Automated annotation of assemblies |
| perl-bio-bigfile |
1.07 |
|
|
Apache |
X | X | | | Low-level interface to BigWig & BigBed files |
| perl-bio-bpwrapper |
1.15 |
|
|
perl_5 |
| | | X | Bio::BPWrapper -- command-line utilities for Bio::Perl |
| perl-bio-cigar |
1.01 |
|
|
gpl_2 |
X | X | | X | Parse CIGAR strings and translate coordinates to/from reference/query |
| perl-bio-coordinate |
1.007001 |
|
|
perl_5 |
X | X | | X | Methods for dealing with genomic coordinates. |
| perl-bio-das |
1.17 |
|
|
artistic_2 |
| | | X | Client-side library for Distributed Genome Annotation System |
| perl-bio-db-embl |
1.7.4 |
|
|
perl_5 |
| | | X | Database object interface for EMBL entry retrieval |
| perl-bio-db-hts |
3.01 |
|
|
Apache |
X | X | | | Read files using HTSlib including BAM/CRAM, Tabix and BCF database files |
| perl-bio-db-refseq |
1.7.4 |
|
|
perl_5 |
| | | X | Database object interface for RefSeq retrieval |
| perl-bio-db-sam |
1.41 |
|
|
Perl |
X | | | | None |
| perl-bio-db-swissprot |
1.7.4 |
|
|
perl_5 |
| | | X | Database object interface to SwissProt retrieval |
| perl-bio-easel |
0.16 |
|
|
BSD |
X | X | | | Perl modules and scripts for interfacing with Sean Eddy's C easel... |
| perl-bio-eutilities |
1.77 |
|
|
perl_5 |
X | X | | X | Webagent which interacts with and retrieves data from NCBI eUtils. |
| perl-bio-featureio |
1.6.905 |
|
|
perl_5 |
X | X | | X | Modules for reading, writing, and manipulating sequence features |
| perl-bio-gff3 |
2.0 |
|
|
perl_5 |
X | X | | X | fast, low-level GFF3 manipulation |
| perl-bio-kmer |
0.55 |
|
|
MIT |
X | X | | | A perl module for helping with kmer analysis. |
| perl-bio-mlst-check |
2.1.1706216 |
|
|
gpl_3 |
X | X | | X | Multilocus sequence type checking using blast |
| perl-bio-phylo |
0.58 |
|
|
perl_5 |
X | X | | X | An object-oriented Perl toolkit for analyzing and manipulating... |
| perl-bio-phylo-cipres |
v0.2.1 |
|
|
perl_5 |
| | | X | Reusable components for CIPRES REST API access |
| perl-bio-phylo-forest-dbtree |
0.58 |
|
|
perl_5 |
| | | X | Tools and API for large phylogenies in SQLite databases. |
| perl-bio-procedural |
1.7.4 |
|
|
perl_5 |
X | X | | | Simple low-dependency procedural interfaces to BioPerl |
| perl-bio-rna-barmap |
0.04 |
|
|
GPL-3.0-or-later |
| | | X | Parse and query BarMap mappings. |
| perl-bio-rna-barriers |
0.03 |
|
|
GPL-3.0-or-later |
| | | X | Parse, query and manipulate output of Barriers |
| perl-bio-rna-rnaalisplit |
0.11 |
|
|
agpl_3 |
X | | | X | Split and deconvolute structural RNA multiple sequence alignments |
| perl-bio-rna-treekin |
0.05 |
|
|
GPL-3.0-or-later |
| | | X | Classes for working with Treekin output. |
| perl-bio-samtools |
1.43 |
|
|
perl_5 |
X | X | | | Read SAM/BAM files |
| perl-bio-searchio-hmmer |
1.7.3 |
|
|
perl_5 |
| | | X | A parser for HMMER2 and HMMER3 output (hmmscan, hmmsearch, hmmpfam) |
| perl-bio-tools-phylo-paml |
1.7.3 |
|
|
perl_5 |
X | X | | X | Parses output from the PAML programs codeml, baseml, basemlg,... |
| perl-bio-tools-run-alignment-clustalw |
1.7.4 |
|
|
perl_5 |
X | X | | X | Object for the calculation of a multiple sequence alignment from a set... |
| perl-bio-tools-run-alignment-tcoffee |
1.7.4 |
|
|
perl_5 |
X | | | X | Object for the calculation of a multiple sequence alignment from a set... |
| perl-bio-tools-run-remoteblast |
1.7.3 |
|
|
perl_5 |
| | | X | Object for remote execution of the NCBI Blast via HTTP |
| perl-bio-trace-abif |
1.06 |
|
|
perl_5 |
| | | X | Bio::Trace::ABIF - Perl extension for reading and parsing ABIF (Applied... |
| perl-bio-viennangs |
0.19.2 |
|
|
perl_5 |
X | X | | X | A Perl distribution for Next-Generation Sequencing (NGS) data analysis |
| perl-bioperl |
1.7.8 |
|
|
perl_5 |
X | X | | X | Bioinformatics Toolkit |
| perl-bioperl-core |
1.007002 |
|
|
perl_5 |
X | X | | X | "Core" packages for the BioPerl toolkit; you really should... |
| perl-bioperl-run |
1.007003 |
|
|
perl_5 |
X | X | | X | BioPerl-Run - wrapper toolkit |
| perl-biosails |
0.02 |
|
|
perl_5 |
X | X | | X | Standard(ized) Analysis Information Layers |
| perl-biox-seq |
0.008009 |
|
|
GPL-3.0-or-later |
X | X | | X | a basic but fast biological sequence object and associated parsers |
| perl-biox-workflow |
1.10 |
|
|
perl_5 |
X | X | | | None |
| perl-biox-workflow-command |
2.4.1 |
|
|
perl_5 |
X | X | | | Opinionated Bioinformatics Genomics Workflow Creator |
| perl-biox-workflow-plugin-filedetails |
0.11 |
|
|
perl_5 |
X | | | | None |
| perl-biox-workflow-plugin-fileexists |
0.13 |
|
|
perl_5 |
X | | | | None |
| perl-bit-vector |
7.4 |
|
|
Perl |
X | X | | X | Efficient bit vector, set of integers and "big int" math library |
| perl-blib |
1.06 |
|
|
perl_5 |
X | X | | X | Use MakeMaker's uninstalled version of a package |
| perl-bloom-faster |
1.7 |
|
|
unknown |
X | X | | | Perl extension for the c library libbloom. |
| perl-border-style |
0.01 |
|
|
perl_5 |
X | X | | X | Border style structure |
| perl-btlib |
0.19 |
|
|
open |
X | X | | | Binary Search Tree library |
| perl-bundle-bioperl |
2.1.9 |
|
|
unknown |
X | X | | X | A bundle to install external CPAN modules used by BioPerl 1.5.2 |
| perl-business-isbn |
3.007 |
|
|
artistic_2 |
X | X | | X | work with International Standard Book Numbers |
| perl-business-isbn-data |
20210112.006 |
|
|
perl_5 |
X | X | | X | data pack for Business::ISBN |
| perl-cache-cache |
1.08 |
|
|
unknown |
X | X | | X | extends Cache::SizeAwareMemoryCache |
| perl-cairo |
1.109 |
|
|
lgpl_2_1 |
X | X | | | Perl interface to the cairo 2d vector graphics library |
| perl-canary-stability |
2013 |
|
|
unknown |
X | X | | X | canary to check perl compatibility for schmorp's modules |
| perl-capture-tiny |
0.48 |
|
|
apache_2_0 |
X | X | | X | Capture STDOUT and STDERR from Perl, XS or external programs |
| perl-carp |
1.38 |
|
|
perl_5 |
X | X | | X | alternative warn and die for modules |
| perl-carp-clan |
6.08 |
|
|
perl_5 |
X | X | | X | Report errors from perspective of caller of a "clan" of modules |
| perl-cg-pipeline |
0.5 |
|
|
GNU |
| | | X | Perl libraries required for CG-Pipeline. |
| perl-cgi |
4.67 |
doc |
|
GPL |
X | X | | | A generic file fetching mechanism. |
| perl-class-accessor |
0.51 |
|
|
perl_5 |
X | X | | X | Automated accessor generation |
| perl-class-data-inheritable |
0.09 |
|
|
perl_5 |
X | X | | X | Inheritable, overridable class data |
| perl-class-inspector |
1.36 |
|
|
perl_5 |
X | X | | X | Get information about a class and its structure |
| perl-class-load |
0.25 |
|
|
perl_5 |
X | X | | X | A working (require "Class::Name") and more |
| perl-class-load-xs |
0.10 |
|
|
artistic_2 |
X | X | | | XS implementation of parts of Class::Load |
| perl-class-method-modifiers |
2.13 |
|
|
perl_5 |
X | X | | X | Provides Moose-like method modifiers |
| perl-class-methodmaker |
2.25 |
|
|
perl_5 |
X | X | | | Create generic methods for OO Perl |
| perl-class-singleton |
1.6 |
|
|
unknown |
X | X | | X | Base class for creating singleton objects |
| perl-class-std |
0.013 |
|
|
perl_5 |
X | X | | X | Support for creating standard "inside-out" classes |
| perl-class-std-fast |
0.0.8 |
|
|
perl_5 |
X | X | | X | faster but less secure than Class::Std |
| perl-class-trigger |
0.15 |
|
|
perl_5 |
| | | X | Mixin to add / call inheritable triggers |
| perl-class-xsaccessor |
1.19 |
|
|
perl_5 |
X | X | | | Generate fast XS accessors without runtime compilation |
| perl-clone |
0.46 |
|
|
perl_5 |
X | X | | | recursively copy Perl datatypes |
| perl-clone-choose |
0.010 |
|
|
perl_5 |
X | X | | X | Choose appropriate clone utility |
| perl-clone-pp |
1.08 |
|
|
perl_5 |
X | X | | X | Recursively copy Perl datatypes |
| perl-color-theme |
0.10.1 |
|
|
perl_5 |
X | X | | X | Color theme structure |
| perl-common-sense |
3.75 |
|
|
perl_5 |
X | X | | X | Sane defaults for Perl programs |
| perl-compress-bgzf |
0.005 |
|
|
gpl_3 |
X | X | | X | Read/write blocked GZIP (BGZF) files |
| perl-compress-raw-bzip2 |
2.201 |
|
|
perl_5 |
X | X | | | Low-Level Interface to bzip2 compression library |
| perl-compress-raw-zlib |
2.105 |
|
|
perl_5 |
X | X | | | Basic utilities for writing tests. |
| perl-config-any |
0.33 |
|
|
perl_5 |
X | X | | | Load configuration from different file formats, transparently |
| perl-config-autoconf |
0.320 |
|
|
perl_5 |
X | X | | | A module to implement some of AutoConf macros in pure perl. |
| perl-config-general |
2.67 |
|
|
perl_5 |
X | X | | X | Generic Config Module |
| perl-config-simple |
4.58 |
|
|
unknown |
X | X | | X | simple configuration file class |
| perl-config-tiny |
2.28 |
|
|
perl_5 |
X | X | | X | Read/Write .ini style files with as little code as possible |
| perl-const-fast |
0.014 |
|
|
perl_5 |
X | X | | X | Facility for creating read-only scalars, arrays, and hashes |
| perl-constant |
1.33 |
|
|
perl_5 |
X | X | | X | Perl pragma to declare constants |
| perl-convert-binary-c |
0.85 |
|
|
perl_5 |
X | X | | | Binary Data Conversion using C Types |
| perl-convert-binhex |
1.125 |
|
|
perl_5 |
X | X | | X | extract data from Macintosh BinHex files |
| perl-cpan-meta |
2.150010 |
|
|
perl_5 |
X | X | | X | the distribution metadata for a CPAN dist |
| perl-cpan-meta-check |
0.014 |
|
|
perl_5 |
X | X | | X | Verify requirements in a CPAN::Meta object |
| perl-cpan-meta-requirements |
2.143 |
|
|
perl_5 |
X | X | | X | a set of version requirements for a CPAN dist |
| perl-cpan-meta-validator |
2.140640 |
|
|
perl_5 |
X | X | | X | validate CPAN distribution metadata structures |
| perl-cpan-meta-yaml |
0.018 |
|
|
perl_5 |
X | X | | X | Read and write a subset of YAML for CPAN Meta files |
| perl-cpan-shell |
5.5004 |
|
|
perl_5 |
X | X | | X | None |
| perl-crypt-openssl-guess |
0.15 |
|
|
perl_5 |
X | X | | X | Guess OpenSSL include path |
| perl-crypt-openssl-random |
0.11 |
|
|
perl_5 |
X | X | | | OpenSSL/LibreSSL pseudo-random number generator access |
| perl-crypt-openssl-rsa |
0.33 |
|
|
perl_5 |
X | X | | | RSA encoding and decoding, using the openSSL libraries |
| perl-crypt-rc4 |
2.02 |
|
|
unknown |
X | X | | X | Perl implementation of the RC4 encryption algorithm |
| perl-data-compare |
1.25 |
|
|
unknown |
X | X | | X | compare perl data structures |
| perl-data-dump |
1.25 |
|
|
perl_5 |
X | X | | | Pretty printing of data structures |
| perl-data-dumper |
2.183 |
|
|
unknown |
X | X | | | seeds germane, yet not germinated |
| perl-data-lock |
1.03 |
|
|
unknown |
| | | X | makes variables (im)?mutable |
| perl-data-match |
0.06 |
|
|
unknown |
X | X | | X | Complex data structure pattern matching |
| perl-data-munge |
0.097 |
|
|
perl_5 |
X | X | | X | various utility functions |
| perl-data-optlist |
0.112 |
|
|
perl_5 |
X | X | | X | parse and validate simple name/value option pairs |
| perl-data-predicate |
2.1.1 |
|
|
BSD |
| | | X | Predicates are a way of composing logic so it eventually reports a... |
| perl-data-stag |
0.14 |
|
|
unknown |
X | X | | X | Structured Tags |
| perl-data-utilities |
0.04 |
|
|
unknown |
X | X | | X | recursively compare Perl datatypes |
| perl-data-uuid |
1.227 |
doc |
|
BSD |
X | X | | | Globally/Universally Unique Identifiers (GUIDs/UUIDs). |
| perl-data-visitor |
0.30 |
|
|
perl_5 |
X | X | | X | Visitor style traversal of Perl data structures |
| perl-data-walk |
2.01 |
|
|
open_source |
X | X | | X | Traverse Perl data structures. |
| perl-date-format |
2.30 |
|
|
perl_5 |
X | X | | | Date formating subroutines |
| perl-date-manip |
6.88 |
|
|
perl_5 |
X | X | | X | Date manipulation routines |
| perl-datetime |
1.65 |
doc |
|
Artistic_2 |
X | X | | | A date and time object for Perl. |
| perl-datetime-format-strptime |
1.75 |
|
|
artistic_2 |
X | X | | X | Parse and format strp and strf time patterns |
| perl-datetime-locale |
1.44 |
|
|
perl_5 |
X | X | | | Localization support for DateTime.pm |
| perl-datetime-timezone |
2.52 |
|
|
perl_5 |
X | X | | | Time zone object base class and factory |
| perl-db-file |
1.855 |
|
|
perl_5 |
X | X | | | Perl5 access to Berkeley DB version 1.x. |
| perl-dbd-mysql |
4.050 |
|
|
perl_5 |
X | X | | | A MySQL driver for the Perl5 Database Interface (DBI) |
| perl-dbd-pg |
3.18.0 |
|
|
perl_5 |
X | X | | | DBI PostgreSQL interface |
| perl-dbd-sqlite |
1.76 |
|
|
Perl |
X | X | | | Self Contained RDBMS in a DBI Driver |
| perl-dbi |
1.643 |
|
|
perl_5 |
X | X | | | Database independent interface for Perl |
| perl-dbm-deep |
2.0019 |
|
|
perl_5 |
X | X | | X | A pure perl multi-level hash/array DBM that supports transactions |
| perl-devel-assert |
1.06 |
|
|
perl_5 |
X | X | | | assertions for Perl >= 5.14 |
| perl-devel-checkbin |
0.04 |
|
|
perl_5 |
X | X | | X | check that a command is available |
| perl-devel-checklib |
1.16 |
|
|
perl_5 |
X | X | | X | check that a library is available |
| perl-devel-checkos |
1.81 |
|
|
unknown |
X | X | | X | check what OS we're running on |
| perl-devel-cover |
1.33 |
|
|
perl_5 |
X | X | | | Code coverage metrics for Perl |
| perl-devel-cycle |
1.12 |
|
|
unknown |
X | X | | X | Find memory cycles in objects |
| perl-devel-globaldestruction |
0.14 |
|
|
perl_5 |
X | X | | X | Provides function returning the equivalent of ${^GLOBAL_PHASE} eq... |
| perl-devel-overloadinfo |
0.007 |
|
|
perl_5 |
X | X | | X | introspect overloaded operators |
| perl-devel-size |
0.84 |
|
|
perl_5 |
X | X | | | Perl extension for finding the memory usage of Perl variables |
| perl-devel-stacktrace |
2.04 |
|
|
artistic_2 |
X | X | | X | An object representing a stack trace |
| perl-devel-symdump |
2.18 |
|
|
perl_5 |
X | X | | X | dump symbol names or the symbol table |
| perl-digest-crc |
0.23 |
|
|
PUBLIC-DOMAIN |
X | X | | | Generic CRC functions |
| perl-digest-crc32 |
0.01 |
|
|
perl_5 |
X | X | | X | Cyclic Redundency Check digests implementation |
| perl-digest-hmac |
1.04 |
|
|
perl_5 |
X | X | | X | Keyed-Hashing for Message Authentication |
| perl-digest-md5 |
2.58 |
|
|
perl_5 |
X | X | | | Perl interface to the MD-5 algorithm |
| perl-digest-md5-file |
0.08 |
|
|
unknown |
X | X | | X | Perl extension for getting MD5 sums for files and urls. |
| perl-digest-perl-md5 |
1.9 |
|
|
unknown |
X | X | | X | Perl Implementation of Rivest's MD5 algorithm |
| perl-digest-sha |
5.88 |
|
|
perl_5 |
X | X | | X | Perl extension for SHA-1/224/256/384/512 |
| perl-digest-sha1 |
2.13 |
|
|
perl_5 |
X | X | | | Perl interface to the SHA-1 algorithm |
| perl-dist-checkconflicts |
0.11 |
|
|
perl_5 |
X | X | | X | declare version conflicts for your dist |
| perl-dumbbench |
0.111 |
|
|
perl_5 |
X | X | | X | More reliable benchmarking with the least amount of thinking |
| perl-dynaloader |
1.25 |
|
|
perl_5 |
X | X | | X | Dynamically load C libraries into Perl code |
| perl-email-date-format |
1.005 |
|
|
perl_5 |
X | X | | X | produce RFC 2822 date strings |
| perl-email-simple |
2.218 |
|
|
perl_5 |
| | | X | simple parsing of RFC2822 message format and headers |
| perl-encode |
3.19 |
|
|
perl_5 |
X | X | | | allows you to write your script in non-ASCII and non-UTF-8 |
| perl-encode-locale |
1.05 |
|
|
perl_5 |
X | X | | X | Determine the locale encoding |
| perl-ensembl-api |
98 |
|
|
apache_2_0 |
| | | X | The Ensembl Core Perl API and |
| perl-ensembl-compara |
98 |
|
|
apache_2_0 |
| | | X | The Ensembl Core Perl API and |
| perl-ensembl-core |
98 |
|
|
apache_2_0 |
| | | X | The Ensembl Core Perl API and |
| perl-ensembl-funcgen |
98 |
|
|
apache_2_0 |
| | | X | The Ensembl Core Perl API and |
| perl-ensembl-genomes |
44 |
|
|
apache_2_0 |
| | | X | The Ensembl Core Perl API and |
| perl-ensembl-io |
98 |
|
|
apache_2_0 |
| | | X | The Ensembl Core Perl API and |
| perl-ensembl-variation |
98 |
|
|
apache_2_0 |
| | | X | The Ensembl Core Perl API and |
| perl-env |
1.04 |
|
|
perl_5 |
X | X | | X | perl module that imports environment variables as scalars or arrays |
| perl-env-path |
0.19 |
|
|
unknown |
X | X | | X | Advanced operations on path variables |
| perl-error |
0.17030 |
|
|
perl_5 |
X | X | | X | Error/exception handling in an OO-ish way |
| perl-escape-houdini |
0.3.0 |
|
|
perl_5 |
X | X | | | Perl API to Houdini, a zero-dependency C web escaping library |
| perl-estscan1 |
1.3 |
|
|
open |
X | X | | | Detects coding regions in DNA sequences even if they are of low... |
| perl-estscan2 |
2.1 |
|
|
open |
X | X | | | Detects coding regions in DNA sequences even if they are of low... |
| perl-eval-closure |
0.14 |
|
|
perl_5 |
X | X | | | safely and cleanly create closures via string eval |
| perl-excel-writer-xlsx |
1.14 |
|
|
perl_5 |
X | X | | X | Create a new file in the Excel 2007+ XLSX format. |
| perl-exception-class |
1.45 |
|
|
perl_5 |
X | X | | X | A module that allows you to declare real exception classes in Perl |
| perl-experimental |
0.034 |
|
|
perl_5 |
X | X | | X | Experimental features made easy |
| perl-exporter |
5.72 |
|
|
perl_5 |
X | X | | X | Implements default import method for modules |
| perl-exporter-tidy |
0.08 |
|
|
unknown |
X | X | | X | Another way of exporting symbols |
| perl-exporter-tiny |
1.002002 |
|
|
perl_5 |
X | X | | X | Exporter with the features of Sub::Exporter but only core dependencies |
| perl-extutils-cbuilder |
0.280230 |
|
|
perl_5 |
X | X | | X | Compile and link C code for Perl modules |
| perl-extutils-config |
0.008 |
|
|
perl_5 |
X | X | | X | A wrapper for perl's configuration |
| perl-extutils-constant |
0.25 |
|
|
perl_5 |
X | X | | | generate XS code to import C header constants |
| perl-extutils-cppguess |
0.26 |
|
|
perl_5 |
X | X | | | guess C++ compiler and flags |
| perl-extutils-depends |
0.8001 |
|
|
perl_5 |
X | X | | X | Easily build XS extensions that depend on XS extensions |
| perl-extutils-helpers |
0.026 |
|
|
perl_5 |
X | X | | X | Various portability utilities for module builders |
| perl-extutils-installpaths |
0.012 |
|
|
perl_5 |
X | X | | X | Build.PL install path logic made easy |
| perl-extutils-makemaker |
7.36 |
|
|
perl_5 |
X | X | | | Create a module Makefile |
| perl-extutils-manifest |
1.73 |
|
|
perl_5 |
X | X | | X | Utilities to write and check a MANIFEST file |
| perl-extutils-parsexs |
3.44 |
|
|
unknown |
X | X | | X | converts Perl XS code into C code |
| perl-extutils-pkgconfig |
1.16 |
|
|
unknown |
X | X | | X | simplistic interface to pkg-config |
| perl-fast |
1.06 |
|
|
Artistic-2.0 |
| | | X | FAST Analysis of Sequences Toolbox |
| perl-fastx-abi |
1.0.1 |
doc |
|
MIT |
| | | X | FASTX::Abi - Read Sanger trace file (.ab1 chromatograms) in FASTQ... |
| perl-fastx-reader |
1.12.0 |
doc |
dev |
gpl_3 |
| | | X | FASTX::Reader, Perl module to parse FASTA and FASTQ files |
| perl-ffi-checklib |
0.28 |
|
|
perl_5 |
| | | X | Check that a library is available for FFI |
| perl-file-chdir |
0.1010 |
|
|
perl_5 |
X | X | | X | a more sensible way to change directories |
| perl-file-compare |
1.1006 |
|
|
perl_5 |
X | X | | X | Compare files or filehandles |
| perl-file-copy-link |
0.200 |
doc |
|
Perl |
X | X | | | Perl extension for replacing a link by a copy of the linked file. |
| perl-file-copy-recursive |
0.45 |
|
|
Perl |
X | X | | | Perl extension for recursively copying files and directories |
| perl-file-copy-recursive-reduced |
0.006 |
|
|
perl_5 |
X | X | | X | Recursive copying of files and directories within Perl 5 toolchain |
| perl-file-details |
0.003 |
|
|
perl_5 |
X | X | | X | File details in an object, stat, hash, etc.. |
| perl-file-fetch |
1.04 |
|
|
perl_5 |
X | X | | X | Generic file fetching code |
| perl-file-find |
1.27 |
|
|
perl_5 |
X | X | | X | Traverse a directory tree. |
| perl-file-find-rule |
0.34 |
|
|
perl_5 |
X | X | | X | Alternative interface to File::Find |
| perl-file-grep |
0.02 |
|
|
unknown |
X | X | | X | Find matches to a pattern in a series of files and related functions |
| perl-file-homedir |
1.004 |
|
|
perl_5 |
X | X | | | Find your home and other directories on any platform |
| perl-file-listing |
6.16 |
|
|
perl_5 |
X | X | | X | parse directory listing |
| perl-file-next |
1.18 |
|
|
artistic_2 |
X | X | | X | File-finding iterator |
| perl-file-path |
2.16 |
|
|
unknown |
X | X | | | Create or remove directory trees |
| perl-file-pushd |
1.016 |
|
|
apache_2_0 |
X | X | | X | change directory temporarily for a limited scope |
| perl-file-readbackwards |
1.06 |
|
|
unknown |
X | X | | X | Read a file backwards by lines. |
| perl-file-remove |
1.57 |
|
|
perl_5 |
X | X | | | Remove files and directories |
| perl-file-share |
0.25 |
|
|
perl_5 |
X | X | | X | Extend File::ShareDir to Local Libraries |
| perl-file-sharedir |
1.118 |
|
|
perl_5 |
X | X | | X | Locate per-dist and per-module shared files |
| perl-file-sharedir-install |
0.13 |
|
|
perl_5 |
X | X | | X | Install shared files |
| perl-file-slurp |
9999.32 |
|
|
perl_5 |
X | X | | X | Simple and Efficient Reading/Writing/Modifying of Complete Files |
| perl-file-slurp-tiny |
0.004 |
|
|
perl_5 |
X | X | | X | A simple, sane and efficient file slurper [DISCOURAGED] |
| perl-file-slurper |
0.014 |
|
|
perl_5 |
X | X | | X | A simple, sane and efficient module to slurp a file |
| perl-file-sort |
1.01 |
|
|
unknown |
X | X | | X | Sort a file or merge sort multiple files |
| perl-file-spec |
3.48_01 |
|
|
perl_5 |
X | X | | X | portably perform operations on file names |
| perl-file-tee |
0.07 |
|
|
unknown |
X | X | | X | replicate data sent to a Perl stream |
| perl-file-temp |
0.2304 |
|
|
perl_5 |
X | X | | | return name and handle of a temporary file safely |
| perl-file-touch |
0.12 |
|
|
perl_5 |
X | X | | X | update file access and modification times, optionally creating files if needed |
| perl-file-util |
4.201720 |
|
|
perl_5 |
X | X | | X | Easy, versatile, portable file handling |
| perl-file-which |
1.23 |
|
|
perl_5 |
X | X | | | Perl implementation of the which utility as an API |
| perl-filedirutil |
0.04 |
|
|
agpl_3 |
X | X | | X | A Moose Role for basic File IO |
| perl-filesys-df |
0.92 |
|
|
unknown |
X | X | | | Perl extension for filesystem disk space information. |
| perl-filter-simple |
0.91 |
|
|
perl_5 |
X | X | | X | Simplified source filtering |
| perl-findbin |
1.51 |
|
|
perl_5 |
X | X | | X | Locate directory of original perl script |
| perl-findbin-libs |
2.017008 |
|
|
perl_5 |
X | X | | X | locate and a 'use lib' or export directories based on $FindBin::Bin. |
| perl-findbin-real |
1.05 |
|
|
perl_5 |
X | X | | X | Locates the full path to the script bin directory to allow the use of... |
| perl-font-afm |
1.20 |
|
|
perl_5 |
X | X | | X | Interface to Adobe Font Metrics files |
| perl-font-ttf |
1.06 |
|
|
artistic_2 |
X | X | | X | TTF font support for Perl |
| perl-forks |
0.36 |
|
|
perl_5 |
X | X | | | drop-in replacement for Perl threads using fork() |
| perl-gd |
2.83 |
|
|
perl_5 |
X | X | | | Perl interface to the gd2 graphics library |
| perl-gd-svg |
0.33 |
|
|
perl_5 |
| | | X | Seamlessly enable SVG output from scripts written using GD |
| perl-gdgraph |
1.54 |
|
|
perl_5 |
X | X | | X | Produces charts with GD |
| perl-gdgraph-histogram |
1.1 |
|
|
unknown |
X | X | | X | Histogram plotting module for Perl5 |
| perl-gdtextutil |
0.86 |
|
|
unknown |
X | X | | | Text utilities for use with GD |
| perl-getopt-argvfile |
1.11 |
|
|
artistic_1 |
X | X | | X | interpolates script options from files into @ARGV or another array |
| perl-getopt-long |
2.58 |
|
|
unknown |
X | X | | X | Module to handle parsing command line options |
| perl-getopt-long-descriptive |
0.111 |
|
|
perl_5 |
X | X | | X | Getopt::Long, but simpler and more powerful |
| perl-gfacs |
1.1.1 |
|
|
GNU |
| | | X | gFACs is a filtering, analysis, and conversion tool to unify genome... |
| perl-git-wrapper |
0.048 |
|
|
perl_5 |
X | X | | X | Wrap git(7) command-line interface |
| perl-git-wrapper-plus |
0.004011 |
|
|
perl_5 |
X | X | | X | A Toolkit for working with Git::Wrapper in an Object Oriented Way. |
| perl-go-perl |
0.15 |
|
|
BSD-3-Clause |
X | X | | X | perl modules for GO and other OBO ontologies |
| perl-graph |
0.9734 |
|
|
perl_5 |
X | X | | X | a Perl extension for keeping data partially sorted |
| perl-graph-readwrite |
2.10 |
|
|
perl_5 |
X | X | | X | modules for reading and writing directed graphs |
| perl-graphics-colornames |
2.11 |
|
|
perl_5 |
X | X | | X | defines RGB values for common color names |
| perl-graphics-colorobject |
0.5.0 |
|
|
unknown |
X | X | | X | convert between color spaces |
| perl-graphviz |
2.24 |
|
|
perl_5 |
X | X | | X | Interface to AT&T's GraphViz. Deprecated. See GraphViz2 |
| perl-grass |
1.1.6 |
|
|
GPLv3 |
X | | | | Gene Rearrangement AnalySiS |
| perl-gtdbtk |
0.1.5 |
|
|
GNU |
X | X | | | Perl script and dependent library files required for GTDB-Tk. |
| perl-hash-merge |
0.302 |
|
|
perl_5 |
X | X | | X | Merges arbitrarily deep hashes into a single hash |
| perl-hash-util-fieldhash-compat |
0.11 |
|
|
perl_5 |
X | X | | X | Use Hash::Util::FieldHash or ties, depending on availability |
| perl-heap |
0.80 |
|
|
perl_5 |
X | X | | X | Perl extensions for keeping data partially sorted |
| perl-heap-simple |
0.13 |
|
|
unknown |
X | X | | X | Fast and easy to use classic heaps |
| perl-heap-simple-perl |
0.14 |
|
|
unknown |
X | X | | X | A pure perl implementation of the Heap::Simple interface |
| perl-heap-simple-xs |
0.10 |
|
|
unknown |
X | X | | | An XS implementation of the Heap::Simple interface |
| perl-hook-lexwrap |
0.26 |
|
|
perl_5 |
X | X | | X | Lexically scoped subroutine wrappers |
| perl-hpc-runner |
2.48 |
|
|
perl_5 |
X | | | | None |
| perl-hpc-runner-command |
3.2.13 |
|
|
perl_5 |
X | X | | X | Create composable bioinformatics hpc analyses. |
| perl-hpc-runner-command-plugin-logger-sqlite |
0.0.3 |
|
|
perl_5 |
X | | | X | Log HPC::Runner workflows to a sqlite DB. |
| perl-hpc-runner-mce |
2.41 |
|
|
perl_5 |
X | X | | | None |
| perl-hpc-runner-pbs |
0.12 |
|
|
perl_5 |
X | X | | | None |
| perl-hpc-runner-scheduler |
0.09 |
|
|
perl_5 |
X | | | | None |
| perl-hpc-runner-slurm |
2.58 |
|
|
perl_5 |
X | X | | | None |
| perl-html-element-extended |
1.18 |
|
|
unknown |
X | X | | X | Perl extension for manipulating a table composed of HTML::Element style... |
| perl-html-entities-numbered |
0.04 |
|
|
unknown |
X | X | | X | Conversion of numbered HTML entities |
| perl-html-form |
6.07 |
|
|
perl_5 |
X | X | | X | Class that represents an HTML form element |
| perl-html-formatter |
2.16 |
|
|
perl_5 |
X | X | | X | Base class for HTML formatters |
| perl-html-parser |
3.83 |
|
|
perl_5 |
X | X | | | HTML parser class |
| perl-html-tableextract |
2.13 |
|
|
unknown |
X | X | | X | Perl module for extracting the content contained in tables within an... |
| perl-html-tagset |
3.20 |
|
|
unknown |
X | X | | X | data tables useful in parsing HTML |
| perl-html-template |
2.97 |
|
|
perl_5 |
X | X | | X | Perl module to use HTML-like templating language |
| perl-html-tidy |
1.60 |
|
|
artistic_2 |
X | X | | | (X)HTML validation in a Perl object |
| perl-html-tree |
5.07 |
|
|
perl_5 |
X | X | | X | Work with HTML in a DOM-like tree structure |
| perl-html-treebuilder-xpath |
0.14 |
|
|
perl_5 |
X | X | | X | add XPath support to HTML::TreeBuilder |
| perl-http-cookies |
6.10 |
|
|
perl_5 |
X | X | | X | HTTP cookie jars |
| perl-http-daemon |
6.16 |
|
|
perl_5 |
X | X | | X | a simple http server class |
| perl-http-date |
6.06 |
|
|
perl_5 |
X | X | | X | date conversion routines |
| perl-http-message |
6.36 |
|
|
perl_5 |
X | X | | X | HTTP style message (base class) |
| perl-http-negotiate |
6.01 |
|
|
perl_5 |
X | X | | X | choose a variant to serve |
| perl-http-server-simple |
0.52 |
|
|
Perl_5 |
X | X | | X | Lightweight HTTP server |
| perl-http-tiny |
0.076 |
|
|
perl_5 |
| | | X | A small, simple, correct HTTP/1.1 client |
| perl-if |
0.0608 |
|
|
perl_5 |
| | | X | use a Perl module if a condition holds |
| perl-image-exiftool |
12.60 |
|
|
perl_5 |
X | X | | X | ExifTool is a platform-independent Perl library plus a command-line... |
| perl-image-info |
1.42 |
|
|
perl_5 |
X | X | | X | Extract meta information from image files |
| perl-image-size |
3.300 |
|
|
perl_5 |
X | X | | X | A library to extract height/width from images |
| perl-import-into |
1.002005 |
|
|
perl_5 |
X | X | | X | Import packages into other packages |
| perl-importer |
0.026 |
|
|
perl_5 |
X | X | | X | Alternative but compatible interface to modules that export symbols. |
| perl-indirect |
0.39 |
|
|
perl_5 |
X | X | | | Lexically warn about using the indirect method call syntax. |
| perl-inline |
0.86 |
|
|
perl_5 |
X | X | | X | Write Perl Subroutines in Other Programming Languages |
| perl-inline-c |
0.81 |
|
|
perl_5 |
X | X | | | C Language Support for Inline |
| perl-integer |
1.01 |
|
|
perl_5 |
X | X | | X | Perl pragma to use integer arithmetic instead of floating point |
| perl-io-all |
0.87 |
|
|
perl_5 |
X | X | | X | Combines all of the best Perl IO modules into a single nifty object... |
| perl-io-compress |
2.201 |
|
|
perl_5 |
X | X | | | IO Interface to compressed data files/buffers |
| perl-io-compress-deflate |
2.064 |
|
|
perl_5 |
X | X | | X | Write RFC 1950 files/buffers |
| perl-io-gzip |
0.20 |
|
|
perl_5 |
X | X | | | Perl extension to provide a PerlIO layer to gzip/gunzip |
| perl-io-handle |
1.42 |
|
|
perl_5 |
X | X | | X | supply object methods for I/O handles |
| perl-io-html |
1.004 |
|
|
perl_5 |
X | X | | X | Open an HTML file with automatic charset detection |
| perl-io-interactive |
1.026 |
|
|
perl_5 |
X | X | | X | Utilities for interactive I/O |
| perl-io-null |
1.01 |
|
|
Perl |
| | | X | class for null filehandles |
| perl-io-pager |
2.10 |
|
|
Artistic |
| | | X | Select a pager (possibly perl-based) & pipe it text if a TTY |
| perl-io-prompt |
0.997004 |
|
|
perl_5 |
X | X | | X | Interactively prompt for user input |
| perl-io-scalar |
2.111 |
|
|
perl_5 |
X | X | | X | IO:: interface for reading/writing a scalar |
| perl-io-sessiondata |
1.03 |
|
|
unknown |
X | X | | X | supporting module for SOAP::Lite |
| perl-io-socket-inet6 |
2.73 |
|
|
perl_5 |
X | X | | X | Object interface for AF_INET/AF_INET6 domain sockets |
| perl-io-socket-ssl |
2.074 |
|
|
perl_5 |
X | X | | X | Nearly transparent SSL encapsulation for IO::Socket::INET. |
| perl-io-string |
1.08 |
|
|
unknown |
X | X | | X | Emulate file interface for in-core strings |
| perl-io-stringy |
2.111 |
|
|
unknown |
X | X | | X | write a file which is updated atomically |
| perl-io-tty |
1.16 |
|
|
perl_5 |
X | X | | | Pseudo ttys and constants |
| perl-io-uncompress-bunzip2 |
2.064 |
|
|
perl_5 |
X | X | | X | Read bzip2 files/buffers |
| perl-io-uncompress-gunzip |
2.064 |
|
|
perl_5 |
X | X | | X | Read RFC 1952 files/buffers |
| perl-io-uncompress-rawinflate |
2.064 |
|
|
perl_5 |
X | X | | X | Read RFC 1951 files/buffers |
| perl-io-zlib |
1.14 |
|
|
unknown |
X | X | | X | IO:: style interface to Compress::Zlib |
| perl-ipc-cmd |
1.04 |
|
|
perl_5 |
X | X | | X | A cross platform way of running (interactive) commandline programs. |
| perl-ipc-run |
20200505.0 |
|
|
perl_5 |
X | X | | X | system() and background procs w/ piping, redirs, ptys (Unix, Win32) |
| perl-ipc-run3 |
0.048 |
|
|
open_source |
X | X | | X | run a subprocess with input/ouput redirection |
| perl-ipc-sharelite |
0.17 |
|
|
perl_5 |
X | X | | | Lightweight interface to shared memory |
| perl-ipc-system-simple |
1.30 |
|
|
perl_5 |
X | X | | X | Run commands simply, with detailed diagnostics |
| perl-jcode |
2.07 |
|
|
unknown |
X | X | | X | Japanese Charset Handler |
| perl-json |
4.10 |
|
dev |
GPL-1.0-or-later |
X | X | | X | JSON (JavaScript Object Notation) encoder/decoder |
| perl-json-create |
0.35 |
|
|
perl_5 |
X | X | | | fast, minimal, UTF-8-only serialization of data to JSON |
| perl-json-maybexs |
1.004003 |
|
|
perl_5 |
X | X | | X | Use Cpanel::JSON::XS with a fallback to JSON::XS and JSON::PP |
| perl-json-parse |
0.62 |
|
|
perl_5 |
X | X | | | Read JSON into a Perl variable |
| perl-json-pp |
4.11 |
|
|
perl_5 |
X | X | | X | JSON::XS compatible pure-Perl module. |
| perl-json-validator |
5.14 |
|
|
artistic_2 |
| | | X | Validate data against a JSON schema |
| perl-json-xs |
4.03 |
|
|
GPL-1.0-or-later |
X | X | | | JSON serialising/deserialising, done correctly and fast |
| perl-lib |
0.63 |
|
|
perl_5 |
X | X | | X | manipulate @INC at compile time |
| perl-libwww-perl |
6.68 |
doc |
dev |
perl_5 |
X | X | | X | The World-Wide Web library for Perl. |
| perl-libxml-perl |
0.08 |
|
|
unknown |
X | X | | X | Perl SAX parser using nsgmls |
| perl-list-compare |
0.53 |
|
|
perl_5 |
X | X | | X | Compare elements of two or more lists |
| perl-list-moreutils |
0.430 |
|
|
apache_2_0 |
X | X | | X | Provide the stuff missing in List::Util |
| perl-list-moreutils-xs |
0.430 |
|
|
apache_2_0 |
X | X | | | Provide the stuff missing in List::Util in XS |
| perl-list-someutils |
0.59 |
|
|
perl_5 |
X | X | | | Provide the stuff missing in List::Util |
| perl-list-uniq |
0.23 |
|
|
perl_5 |
X | X | | X | extract the unique elements of a list |
| perl-list-util |
1.38 |
|
|
perl_5 |
X | X | | | A selection of general-utility list subroutines |
| perl-local-lib |
2.000029 |
|
|
perl_5 |
X | X | | X | create and use a local lib/ for perl modules with PERL5LIB |
| perl-locale |
1.03 |
|
|
perl_5 |
X | X | | X | Perl pragma to use or avoid POSIX locales for built-in operations |
| perl-locale-maketext-simple |
0.21 |
|
|
perl_5 |
X | X | | X | Simple interface to Locale::Maketext::Lexicon |
| perl-lockfile-simple |
0.208 |
|
|
unknown |
| | | X | simple file locking scheme |
| perl-log-any |
1.710 |
|
|
perl_5 |
X | X | | X | Bringing loggers and listeners together |
| perl-log-log4perl |
1.55 |
|
|
unknown |
X | X | | X | Log4j implementation for Perl |
| perl-logger-simple |
2.0 |
|
|
perl_5 |
X | X | | X | Implementation of the Simran-Log-Log and Simran-Error-Error modules |
| perl-lwp-mediatypes |
6.04 |
|
|
perl_5 |
X | X | | X | guess media type for a file or a URL |
| perl-lwp-protocol-https |
6.10 |
|
|
Perl |
X | X | | X | Provide https support for LWP::UserAgent |
| perl-lwp-simple |
6.67 |
|
|
Perl |
X | X | | X | simple procedural interface to LWP |
| perl-lyve-set |
2.0.1 |
|
|
MIT |
| | | X | Perl libraries required for Lyve-SET. |
| perl-mac-propertylist |
1.504 |
|
|
artistic_2 |
X | X | | X | work with Mac plists at a low level |
| perl-mac-systemdirectory |
0.10 |
|
|
perl_5 |
| X | | | Locate Mac OS X Standard System Directories |
| perl-mailtools |
2.21 |
|
|
perl_5 |
X | X | | X | Various e-mail related modules |
| perl-math-base-convert |
0.11 |
|
|
unknown |
X | X | | X | very fast base to base conversion |
| perl-math-bezier |
0.01 |
|
|
unknown |
X | X | | X | solution of Bezier Curves |
| perl-math-bigint |
2.004001 |
|
|
perl_5 |
X | X | | X | Arbitrary size floating point math package |
| perl-math-bigrat |
0.2624 |
|
|
perl_5 |
X | X | | X | Arbitrary big rational numbers |
| perl-math-cdf |
0.1 |
|
|
Public |
X | X | | | Generate probabilities and quantiles from several statistical... |
| perl-math-combinatorics |
0.09 |
|
|
unknown |
X | X | | X | Perform combinations and permutations on lists |
| perl-math-complex |
1.59 |
|
|
perl_5 |
X | X | | X | trigonometric functions |
| perl-math-derivative |
1.01 |
|
|
perl_5 |
X | X | | X | Numeric 1st and 2nd order differentiation. |
| perl-math-matrix |
0.94 |
|
|
unknown |
| | | X | Multiply and invert Matrices |
| perl-math-matrixreal |
2.13 |
|
|
perl_5 |
| | | X | Manipulate NxN matrices of real numbers |
| perl-math-random |
0.72 |
|
|
unknown |
X | X | | | Random Number Generators |
| perl-math-random-mt-auto |
6.23 |
|
|
unrestricted |
X | X | | | Auto-seeded Mersenne Twister PRNGs |
| perl-math-round |
0.07 |
|
|
unknown |
X | X | | X | Perl extension for rounding numbers |
| perl-math-spline |
0.02 |
|
|
perl_5 |
X | X | | X | Cubic Spline Interpolation of data |
| perl-math-utils |
1.14 |
|
|
perl_5 |
X | X | | X | Useful mathematical functions not in Perl |
| perl-math-vecstat |
0.08 |
|
|
unknown |
X | X | | X | Some basic numeric stats on vectors |
| perl-mce |
1.901 |
|
|
perl_5 |
X | X | | X | Many-Core Engine for Perl providing parallel processing capabilities |
| perl-mce-shared |
1.893 |
|
|
perl_5 |
X | X | | X | MCE extension for sharing data supporting threads and processes |
| perl-memoize |
1.09 |
|
|
perl_5 |
X | X | | X | Make functions faster by trading space for time |
| perl-metabolomics-fragment-annotation |
0.6.9 |
|
|
perl_5 |
| | | X | Perl extension for fragment annotation in metabolomics |
| perl-mime-base64 |
3.16 |
|
|
perl_5 |
X | X | | | The RFC 2045 encodings; base64 and quoted-printable |
| perl-mime-lite |
3.030 |
|
|
perl_5 |
X | X | | X | Handy-dandy MIME mailing class |
| perl-mime-quotedprint |
3.13 |
|
|
perl_5 |
X | X | | X | Encoding and decoding of quoted-printable strings |
| perl-mime-tools |
5.508 |
|
|
perl_5 |
X | X | | X | Tools to manipulate MIME messages |
| perl-mime-types |
2.27 |
|
|
perl_5 |
X | X | | X | Definition of MIME types |
| perl-minion |
10.31 |
|
|
Artistic-2.0 |
| | | X | Job queue |
| perl-minion-backend-sqlite |
5.0.7 |
|
|
Artistic-2.0 |
| | | X | SQLite backend for Minion job queue |
| perl-mixin-linewise |
0.111 |
|
|
perl_5 |
X | X | | X | write your linewise code for handles; this does the rest |
| perl-mldbm |
2.05 |
|
|
perl_5 |
X | X | | X | store multi-level Perl hash structure in single level tied hash |
| perl-mldbm-sync |
0.30 |
|
|
unknown |
X | X | | X | safe concurrent access to MLDBM databases |
| perl-module-build |
0.4231 |
|
|
perl_5 |
X | X | | X | Build and install Perl modules |
| perl-module-build-tiny |
0.039 |
|
|
perl_5 |
X | X | | X | A tiny replacement for Module::Build |
| perl-module-corelist |
5.20220620 |
|
|
perl_5 |
X | X | | X | what modules shipped with versions of perl |
| perl-module-extract-use |
1.043 |
|
|
artistic_2 |
X | X | | X | Pull out the modules a module explicitly uses |
| perl-module-fromperlver |
0.008002 |
|
|
perl_5 |
X | X | | X | install modules compatible with the running perl. |
| perl-module-implementation |
0.09 |
|
|
artistic_2 |
X | X | | X | Loads one of several alternate underlying implementations for a module |
| perl-module-list |
0.004 |
|
|
perl_5 |
X | X | | X | module `directory' listing |
| perl-module-load |
0.34 |
|
|
perl_5 |
X | X | | X | Load modules in a DWIM style |
| perl-module-load-conditional |
0.68 |
|
|
perl_5 |
X | X | | X | Looking up module information / loading at runtime |
| perl-module-loaded |
0.08 |
|
|
perl_5 |
X | X | | X | Mark modules as loaded/unloaded |
| perl-module-metadata |
1.000038 |
|
|
perl_5 |
X | X | | X | Gather package and POD information from perl module files |
| perl-module-pluggable |
5.2 |
|
|
perl_5 |
X | X | | X | automatically give your module the ability to have plugins |
| perl-module-runtime |
0.016 |
|
|
perl_5 |
X | X | | X | runtime module handling |
| perl-module-runtime-conflicts |
0.003 |
|
|
perl_5 |
X | X | | X | Provide information on conflicts for Module::Runtime |
| perl-module-scandeps |
1.33 |
|
|
perl_5 |
X | X | | X | Recursively scan Perl code for dependencies |
| perl-module-util |
1.09 |
|
|
perl_5 |
X | X | | X | Module name tools and transformations |
| perl-mojo-pg |
4.27 |
|
|
Artistic-2.0 |
| | | X | Mojolicious PostgreSQL |
| perl-mojo-sqlite |
3.009 |
|
|
Artistic-2.0 |
| | | X | A tiny Mojolicious wrapper for SQLite |
| perl-moo |
2.005004 |
|
|
perl_5 |
X | X | | X | Minimalist Object Orientation (with Moose compatibility) |
| perl-moose |
2.2202 |
|
|
perl_5 |
X | X | | | A postmodern object system for Perl 5 |
| perl-moosex-app |
1.3701 |
|
|
perl_5 |
X | X | | X | Write user-friendly command line apps with even less suffering |
| perl-moosex-app-role-log4perl |
0.03 |
|
|
perl_5 |
X | | | X | Add basic Log::Log4perl logging to a MooseX::App application as a role. |
| perl-moosex-clone |
0.06 |
|
|
perl_5 |
X | X | | X | Fine-grained cloning support for Moose objects. |
| perl-moosex-fileattribute |
0.03 |
|
|
perl_5 |
X | X | | X | Sugar for classes that have file or directory attributes |
| perl-moosex-getopt |
0.75 |
|
|
perl_5 |
X | X | | X | A Moose role for processing command line options |
| perl-moosex-nonmoose |
0.26 |
|
|
perl_5 |
X | X | | X | MooseX::NonMoose - easy subclassing of non-Moose classes |
| perl-moosex-object-pluggable |
0.0014 |
|
|
perl_5 |
X | X | | X | Make your classes pluggable |
| perl-moosex-role-parameterized |
1.11 |
|
|
perl_5 |
X | X | | X | Moose roles with composition parameters |
| perl-moosex-role-withoverloading |
0.17 |
|
|
perl_5 |
X | X | | | (DEPRECATED) Roles which support overloading |
| perl-moosex-singleton |
0.30 |
|
|
perl_5 |
X | X | | X | Turn your Moose class into a singleton |
| perl-moosex-strictconstructor |
0.21 |
|
|
artistic_2 |
| | | X | Make your object constructors blow up on unknown attributes |
| perl-moosex-types |
0.50 |
|
|
perl_5 |
X | X | | X | Organise your Moose types in libraries |
| perl-moosex-types-path-class |
0.09 |
|
|
perl_5 |
X | X | | X | A Path::Class type library for Moose |
| perl-moosex-types-path-tiny |
0.012 |
|
|
perl_5 |
X | X | | X | MooseX::Types::Path::Tiny - Path::Tiny types and coercions for Moose |
| perl-moosex-types-stringlike |
0.003 |
|
|
apache_2_0 |
X | X | | X | Moose type constraints for strings or string-like objects |
| perl-mozilla-ca |
20211001 |
|
|
unknown |
X | X | | X | Mozilla's CA cert bundle in PEM format |
| perl-mro-compat |
0.15 |
|
|
perl_5 |
X | X | | X | mro::* interface compatibility for Perls < 5.9.5 |
| perl-ms |
0.207003 |
|
|
GPL-3.0-or-later |
| | | X | Namespace for mass spectrometry-related libraries |
| perl-namespace-autoclean |
0.31 |
|
|
perl_5 |
X | X | | | Keep imports out of your namespace |
| perl-namespace-clean |
0.27 |
|
|
perl_5 |
X | X | | | Keep imports and functions out of your namespace |
| perl-net-ftp |
2.79 |
|
|
perl_5 |
X | X | | X | FTP Client class |
| perl-net-ftp-recursive |
2.04 |
|
|
Perl |
X | X | | X | Recursive FTP Client class |
| perl-net-http |
6.22 |
|
|
perl_5 |
X | X | | X | Low-level HTTP connection (client) |
| perl-net-netrc |
2.14 |
|
|
perl_5 |
X | X | | X | OO interface to users netrc file |
| perl-net-ssleay |
1.92 |
|
|
perl_5 |
X | X | | | Perl extension for using OpenSSL |
| perl-ntlm |
1.09 |
|
|
perl_5 |
X | X | | X | An NTLM authentication module |
| perl-number-compare |
0.03 |
|
|
perl_5 |
X | X | | X | Numeric comparisons |
| perl-number-format |
1.76 |
|
|
perl_5 |
X | X | | X | Perl extension for formatting numbers |
| perl-number-misc |
1.2 |
|
|
perl_5 |
X | X | | X | Number::Misc - handy utilities for numbers |
| perl-number-range |
0.12 |
|
|
perl_5 |
X | X | | X | Perl extension defining ranges of numbers and testing if a number is... |
| perl-number-witherror |
1.01 |
|
|
perl_5 |
X | X | | X | Numbers with error propagation and scientific rounding |
| perl-object-insideout |
4.05 |
|
|
perl_5 |
X | X | | X | Comprehensive inside-out object support module |
| perl-obogaf-parser |
1.373 |
doc |
dev |
perl_5 |
| | | X | a perl5 module to handle obo and gaf file |
| perl-ole-storage_lite |
0.22 |
|
|
unknown |
X | X | | X | Read and write OLE storage files. |
| perl-onto-perl |
1.45 |
|
|
perl_5 |
X | X | | X | PERL modules for manipulating OBO-formatted ontologies, such as the... |
| perl-package-deprecationmanager |
0.17 |
|
|
artistic_2 |
X | X | | X | Manage deprecation warnings for your distribution |
| perl-package-stash |
0.40 |
|
|
perl_5 |
X | X | | | routines for manipulating stashes |
| perl-package-stash-xs |
0.29 |
|
|
perl_5 |
X | X | | | faster and more correct implementation of the Package::Stash API |
| perl-padwalker |
2.5 |
|
|
unknown |
X | X | | | play with other peoples' lexical variables |
| perl-par |
1.014 |
|
|
perl_5 |
X | X | | X | Perl Archive Tookit |
| perl-par-dist |
0.49 |
|
|
unknown |
X | X | | X | Create and manipulate PAR distributions |
| perl-par-packer |
1.036 |
|
|
perl_5 |
X | | | | PAR Packager |
| perl-parallel-forkmanager |
2.03 |
|
|
perl_5 |
X | X | | X | A simple parallel processing fork manager |
| perl-parallel-iterator |
1.00 |
|
|
perl_5 |
X | X | | X | Simple parallel execution |
| perl-parallel-loops |
0.12 |
|
|
perl_5 |
X | X | | X | Execute loops using parallel forked subprocesses |
| perl-params-check |
0.38 |
|
|
perl_5 |
X | X | | X | Templated based param validation |
| perl-params-coerce |
0.14 |
|
|
perl_5 |
X | X | | X | Allows your classes to do coercion of parameters |
| perl-params-util |
1.102 |
|
|
perl_5 |
X | X | | | Simple, compact and correct param-checking functions |
| perl-params-validate |
1.31 |
|
|
artistic_2 |
X | X | | | Validate method/function parameters |
| perl-params-validationcompiler |
0.31 |
|
|
artistic_2 |
X | X | | X | Build an optimized subroutine parameter validator once, use it forever |
| perl-parent |
0.236 |
|
|
perl_5 |
X | X | | X | Establish an ISA relationship with base classes at compile time |
| perl-parse-recdescent |
1.967015 |
|
|
unknown |
X | X | | X | Generate Recursive-Descent Parsers |
| perl-parse-yapp |
1.21 |
|
|
unknown |
X | X | | X | A perl frontend to the Parse::Yapp module |
| perl-path-class |
0.37 |
|
|
perl_5 |
X | X | | X | Cross-platform path specification manipulation |
| perl-path-tiny |
0.122 |
|
|
apache_2_0 |
X | X | | X | File path utility |
| perl-pathtools |
3.75 |
|
|
perl_5 |
X | X | | | Tools for working with directory and file names |
| perl-pbkdf2-tiny |
0.005 |
|
|
apache_2_0 |
X | | | X | Minimalist PBKDF2 (RFC 2898) with HMAC-SHA1 or HMAC-SHA2 |
| perl-pcap |
3.5.2 |
|
|
GPLv3 |
X | | | | NGS reference implementations and helper code for the IGCG/TCGA... |
| perl-pdf-api2 |
2.043 |
|
|
lgpl_2_1 |
X | X | | X | Facilitates the creation and modification of PDF files |
| perl-pdf-table |
1.005 |
|
|
perl_5 |
| | | X | A utility class for building table layouts in a PDF::API2 object. |
| perl-pegex |
0.61 |
|
|
perl_5 |
X | X | | X | Pegex Grammar for the Pegex Grammar Language |
| perl-perl-osnames |
0.122 |
|
|
perl_5 |
X | X | | X | List possible $^O ($OSNAME) values, with description |
| perl-perl-ostype |
1.010 |
|
|
perl_5 |
X | X | | X | Map Perl operating system names to generic types |
| perl-perl-unsafe-signals |
0.03 |
|
|
perl_5 |
X | X | | | Allow unsafe handling of signals in selected blocks |
| perl-perl-version |
1.018 |
|
|
perl_5 |
X | X | | X | Parse and manipulate Perl version strings |
| perl-perl4-corelibs |
0.004 |
|
|
GPL-3.0 |
X | X | | | libraries historically supplied with Perl 4 |
| perl-perldoc |
0.20 |
|
|
perl_5 |
| | | X | Documentation Framework for Perl |
| perl-perlio |
1.09 |
|
|
perl_5 |
X | X | | X | On demand loader for PerlIO layers and root of PerlIO::* name space |
| perl-perlio-encoding |
0.18 |
|
|
perl_5 |
X | X | | X | encoding layer |
| perl-perlio-gzip |
0.20 |
|
|
perl_5 |
X | X | | | PerlIO interface to gzip/gunzip |
| perl-perlio-utf8_strict |
0.009 |
|
|
perl_5 |
X | X | | | Fast and correct UTF-8 IO |
| perl-pod-checker |
1.60 |
|
|
perl_5 |
X | X | | X | Pod::Checker verifies POD documentation contents for compliance with... |
| perl-pod-coverage |
0.23 |
|
|
unknown |
X | X | | X | Checks if the documentation of a module is comprehensive |
| perl-pod-coverage-trustpod |
0.100006 |
|
|
perl_5 |
X | X | | X | allow a module's pod to contain Pod::Coverage hints |
| perl-pod-elemental |
0.103006 |
|
|
perl_5 |
X | X | | | work with nestable Pod elements |
| perl-pod-escapes |
1.07 |
|
|
perl_5 |
X | X | | X | for resolving Pod Elt...gt sequences |
| perl-pod-eventual |
0.094003 |
|
|
perl_5 |
| | | X | read a POD document as a series of trivial events |
| perl-pod-parser |
1.63 |
|
|
unknown |
X | X | | X | Modules for parsing/translating POD format documents |
| perl-pod-plaintext |
2.07 |
|
|
perl_5 |
X | X | | X | Convert POD data to formatted ASCII text |
| perl-pod-simple |
3.35 |
|
|
perl_5 |
X | X | | X | framework for parsing Pod |
| perl-pod-simple-text |
3.28 |
|
|
perl_5 |
X | X | | X | format Pod as plaintext |
| perl-pod-usage |
2.03 |
|
|
perl_5 |
X | X | | X | print a usage message from embedded pod documentation |
| perl-posix |
1.38_03 |
|
|
perl_5 |
X | X | | X | None |
| perl-postscript |
0.06 |
|
|
unknown |
X | X | | X | helper module for PostScript::TextBlock |
| perl-ppi |
1.236 |
|
|
perl_5 |
X | X | | X | Parse, Analyze and Manipulate Perl (without perl) |
| perl-prefork |
1.05 |
|
|
perl_5 |
X | X | | X | Optimized module loading for forking or non-forking processes |
| perl-probe-perl |
0.03 |
|
|
perl_5 |
X | X | | X | Information about the currently running perl |
| perl-proc-fork |
0.806 |
|
|
perl_5 |
X | X | | X | simple, intuitive interface to the fork() system call |
| perl-readonly |
2.05 |
|
|
perl_5 |
X | X | | X | Facility for creating read-only scalars, arrays, hashes |
| perl-regexp-common |
2017060201 |
|
|
mit |
X | X | | X | Provide commonly requested regular expressions |
| perl-rest-client |
281 |
|
|
perl_5 |
| | | X | A simple client for interacting with RESTful http/https resources |
| perl-retroseq |
1.5 |
|
|
GPL |
| | | X | RetroSeq: discovery and genotyping of TEVs from reads in BAM format. |
| perl-return-multilevel |
0.08 |
|
|
perl_5 |
X | X | | X | return across multiple call levels |
| perl-role-tiny |
2.002004 |
|
|
perl_5 |
X | X | | X | Roles. Like a nouvelle cuisine portion size slice of Moose. |
| perl-role-tiny-with |
2.000005 |
|
|
perl_5 |
X | X | | X | Neat interface for consumers of Role::Tiny roles |
| perl-safe |
2.37 |
|
|
unknown |
X | X | | X | Compile and execute code in restricted compartments |
| perl-sanger-allelecount |
2.1.2 |
|
|
GPLv3 |
X | | | | None |
| perl-sanger-cgp-allelecount |
4.3.0 |
|
|
GPLv3 |
X | | | | Support code for NGS copy number algorithm |
| perl-sanger-cgp-battenberg |
1.4.1 |
|
|
GPLv3 |
X | | | | detect subclonality and copy number in matched NGS data |
| perl-sanger-cgp-vagrent |
3.7.0 |
|
|
GPL3 |
X | | | | A toolset for comparing genomic variants to reference genome annotation... |
| perl-sanger-cgp-vcf |
2.2.1 |
|
|
GPLv3 |
X | X | | | a set of common perl utilities for generating consistent Vcf headers |
| perl-scalar-list-utils |
1.62 |
|
|
perl_5 |
X | X | | | Common Scalar and List utility subroutines |
| perl-scalar-util-numeric |
0.40 |
|
|
perl_5 |
X | X | | | numeric tests for perl scalars |
| perl-scope-guard |
0.21 |
|
|
perl_5 |
X | X | | X | lexically-scoped resource management |
| perl-sereal |
4.019 |
|
|
perl_5 |
X | X | | X | Fast, compact, powerful binary (de-)serialization |
| perl-sereal-decoder |
4.025 |
|
|
perl_5 |
X | X | | | Fast, compact, powerful binary deserialization |
| perl-sereal-encoder |
4.025 |
|
|
perl_5 |
X | X | | | Fast, compact, powerful binary serialization |
| perl-set-intervaltree |
0.12 |
|
|
perl_5 |
X | X | | | An interval tree implementation in PERL. |
| perl-set-intspan |
1.19 |
|
|
unknown |
X | X | | X | Manages sets of integers, newsrc style |
| perl-set-object |
1.42 |
|
|
artistic_2 |
X | X | | | Unordered collections (sets) of Perl Objects |
| perl-set-scalar |
1.29 |
|
|
perl_5 |
X | X | | X | basic set operations |
| perl-slurp |
0.4 |
|
|
unknown |
X | X | | X | Slurp entire files into variables |
| perl-snap |
2.1.1 |
|
|
Custom |
X | X | | X | SNAP calculates pairwise synonymous and nonsynonymous distances... |
| perl-soap-lite |
1.27 |
|
|
perl_5 |
X | X | | X | Perl's Web Services Toolkit |
| perl-socket |
2.027 |
|
|
perl_5 |
X | X | | | networking constants and support functions |
| perl-socket6 |
0.29 |
|
|
unknown |
X | X | | | IPv6 related part of the C socket.h defines and structure manipulators |
| perl-sort-key |
1.33 |
|
|
Artistic-1.0-Perl |
X | X | | | the fastest way to sort anything in Perl |
| perl-sort-mergesort |
0.31 |
|
|
Artistic-2.0 |
| | | X | Merge sorted streams to create a new stream |
| perl-sort-naturally |
1.03 |
|
|
perl_5 |
X | X | | X | sort lexically, but sort numeral parts numerically |
| perl-sort-versions |
1.62 |
|
|
perl_5 |
X | X | | X | a perl 5 module for sorting of revision-like numbers |
| perl-specio |
0.50 |
|
|
artistic_2 |
X | X | | X | Type constraints and coercions for Perl |
| perl-specio-exporter |
0.36 |
|
|
perl_5 |
X | X | | | Base class for type libraries |
| perl-spiffy |
0.46 |
|
|
perl_5 |
X | X | | X | Spiffy Perl Interface Framework For You |
| perl-spreadsheet-parseexcel |
0.66 |
|
|
perl_5 |
X | X | | X | Read information from an Excel file. |
| perl-spreadsheet-writeexcel |
2.40 |
|
|
perl_5 |
X | X | | X | Write to a cross platform Excel binary file |
| perl-sql-abstract |
2.000001 |
|
|
GPL-1.0-or-later |
| | | X | Generate SQL from Perl data structures |
| perl-sql-abstract-pg |
1.0 |
|
|
Artistic-2.0 |
| | | X | PostgreSQL features for SQL::Abstract |
| perl-sql-statement |
1.414 |
|
|
perl_5 |
X | X | | X | SQL parsing and processing engine |
| perl-statistics-basic |
1.6611 |
|
|
open_source |
X | X | | X | None |
| perl-statistics-caseresampling |
0.15 |
|
|
unknown |
X | X | | | Efficient resampling and calculation of medians with confidence intervals |
| perl-statistics-descriptive |
3.0801 |
|
|
perl_5 |
X | X | | X | Module of basic descriptive statistical functions. |
| perl-statistics-distributions |
1.02 |
|
|
perl_5 |
X | X | | X | Perl module for calculating critical values and upper probabilities of... |
| perl-statistics-frequency |
0.04 |
|
|
perl_5 |
X | X | | X | simple counting of elements |
| perl-statistics-lite |
3.62 |
|
|
perl_5 |
X | X | | X | Small stats stuff. |
| perl-statistics-r |
0.34 |
|
|
Perl5 |
X | X | | X | Statistics::R - Perl interface with the R statistical program |
| perl-statistics-ttest |
1.1 |
|
|
perl_5 |
X | X | | X | Perl module to perform T-test on 2 independent samples... |
| perl-storable |
3.15 |
|
|
perl_5 |
X | X | | | persistence for Perl data structures |
| perl-string-approx |
3.27 |
|
|
unknown |
X | X | | | Perl extension for approximate matching (fuzzy matching) |
| perl-string-diff |
0.11 |
|
|
perl_5 |
| | | X | Simple diff to String |
| perl-string-escape |
2010.002 |
|
|
perl_5 |
X | X | | X | Backslash escapes, quoted phrase, word elision, etc. |
| perl-string-random |
0.30 |
|
|
perl_5 |
X | X | | X | Perl module to generate random strings based on a pattern |
| perl-string-rewriteprefix |
0.009 |
|
|
perl_5 |
X | X | | X | rewrite strings based on a set of known prefixes |
| perl-string-truncate |
1.100603 |
|
|
perl_5 |
X | X | | X | a module for when strings are too long to be displayed in... |
| perl-string-util |
1.26 |
|
|
perl_5 |
X | X | | X | String::Util -- String processing utilities |
| perl-sub-attribute |
0.07 |
|
|
perl_5 |
X | X | | | Reliable subroutine attribute handlers |
| perl-sub-exporter |
0.988 |
|
|
perl_5 |
X | X | | X | a sophisticated exporter for custom-built routines |
| perl-sub-exporter-formethods |
0.100055 |
|
|
perl_5 |
X | X | | X | helper routines for using Sub::Exporter to build methods |
| perl-sub-exporter-progressive |
0.001013 |
|
|
perl_5 |
X | X | | X | Only use Sub::Exporter if you need it |
| perl-sub-identify |
0.14 |
|
|
perl_5 |
X | X | | | Retrieve names of code references |
| perl-sub-info |
0.002 |
|
|
perl_5 |
X | X | | X | Tool for inspecting subroutines. |
| perl-sub-install |
0.928 |
|
|
perl_5 |
X | X | | X | install subroutines into packages easily |
| perl-sub-name |
0.21 |
|
|
perl_5 |
X | X | | | (Re)name a sub |
| perl-sub-quote |
2.006006 |
|
|
perl_5 |
X | X | | X | Efficient generation of subroutines via string eval |
| perl-sub-uplevel |
0.2800 |
|
|
perl_5 |
X | X | | | apparently run a function in a higher stack frame |
| perl-super |
1.20190531 |
|
|
perl_5 |
X | X | | X | control superclass method dispatch |
| perl-svg |
2.87 |
|
|
perl_5 |
X | X | | X | Perl extension for generating Scalable Vector Graphics (SVG) documents |
| perl-svg-graph |
0.02 |
|
|
unknown |
X | X | | X | Visualize your data in Scalable Vector Graphics (SVG) format. |
| perl-symbol |
1.07 |
|
|
perl_5 |
X | X | | X | manipulate Perl symbols and their names |
| perl-symbol-util |
0.0203 |
|
|
perl_5 |
X | X | | | Additional utils for Perl symbols manipulation |
| perl-sys-info |
0.7811 |
|
|
perl_5 |
X | X | | X | Fetch information from the host system |
| perl-sys-info-base |
0.7807 |
|
|
perl_5 |
X | X | | X | Base class for Sys::Info |
| perl-sys-info-driver-linux |
0.7905 |
|
|
perl_5 |
X | | | X | Linux driver for Sys::Info |
| perl-sys-info-driver-osx |
0.7960 |
|
|
perl_5 |
| X | | | OSX driver for Sys::Info |
| perl-sys-sigaction |
0.23 |
|
|
perl_5 |
X | X | | X | Perl extension for Consistent Signal Handling |
| perl-tap-harness-env |
3.30 |
|
|
perl_5 |
X | X | | X | Parsing harness related environmental variables where appropriate |
| perl-task-weaken |
1.06 |
|
|
perl_5 |
X | X | | X | Ensure that a platform has weaken support |
| perl-template-toolkit |
3.102 |
doc |
|
perl_5 |
X | X | | | Comprehensive template processing system. |
| perl-term-app-roles |
0.031 |
|
|
perl_5 |
X | X | | X | Collection of roles for terminal-based application |
| perl-term-detect-software |
0.223 |
|
|
perl_5 |
X | X | | X | Detect terminal (emulator) software and its capabilities |
| perl-term-encoding |
0.03 |
|
|
perl_5 |
X | X | | X | Detect encoding of the current terminal |
| perl-term-progressbar |
2.22 |
|
|
perl_5 |
X | X | | X | provide a progress meter on a standard terminal |
| perl-term-table |
0.024 |
|
|
perl_5 |
X | X | | X | Format a header and rows into a table |
| perl-termreadkey |
2.38 |
|
|
perl_5 |
X | X | | | A perl module for simple terminal control |
| perl-test |
1.26 |
|
|
unknown |
X | X | | X | provides a simple framework for writing test scripts |
| perl-test-base |
0.89 |
|
|
perl_5 |
X | X | | X | A Data Driven Testing Framework |
| perl-test-builder-tester |
1.23_002 |
|
|
unknown |
X | X | | X | test testsuites that have been built with Test::Builder |
| perl-test-class-moose |
0.99 |
|
|
perl_5 |
X | X | | X | Serious testing for serious Perl |
| perl-test-classapi |
1.07 |
|
|
perl_5 |
X | X | | X | Provides basic first-pass API testing for large class trees |
| perl-test-cleannamespaces |
0.24 |
|
|
perl_5 |
X | X | | X | Check for uncleaned imports |
| perl-test-cpan-meta |
0.25 |
|
|
artistic_2 |
X | X | | X | Validate your CPAN META.json files |
| perl-test-deep |
1.130 |
|
|
perl_5 |
X | X | | X | Extremely flexible deep comparison |
| perl-test-differences |
0.69 |
|
|
Perl |
X | X | | X | Test strings and data structures and show differences if not ok |
| perl-test-eol |
2.02 |
|
|
perl_5 |
X | X | | X | Check the correct line endings in your project |
| perl-test-exception |
0.43 |
|
|
perl_5 |
X | X | | X | Test exception-based code |
| perl-test-exec |
0.04 |
|
|
perl_5 |
X | X | | X | Test that some code calls exec without terminating testing |
| perl-test-fatal |
0.016 |
|
|
perl_5 |
X | X | | X | incredibly simple helpers for testing code with exceptions |
| perl-test-file |
1.994 |
|
|
perl_5 |
X | X | | X | test file attributes |
| perl-test-file-contents |
0.23 |
|
|
perl_5 |
X | X | | X | Test routines for examining the contents of files |
| perl-test-files |
0.15 |
|
|
unknown |
X | X | | X | A Test::Builder based module to ease testing with files and dirs |
| perl-test-fork |
0.02 |
|
|
perl_5 |
X | X | | X | test code which forks |
| perl-test-harness |
3.44 |
|
|
perl_5 |
X | X | | X | contributing to TAP::Harness |
| perl-test-inter |
1.10 |
|
|
perl_5 |
X | X | | X | framework for more readable interactive test scripts |
| perl-test-leaktrace |
0.17 |
|
|
perl_5 |
X | X | | | Traces memory leaks |
| perl-test-lectrotest |
0.5001 |
|
|
perl_5 |
X | X | | X | Easy, automatic, specification-based tests |
| perl-test-longstring |
0.17 |
|
|
perl_5 |
X | X | | X | tests strings for equality, with more helpful failures |
| perl-test-memory-cycle |
1.06 |
|
|
unknown |
X | X | | X | Verifies code hasn't left circular references |
| perl-test-mockmodule |
0.13 |
|
|
gpl_3 |
X | X | | X | Override subroutines in a module for unit testing |
| perl-test-more |
1.001002 |
|
|
perl_5 |
X | X | | X | yet another framework for writing test scripts |
| perl-test-most |
0.38 |
|
|
unknown |
X | X | | X | Most commonly needed test functions and features |
| perl-test-needs |
0.002009 |
|
|
perl_5 |
X | X | | X | Skip tests when modules not available |
| perl-test-notabs |
2.02 |
|
|
perl_5 |
X | X | | X | Check the presence of tabs in your project |
| perl-test-nowarnings |
1.06 |
|
|
Perl |
X | X | | X | Make sure you didn't emit any warnings while testing |
| perl-test-object |
0.08 |
|
|
perl_5 |
X | X | | X | Thoroughly testing objects via registered handlers |
| perl-test-output |
1.031 |
|
|
perl_5 |
X | X | | X | Utilities to test STDOUT and STDERR messages. |
| perl-test-pod |
1.52 |
|
|
perl_5 |
X | X | | X | check for POD errors in files |
| perl-test-pod-coverage |
1.10 |
|
|
artistic_2 |
X | X | | | Check for pod coverage in your distribution |
| perl-test-prereq |
2.002 |
|
|
artistic_2 |
X | X | | X | check if Makefile.PL has the right pre-requisites |
| perl-test-requires |
0.11 |
|
|
perl_5 |
X | X | | X | Checks to see if the module can be loaded |
| perl-test-requiresinternet |
0.05 |
|
|
perl_5 |
X | X | | X | Easily test network connectivity |
| perl-test-script |
1.29 |
|
|
perl_5 |
X | X | | X | Basic cross-platform tests for scripts |
| perl-test-simple |
1.302190 |
|
|
perl_5 |
X | X | | X | Basic utilities for writing tests. |
| perl-test-subcalls |
1.10 |
|
|
perl_5 |
X | X | | X | Track the number of times subs are called |
| perl-test-sys-info |
0.23 |
|
|
perl_5 |
X | X | | X | Centralized test suite for Sys::Info. |
| perl-test-toolbox |
0.4 |
|
|
perl_5 |
X | X | | X | Test::Toolbox - tools for testing |
| perl-test-trap |
0.3.3 |
|
|
perl_5 |
X | X | | X | Trap exit codes, exceptions, output, etc. |
| perl-test-unit-lite |
0.1202 |
|
|
perl_5 |
X | X | | X | Unit testing without external dependencies |
| perl-test-utf8 |
1.03 |
|
|
perl_5 |
X | X | | X | handy utf8 tests |
| perl-test-warn |
0.36 |
|
|
perl_5 |
X | X | | X | Perl extension to test methods for warnings |
| perl-test-warnings |
0.031 |
|
|
perl_5 |
X | X | | X | Test for warnings and the lack of them |
| perl-test-without-module |
0.20 |
|
|
perl_5 |
X | X | | X | Test fallback behaviour in absence of modules |
| perl-test-xml |
0.08 |
|
|
perl_5 |
X | X | | X | Compare XML in perl tests |
| perl-test-yaml |
1.07 |
|
|
perl_5 |
X | X | | X | Testing Module for YAML Implementations |
| perl-test2 |
1.302075 |
|
|
perl_5 |
X | X | | X | Framework for writing test tools that all work together. |
| perl-test2-plugin-nowarnings |
0.09 |
|
|
artistic_2 |
| | | X | Fail if tests warn |
| perl-test2-suite |
0.000163 |
|
|
perl_5 |
X | X | | X | Distribution with a rich set of tools built upon the Test2 framework. |
| perl-text-abbrev |
1.02 |
|
|
perl_5 |
X | X | | X | abbrev - create an abbreviation table from a list |
| perl-text-ansitable |
0.48 |
|
|
perl_5 |
X | X | | X | Create nice formatted tables using extended ASCII and ANSI colors |
| perl-text-asciitable |
0.22 |
|
|
perl_5 |
X | X | | X | Create a nice formatted table using ASCII characters. |
| perl-text-balanced |
2.06 |
|
|
perl_5 |
X | X | | X | Extract delimited text sequences from strings |
| perl-text-csv |
2.01 |
|
|
perl_5 |
X | X | | X | comma-separated values manipulator (using XS or PurePerl) |
| perl-text-csv_xs |
1.48 |
|
|
perl_5 |
X | X | | | Text::CSV_XS - comma-separated values manipulation routines |
| perl-text-diff |
1.45 |
|
|
perl_5 |
X | X | | X | Perform diffs on files and record sets |
| perl-text-format |
0.62 |
|
|
perl_5 |
X | X | | X | Format text |
| perl-text-glob |
0.11 |
|
|
perl_5 |
X | X | | X | match globbing patterns against text |
| perl-text-levenshtein |
0.13 |
|
|
perl_5 |
X | X | | X | calculate the Levenshtein edit distance between two strings |
| perl-text-levenshteinxs |
0.03 |
|
|
Perl |
X | X | | | An XS implementation of the Levenshtein edit distance |
| perl-text-nsp |
1.31 |
|
|
open_source |
X | X | | X | Extract collocations and Ngrams from text |
| perl-text-parsewords |
3.31 |
|
|
perl_5 |
X | X | | X | parse text into an array of tokens or array of arrays |
| perl-text-tabs |
2013.0523 |
|
|
perl_5 |
X | X | | X | expand and unexpand tabs like unix expand(1) and unexpand(1) |
| perl-text-tabs-wrap |
2021.0814 |
|
|
unknown |
X | X | | X | Expand tabs and do simple line wrapping |
| perl-text-template |
1.46 |
|
|
unknown |
X | X | | X | Expand template text with embedded Perl |
| perl-text-template-simple |
0.91 |
|
|
perl_5 |
X | X | | X | Simple text template engine |
| perl-text-wrap |
2021.0814 |
|
|
perl_5 |
X | X | | X | line wrapping to form simple paragraphs |
| perl-threaded |
5.32.1 |
|
|
Perl |
X | X | | X | The Perl language. |
| perl-tie-cache |
0.21 |
|
|
unknown |
X | X | | X | LRU Cache in Memory |
| perl-tie-cacher |
0.09 |
|
|
perl_5 |
X | X | | X | Cache a (sub)set of key/value pairs. Tie and OO interface. |
| perl-tie-hash |
1.05 |
|
|
perl_5 |
X | X | | X | None |
| perl-tie-hash-indexed |
0.08 |
|
|
perl_5 |
X | X | | | Ordered hashes for Perl |
| perl-tie-ixhash |
1.23 |
|
|
perl_5 |
X | X | | X | ordered associative arrays for Perl |
| perl-tie-log4perl |
0.1 |
|
|
perl_5 |
X | X | | X | Tie a filehandle to log via Log4perl |
| perl-tie-refhash |
1.39 |
|
|
perl_5 |
X | X | | X | use references as hash keys |
| perl-tie-refhash-weak |
0.09 |
|
|
unknown |
X | X | | X | A Tie::RefHash subclass with weakened references in the keys. |
| perl-tie-toobject |
0.03 |
|
|
perl_5 |
X | X | | X | Tie to an existing object. |
| perl-time-hires |
1.9764 |
|
|
perl_5 |
X | X | | | High resolution alarm, sleep, gettimeofday, interval timers |
| perl-time-local |
1.2300 |
|
|
perl_5 |
X | X | | X | efficiently compute time from local and GMT time |
| perl-time-piece |
1.27 |
|
|
perl_5 |
X | X | | X | Object Oriented time objects |
| perl-timedate |
2.33 |
|
|
perl_5 |
X | X | | X | Date formating subroutines |
| perl-tree-dag_node |
1.32 |
|
|
artistic_2 |
X | X | | X | An N-ary tree |
| perl-try-tiny |
0.31 |
|
|
mit |
X | X | | X | minimal try/catch with proper preservation of $@ |
| perl-try-tiny-retry |
0.004 |
|
|
Apache-2.0 |
X | X | | X | Just like Try::Tiny, but with retry instead of try. |
| perl-type-tiny |
1.016006 |
|
|
perl_5 |
X | X | | X | tiny, yet Moo(se)-compatible type constraint |
| perl-types-serialiser |
1.01 |
|
|
perl_5 |
X | X | | X | Simple data types for common serialisation formats |
| perl-types-standard |
1.002001 |
|
|
perl_5 |
X | X | | | bundled set of built-in types for Type::Tiny |
| perl-unicode-map |
0.112 |
|
|
unknown |
X | X | | | An utility to map texts from and to unicode |
| perl-unicode-normalize |
1.26 |
|
|
perl_5 |
X | X | | | Unicode Normalization Forms |
| perl-unicode-stringprep |
1.105 |
|
|
perl_5 |
X | X | | X | Preparation of Internationalized Strings (RFC 3454) |
| perl-unicode-utf8 |
0.62 |
|
|
perl_5 |
X | X | | | Encoding and decoding of UTF-8 encoding form |
| perl-uri |
5.12 |
|
|
perl_5 |
X | X | | X | Uniform Resource Identifiers (absolute and relative) |
| perl-uri-db |
0.23 |
|
|
GPL-1.0-or-later |
| | | X | Database URIs |
| perl-uri-nested |
0.10 |
|
|
perl_5 |
| | | X | Nested URIs |
| perl-url-encode |
0.03 |
|
|
perl_5 |
X | X | | | Encoding and decoding of application/x-www-form-urlencoded encoding. |
| perl-util-properties |
0.18 |
|
|
open_source |
| | | X | Java.util.properties like class |
| perl-variable-magic |
0.63 |
|
|
perl_5 |
X | X | | | Associate user-defined magic to variables from Perl. |
| perl-vars |
1.03 |
|
|
perl_5 |
X | X | | X | Perl pragma to predeclare global variable names |
| perl-vcftools-vcf |
0.1.16 |
|
|
LGPLv3 |
X | X | | X | cpanm ready distribution of VCFtools Perl libraries |
| perl-velvetoptimiser |
2.2.6 |
|
|
GPLv2 |
X | X | | X | Automatically optimise three of Velvet's assembly parameters. |
| perl-version |
0.9924 |
|
|
perl_5 |
X | X | | | Structured version objects |
| perl-version-next |
1.000 |
|
|
apache_2_0 |
X | X | | X | increment module version numbers simply and correctly |
| perl-want |
0.29 |
|
|
perl_5 |
X | X | | | This module generalises the mechanism of the wantarray function,... |
| perl-warnings-register |
1.03 |
|
|
perl_5 |
X | X | | X | warnings import function |
| perl-www-mechanize |
1.91 |
|
|
perl_5 |
X | X | | X | Handy web browsing in a Perl object |
| perl-www-robotrules |
6.02 |
|
|
perl_5 |
X | X | | X | database of robots.txt-derived permissions |
| perl-xml-dom |
1.46 |
|
|
unknown |
X | X | | X | A perl module for building DOM Level 1 compliant document structures |
| perl-xml-dom-xpath |
0.14 |
|
|
unknown |
X | X | | X | Perl extension to add XPath support to XML::DOM, using XML::XPath engine |
| perl-xml-entities |
1.0002 |
|
|
perl_5 |
X | X | | X | Mapping of XML entities to Unicode |
| perl-xml-filter-buffertext |
1.01 |
|
|
unknown |
X | X | | X | Filter to put all characters() in one event |
| perl-xml-libxml |
2.0210 |
|
|
Perl |
X | X | | | Interface to Gnome libxml2 xml parsing and DOM library |
| perl-xml-libxslt |
2.003000 |
|
|
perl_5 |
X | X | | | Interface to GNOME libxslt library |
| perl-xml-namespacesupport |
1.12 |
|
|
perl_5 |
X | X | | X | a simple generic namespace support class |
| perl-xml-parser |
2.44 |
|
|
perl_5 |
X | X | | | A perl module for parsing XML documents |
| perl-xml-parser-lite |
0.722 |
|
|
perl_5 |
X | X | | X | Lightweight pure-perl XML Parser (based on regexps) |
| perl-xml-regexp |
0.04 |
|
|
unknown |
X | X | | X | Regular expressions for XML tokens |
| perl-xml-sax |
1.02 |
|
|
unknown |
X | X | | X | Simple API for XML |
| perl-xml-sax-base |
1.09 |
|
|
perl_5 |
X | X | | X | Base class for SAX Drivers and Filters |
| perl-xml-sax-expat |
0.51 |
|
|
perl_5 |
X | X | | X | SAX Driver for Expat |
| perl-xml-sax-writer |
0.57 |
|
|
perl_5 |
X | X | | X | SAX2 XML Writer |
| perl-xml-semanticdiff |
1.0007 |
|
|
perl_5 |
X | X | | X | Perl extension for comparing XML documents. |
| perl-xml-simple |
2.25 |
|
|
perl_5 |
X | X | | X | An API for simple XML files |
| perl-xml-twig |
3.52 |
|
|
perl_5 |
X | X | | X | XML, The Perl Way |
| perl-xml-writer |
0.900 |
|
|
unrestricted |
X | X | | X | Easily generate well-formed, namespace-aware XML. |
| perl-xml-xpath |
1.47 |
|
|
Artistic-2.0 |
X | X | | X | Parse and evaluate XPath statements. |
| perl-xml-xpathengine |
0.14 |
|
|
unknown |
X | X | | X | a re-usable XPath engine for DOM-like trees |
| perl-xsloader |
0.24 |
|
|
perl_5 |
X | X | | | Dynamically load C libraries into Perl code |
| perl-xxx |
0.35 |
|
|
perl |
| | | X | See Your Data in the Nude |
| perl-yaml |
1.30 |
|
|
perl_5 |
X | X | | X | YAML Ain't Markup Language™ |
| perl-yaml-libyaml |
0.66 |
|
|
perl_5 |
X | X | | | Perl YAML Serialization using XS and libyaml |
| perl-yaml-pp |
0.021 |
|
|
perl |
| | | X | YAML 1.2 Processor |
| perl-yaml-tiny |
1.73 |
|
|
perl |
X | X | | X | Read/Write YAML files with as little code as possible |
| pfam_scan |
1.6 |
|
|
GPL |
X | X | | X | pfam_scan.pl is a Perl script calling HMMER v3 to search a FASTA file... |
| pfp |
0.3.9 |
|
|
MIT |
X | X | | | Prefix Free Parsing. |
| pftools |
3.2.12 |
|
dev |
GPLv2 |
X | X | | | A generalized profile syntax for biomolecular sequence motifs and its... |
| pgcgap |
1.0.35 |
doc |
dev |
GPLv3 |
| | | X | A prokaryotic genomics and comparative genomics analysis pipeline |
| pgdspider |
2.1.1.5 |
|
|
BSD-3-clause |
| | | X | An automated data conversion tool for connecting population genetics... |
| pgenlib |
0.91.0 |
doc |
dev |
LGPL-3.0-or-later |
X | X | | | Python wrapper for pgenlib's basic reader and writer. |
| pggb |
0.7.2 |
|
|
MIT |
X | | | X | PanGenome Graph Building pipeline renders |
| pgma-simple |
0.1 |
|
|
GNUv3 |
X | X | | | Pgma is a simple program for building WPGMA trees. |
| pgr-tk |
0.5.1 |
|
|
CC |
X | | | | A PanGenomic Research Took Kit. This repository is a project to provide... |
| pgrc |
2.0.2 |
|
dev |
GPL-3.0-or-later |
X | X | | | A tool for compressing the DNA stream of FASTQ datasets. |
| pgsa |
1.2 |
|
|
Creative |
X | X | | | Pseudogenome Suffix Array is a compact index for collections of reads... |
| pgscatalog-utils |
1.4.4 |
doc |
|
Apache-2.0 |
| | | X | Utilities for working with PGS Catalog API and scoring files |
| pgscatalog.calc |
0.3.0 |
|
|
Apache-2.0 |
| | | X | Libraries and applications for working with calculated polygenic scores |
| pgscatalog.core |
0.3.3 |
|
|
Apache-2.0 |
| | | X | Core tools for working with polygenic scores (PGS) and the PGS Catalog |
| pgscatalog.match |
0.3.3 |
doc |
|
MIT |
| | | X | Tools for matching variants in PGS scoring files and target variant... |
| pgx-pipe-helper |
0.0.4 |
|
|
MIT |
| | | X | A helper module for wrapping functionality which is common to all... |
| pgx-variant-tools |
0.0.5 |
|
|
MIT |
| | | X | This library contains various methods and utilities for the calling and... |
| phables |
1.4.1 |
doc |
dev |
MIT |
X | X | | X | Phables: from fragmented assemblies to high-quality bacteriophage genomes |
| phabox |
2.1.10 |
doc |
dev |
AFL-3.0 |
| | | X | Virus identification and analysis tool set |
| phamb |
1.0.1 |
|
|
GNU |
| | | X | phamb discovery approach used to isolate metagenome derived viromes and... |
| phame |
1.0.3 |
|
|
GPLV2 |
X | X | | X | A tool to derive SNP matrices and phylogenetic tree from raw reads,... |
| phanotate |
1.6.7 |
doc |
dev |
GPL-3.0-only |
X | X | | | Phanotate gene caller for phages |
| phantasm |
1.1.3 |
|
|
MIT |
| | | X | PHANTASM: PHylogenomic ANalyses for the TAxonomy and Systematics of Microbes |
| phantasm-xenogi |
3.1.2 |
|
|
GPL-3.0 |
| | | X | xenoGI for PHANTASM |
| phantompeakqualtools |
1.2.2 |
|
|
BSD-3-Clause |
X | X | | X | This package computes informative enrichment and quality measures for... |
| pharokka |
1.7.5 |
doc |
dev |
MIT |
| | | X | Fast Phage Annotation Program |
| phaser |
0.1.1ad5f89 |
|
|
file |
X | X | | | phASEr performs haplotype phasing and provides measures of haplotypic... |
| phasius |
0.5.0 |
|
|
MIT |
X | | | | A rust tool to create phase-block maps from phased cram/bam files |
| phast |
1.5 |
|
|
BSD |
X | X | | | PHAST is a freely available software package for comparative and... |
| phastaf |
0.1.0 |
|
dev |
GPLv3 |
| | | X | Identify phage regions in bacterial genomes for masking purposes |
| phate |
1.0.11 |
doc |
dev |
GPL-2.0 |
| | | X | PHATE (Potential of Heat-diffusion for Affinity-based Transition... |
| phava |
0.2.3 |
|
dev |
MIT |
| | | X | Detection of invertons from long-read sequencing datasets |
| phcue-ck |
0.2.0 |
|
|
MIT |
X | X | | | phcue-ck (pronounced "F-Q-Seek") is a simple tool to get FTP... |
| pheniqs |
2.1.0 |
doc |
dev |
GPL3 |
X | X | | | Pheniqs is a flexible generic barcode classifier for high-throughput... |
| phenix |
1.4.1a |
|
|
GPL3 |
X | X | | | Public Health England SNP calling pipeline |
| phenograph |
1.5.7 |
doc |
dev |
MIT |
| | | X | Graph-based clustering for high-dimensional single-cell data. |
| phertilizer |
0.1.0 |
|
|
BSD-3 |
| | | X | Phertilizer is a method to grow a clonal tree from ultra-low coverage... |
| phiercc |
1.24 |
|
|
GNU |
| | | X | Hierarchical Clustering of cgMLST profiles |
| phigaro |
2.4.0 |
doc |
|
MIT |
| | | X | Phigaro is a scalable command-line tool for predicting phages and prophages. |
| phip-stat |
0.5.1 |
|
|
Apache-2.0 |
| | | X | PhIP-seq analysis tools |
| phipack |
1.1 |
|
|
GPL3 |
X | X | | | Simple, rapid, and statistically efficient test for recombination. |
| phirbo |
1.0 |
|
|
GPL3 |
| | | X | Predict prokaryotic hosts for phage (meta) genomic sequences |
| phispy |
4.2.21 |
doc |
dev |
MIT |
X | X | | | Prophage finder using multiple metrics |
| phist |
1.0.0 |
|
|
GPL-3 |
X | X | | | Phage-Host Interaction Search Tool. |
| phizz |
0.2.3 |
|
|
MIT |
X | X | | X | Tool to query hpo database and some other sources |
| phold |
0.2.0 |
doc |
|
MIT |
| | | X | Phage annotation using protein structures |
| phonenumbers |
7.2.4 |
|
|
Apache |
X | X | | | None |
| phyclone |
0.7.0 |
|
|
GPL-3.0-or-later |
| | | X | Accurate Bayesian reconstruction of cancer phylogenies from bulk sequencing. |
| phykit |
2.0.1 |
doc |
dev |
MIT |
| | | X | PhyKIT is a UNIX shell toolkit for processing and analyzing phylogenomic data. |
| phylics |
1.0.7 |
|
|
AGPL3 |
X | X | | X | Single-cell CNV data analysis toolkit |
| phylip |
3.697 |
|
|
BSD |
X | X | | | Package of programs for inferring phylogenies |
| phyloacc |
2.4.2 |
doc |
dev |
GPL-3.0-or-later |
X | X | | | Bayesian estimation of substitution rate shifts in non-coding regions |
| phyloaln |
1.0.0 |
|
|
MIT |
| | | X | PhyloAln: a reference-based multiple sequence alignment tool for phylogeny |
| phylobayes-mpi |
1.9 |
|
|
GPL2 |
X | X | | | A Bayesian software for phylogentic reconstrunction using mixture models |
| phylocsf |
1.0.1 |
|
|
AGPL-3.0 |
X | X | | | Phylogenetic analysis of multi-species genome sequence alignments to... |
| phylocsfpp |
1.2.0_9643238d |
|
|
AGPLv3 |
X | X | | | A fast and user-friendly implementation of PhyloCSF with annotation tools. |
| phylodeep |
0.9 |
doc |
dev |
GPL-3.0-or-later |
| | | X | Deep-learning parameter estimation and model selection from phylogenetic trees. |
| phylodeep_data_bd |
0.6 |
|
|
GPL-3.0-or-later |
| | | X | Package containing data for the phylodeep package. |
| phylodeep_data_bdei |
0.4 |
|
|
GPL-3.0-or-later |
| | | X | Package containing data for the phylodeep package. |
| phylodeep_data_bdss |
0.4 |
|
|
GPL-3.0-or-later |
| | | X | Package containing data for the phylodeep package. |
| phylodm |
3.2.0 |
|
dev |
GPL-3.0-only |
X | X | | X | Efficient calculation of phylogenetic distance matrices. |
| phylofisher |
1.2.14 |
doc |
dev |
MIT |
| | | X | A package for the creation, analysis, and visualization of eukaryotic... |
| phyloflash |
3.4.2 |
|
|
GPLv3 |
X | X | | X | phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and... |
| phylogenetics |
0.5.0 |
|
|
BSD-3-Clause |
| | | X | Python API for managing a phylogenetics projects. |
| phylogenize |
0.91 |
|
|
MIT |
| | | X | Phylogenize is a tool that allows users to link microbial genes to... |
| phylommand |
1.1.0 |
|
|
GPLv3 |
X | X | | | Command-line phylogenetics tools. |
| phylopandas |
0.8.0 |
|
|
MIT |
X | X | | X | Pandas for phylogenetics |
| phylophlan |
3.1.1 |
|
|
MIT |
| | | X | Precise phylogenetic analysis of microbial isolates and genomes from metagenomes |
| phylorank |
0.1.12 |
|
|
GNU |
| | | X | PhyloRank provides functionality for calculating the relative... |
| phylornn |
1.1 |
|
|
LPGL-2.1-only |
| | | X | PhyloRNN |
| phylotoast |
1.4.0rc2 |
|
|
MIT |
X | X | | | Tools for phylogenetic data analysis including visualization and... |
| phylovega |
0.3 |
|
|
MIT |
| | | X | Interactive Phylogenetic trees in Vega. |
| phylowgs |
20181105 |
|
|
GPLv3 |
X | X | | | Application for inferring subclonal composition and evolution from... |
| phyluce |
1.6.8 |
|
|
BSD |
X | X | | X | Software for UCE (and general) phylogenomics. |
| phyml |
3.3.20220408 |
doc |
dev |
GPL-3.0-only |
X | X | | | Phylogenetic estimation using (Maximum) Likelihood |
| phynder |
1.0 |
|
dev |
MIT |
X | X | | | Efficient likelihood calculations to place samples into a phylogenetic tree. |
| phynteny |
0.1.13 |
|
dev |
MIT |
| | | X | Phynteny: Synteny-based prediction of bacteriophage genes |
| phyphy |
0.4.3 |
|
|
BSD-3-Clause |
| | | X | Facilitating the execution and parsing of standard HyPhy (>=2.3.7) analyses |
| physher |
2.0.1 |
|
|
GPL-2.0-or-later |
X | X | | | A multi-algorithmic framework for phylogenetic inference |
| physiofit |
3.4.0 |
doc |
dev |
GPL-3.0-only |
| | | X | Calculate extracellular fluxes from metabolite concentrations and biomass data |
| physiofit4galaxy |
2.2.1 |
|
|
GPL-3.0 |
| | | X | Calculate extracellular fluxes from metabolite concentrations and biomass data |
| physiofit_data_manager |
1.0.1 |
|
|
GPL-3.0 |
| | | X | Handle data input management for physiofit4galaxy |
| physlr |
1.0.4 |
doc |
dev |
GPL3 |
X | X | | | Physlr; Next-generation Physical Maps |
| phytest |
1.4.1 |
doc |
dev |
MIT |
| | | X | Quality control for phylogenetic pipelines using pytest |
| phytop |
0.3 |
|
|
GPL-3.0-or-later |
| | | X | Phytop: A tool for visualizing and recognizing signals of incomplete... |
| phyx |
1.1 |
|
|
GPL3 |
X | X | | | Phylogenetics tools for linux (and other mostly posix compliant) computers |
| pia |
1.5.5 |
|
|
BSD-3-Clause |
| | | X | PIA is a toolbox for MS based protein inference and identification analysis. |
| piawka |
0.8.11 |
doc |
dev |
MIT |
| | | X | The powerful AWK script to calculate population statistics in VCF files... |
| picard |
3.3.0 |
|
dev |
MIT |
X | X | | X | Java tools for working with NGS data in the BAM format |
| picard-slim |
3.3.0 |
|
dev |
MIT |
| | | X | Java tools for working with NGS data in the BAM format. |
| picopore |
1.2.0 |
|
|
GNU |
X | X | | X | A tool for reducing the size of Oxford Nanopore Technologies'... |
| picrust |
1.1.4 |
|
|
GPL-3.0 |
X | X | | X | PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of... |
| picrust2 |
2.6.1 |
|
dev |
GNU |
| | | X | PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of... |
| pictrust |
1.0.1 |
|
|
GPL |
X | X | | | PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of... |
| piemmer |
1.0.5 |
doc |
dev |
BSD-3-Clause |
| | | X | A algorithm to simplify the input for principal component analysis |
| pifcosm |
0.1.1 |
|
|
GPL-3.0-only |
| | | X | PisCoSm is a pipeline to construct supermatrix trees from GenBank data |
| pigpen |
0.0.6 |
|
|
MIT |
X | X | | | A package to quantify RNA localization using OINC-seq data |
| pilea |
0.1.0 |
|
|
MIT |
| | | X | Pilea: profiling bacterial growth dynamics from metagenomes with sketching |
| pileometh |
0.1.13 |
|
|
MIT |
X | X | | | A (mostly) universal methylation extractor for BS-seq experiments. |
| piler |
0.1 |
|
|
public |
X | X | | | PILER is public domain software for analyzing repetitive DNA found in... |
| piler-cr |
1.06 |
|
|
Public |
X | X | | | Identification and analysis of CRISPR repeats. |
| pileuppy |
1.2.0 |
|
|
MIT |
| | | X | Colorful and fast tool designed to draw alignment pileup. |
| pilon |
1.24 |
|
|
GPLv2 |
X | X | | X | Pilon is an automated genome assembly improvement and variant detection tool. |
| pin_hic |
3.0.0 |
|
|
MIT |
X | X | | | A Hi-C scaffolding method |
| pindel |
0.2.5b9 |
|
|
GPLv3 |
X | | | | Pindel can detect breakpoints of large deletions, medium sized... |
| pio_mpich |
2.6.2 |
|
|
Apache-2.0 |
X | | | | ParallelIO - High-level parallel I/O library |
| pipelign |
0.2 |
|
|
MIT |
X | X | | X | A pipeline for automated multiple sequence alignment, particularly of... |
| piper |
0.14.4 |
doc |
dev |
BSD-2-Clause |
| | | X | A lightweight python toolkit for gluing together restartable, robust... |
| pipits |
3.1 |
|
|
GNU |
X | X | | X | PIPITS: An automated pipeline for analyses of fungal internal... |
| pipmir |
1.1 |
|
|
PIPmiR |
X | | | X | We developed the PIPmiR algorithm to identify novel plant miRNA genes... |
| piranha |
1.2.1 |
|
|
GNU |
X | | | | Piranha is a peak-caller for CLIP- and RIP-Seq data. |
| piranha-polio |
1.4.2 |
|
|
GPL-3.0-only |
| | | X | Poliovirus Investigation Resource Automating Nanopore Haplotype Analysis |
| pirate |
1.0.5 |
|
|
GPL3 |
| | | X | Pangenome analysis and threshold evaluation toolbox |
| piret |
0.3.4 |
|
|
GPLV2 |
X | X | | X | A tool for conducting RNA seq analysis. |
| pirs |
2.0.2 |
|
|
GPL-2.0 |
X | | | | pIRS is a program for simulating Illumina PE reads. |
| piscem |
0.12.2 |
|
|
BSD |
X | X | | | piscem is a next-generation compacted colored de Bruijn Graph-based... |
| piscem-infer |
0.6.0 |
|
|
BSD-3-Clause |
X | X | | | piscem-infer is a flexible tool to perform target quantification from... |
| pisces |
5.2.10.49 |
|
|
GPLv3 |
X | X | | X | Somatic and germline variant caller for amplicon data. Recommended... |
| pispino |
1.1 |
|
|
GNU |
X | X | | X | PISPINO (PIpits SPIN-Off tools): Bioinformatics toolkits for processing NGS data |
| pixelator |
0.19.0 |
|
dev |
MIT |
| | | X | A command-line tool and library to process and analyze sequencing data... |
| pizzly |
0.37.3 |
|
|
BSD-2 |
X | X | | | Fast fusion detection using kallisto |
| pkiss |
2.3.0 |
|
|
GPL-3.0-or-later |
X | X | | | RNA secondary structure prediction including K-type and kissing... |
| planemo |
0.75.27 |
doc |
dev |
MIT |
X | X | | X | Command-line utilities to assist in building tools for the Galaxy... |
| plannotate |
1.2.3 |
|
|
GPL-3.0-or-later |
| | | X | Webserver and command line tool for annotating engineered plasmids |
| plant_tribes_assembly_post_processor |
1.0.4 |
|
|
GNU |
X | | | | Transcriptome assembly post processing pipeline |
| plant_tribes_gene_family_aligner |
1.0.4 |
|
|
GNU |
X | X | | X | Gene family aligner pipeline |
| plant_tribes_gene_family_classifier |
1.0.4 |
|
|
GNU |
X | X | | X | Gene family classifier pipeline |
| plant_tribes_gene_family_integrator |
1.0.4 |
|
|
GNU |
X | X | | X | Gene family integrator pipeline |
| plant_tribes_gene_family_phylogeny_builder |
1.0.4 |
|
|
GNU |
X | X | | X | Gene family phylogeny builder pipeline |
| plant_tribes_kaks_analysis |
1.0.4 |
|
|
GNU |
X | | | X | KaKs Analysis pipeline |
| plantcv |
3.8.0 |
doc |
dev |
MIT |
| | | X | An image processing package for plant phenotyping. |
| plasann |
1.0.3 |
|
|
MIT |
| | | X | A tool for plasmid annotation and visualization |
| plasclass |
0.1.1 |
|
|
MIT |
| | | X | Classification of plasmid sequences |
| plascope |
1.3.1 |
|
|
GPL |
X | X | | X | PlaScope is a targeted approach to assess the plasmidome of bacteria. |
| plasflow |
1.1.0 |
|
|
GNU |
X | | | | PlasFlow - predicting plasmid sequences in metagenomic data |
| plasmidfinder |
2.1.6 |
|
|
Apache-2.0 |
| | | X | PlasmidFinder allows identification of plasmids in total or partial... |
| plasmidhawk |
1.0.3 |
|
|
MIT |
| | | X | Plasmidhawk is a program for detecting lab-of-origin of input plasmids... |
| plasmidid |
1.6.5 |
|
|
GPLv3 |
| | | X | Pipeline for plasmid identification and reconstruction |
| plasmidtron |
0.4.1 |
|
|
GNU |
X | X | | X | PlasmidTron: assembling the cause of phenotypes from NGS data |
| plasnet |
0.6.0 |
|
|
MIT |
| | | X | Clustering, visualising and exploring plasmid networks |
| plass |
5.cf8933 |
|
|
GPLv3 |
X | X | | | Plass (Protein-Level ASSembler) and PenguiN (Protein-guided Nucleotide... |
| plassembler |
1.6.2 |
doc |
dev |
MIT |
| | | X | Quickly and accurately assemble plasmids in hybrid sequenced bacterial isolates |
| plastedma |
0.2.1 |
doc |
dev |
MIT |
| | | X | Plastic Enzymes Degrading in Metagenomic databases Analysis |
| plastid |
0.6.1 |
|
|
BSD |
X | X | | | plastid is a Python library for genomic analysis -- in particular,... |
| platon |
1.7 |
|
dev |
GPLv3 |
| | | X | Plasmid contig classification and characterization for short read draft... |
| platypus-conquistador |
0.9.0 |
|
|
BSD-3-Clause |
X | | | X | Platypus Conquistador: Confirming specific taxonomic groups within your... |
| platypus-variant |
0.8.1.2 |
|
|
GPLv3 |
X | X | | | A Haplotype-Based Variant Caller For Next Generation Sequence Data |
| plek |
1.2 |
|
dev |
GPL-3.0-or-later |
X | X | | | Predictor of long non-coding RNAs and mRNAs based on k-mer scheme. |
| pling |
2.0.0 |
|
|
LICENSE |
| | | X | Pling computes the rearrangement distance between plasmids and clusters... |
| plink |
1.90b7.7 |
|
|
GPL |
X | X | | | Whole genome association analysis toolset, designed to perform a range... |
| plink2 |
2.00a5.12 |
|
|
GPL-3 |
X | X | | | Whole genome association analysis toolset |
| plinkio |
0.9.8 |
|
|
BSD-3-Clause |
X | X | | | A library for parsing plink genotype files |
| plmc |
20221105 |
|
|
MIT |
X | X | | | Inference of couplings in proteins and RNAs from sequence variation. |
| plncpro |
1.2.2 |
doc |
|
GNU |
X | X | | | PlncPRO is a program to predict long non-coding (lncRNAs) transcripts... |
| plotcritic |
1.0.1 |
|
|
MIT |
| | | X | Python deployment tool for bespoke image curation projects, oriented... |
| plothic |
0.5.0 |
doc |
dev |
GPL-3.0-only |
| | | X | Plot Whole genome Hi-C contact matrix heatmap. |
| plotsr |
1.1.1 |
|
|
MIT |
| | | X | Visualiser for structural annotations between multiple genomes |
| pm4ngs |
0.0.21 |
|
dev |
Public |
| | | X | PM4NGS generates a standard organizational structure for Next... |
| pmdtools |
0.60 |
|
|
GPL-3.0 |
| | | X | Compute postmortem damage patterns and decontaminate ancient genomes |
| pmga |
3.0.2 |
|
|
AGPL-2.0 |
| | | X | Command-line version of PMGA (PubMLST Genome Annotator) for all... |
| pmlst |
2.0.3 |
|
|
APACHE-2.0 |
| | | X | Plasmid Multi-Locus Sequence Typing |
| pmmrcalculator |
1.1.0 |
|
|
GPL-3.0 |
| | | X | A small python tool to calculate pairwise mismatch rate between all... |
| pmultiqc |
0.0.25 |
doc |
dev |
MIT |
| | | X | Python package for quality control of proteomics datasets, based on... |
| pmx_biobb |
4.1.3 |
|
|
GNU |
X | X | | | Toolkit for free-energy calculation setup/analysis and biomolecular... |
| pnetcdf_mpich |
1.14.0 |
|
|
PnetCDF |
X | | | | PnetCDF - Parallel netCDF |
| pneumo-typer |
1.0.3 |
doc |
|
GNU |
| | | X | Pneumo-Typer: An integrated tool for simultaneous identification of... |
| pneumocat |
1.2.1 |
|
|
GPL-3.0 |
X | X | | X | PneumoCaT (Pneumococcal Capsular Typing) uses a two-step step approach... |
| poa |
2.0 |
|
dev |
GPL-2.0-or-later |
X | X | | | POA is Partial Order Alignment, a fast program for multiple sequence... |
| pod5 |
0.3.15 |
doc |
dev |
MPL-2.0 |
| | | X | Oxford Nanopore Technologies Pod5 File Format Python API and Tools. |
| polap |
0.4.1.1 |
doc |
dev |
GPL-3.0-or-later |
| | | X | POLAP: plant organelle long-read assembly pipeline |
| poly-qtlseq |
1.0.2 |
|
|
MIT |
| | | X | PolyploidQtlSeq is a program that extends QTL-seq for polyploid F1 populations. |
| polymutt |
0.18 |
|
|
custom |
X | | | | Li B, Chen W, Zhan X, Busonero F, Sanna S, et al. (2012) A... |
| polypolish |
0.6.0 |
doc |
dev |
GPL-3.0-or-later |
X | X | | | Polishing genome assemblies with short reads. |
| polystest |
1.3.4 |
|
|
GPL |
| | | X | Interactive tool for statistical testing, data browsing and interactive... |
| pomegranate |
0.3.7 |
|
|
LICENSE.txt |
X | X | | | Pomegranate is a graphical models library for Python, implemented in... |
| pomoxis |
0.3.16 |
doc |
dev |
MPL-2.0 |
| | | X | Assembly, consensensus, and analysis tools by ONT research |
| poolsnp |
1.0.1 |
|
|
Apache-2.0 |
| | | X | PoolSNP is a heuristic SNP caller, which uses an MPILEUP file and a... |
| popdel |
1.5.0 |
|
|
GPL-3.0 |
X | X | | | Fast structural deletion calling on population-scale short read... |
| popera |
1.0.3 |
|
dev |
MIT |
| | | X | A software for DNase I hypersensitive sites identification. |
| popgen-entropy |
2.0 |
|
|
GPLv3 |
X | X | | | This program is for inferring population structure from autopolyploid... |
| popins2 |
0.13.0 |
doc |
|
GPL-2.0-only |
X | | | | Population-scale detection of non-reference sequence variants using... |
| poplddecay |
3.43 |
doc |
dev |
MIT |
X | X | | | PopLDdecay: a fast and effective tool for linkage disequilibrium decay... |
| popoolation2 |
1.201 |
|
|
BSD-3 |
| | | X | PoPoolation2 allows to compare allele frequencies for SNPs between two... |
| poppunk |
2.7.5 |
doc |
dev |
Apache-2.0 |
X | X | | X | PopPUNK (POPulation Partitioning Using Nucleotide Kmers) |
| popscle |
0.1 |
|
|
MIT |
X | X | | | A suite of population scale analysis tools for single-cell genomics... |
| popt |
1.16 |
|
|
GPL |
X | X | | | Popt is a C library for parsing command line parameters. |
| pore-c |
0.4.0 |
|
dev |
Mozilla |
| | | X | Toolkit for processing Pore-C concatemers |
| porechop |
0.2.4 |
doc |
dev |
GPL-3.0-only |
X | X | | | Adapter removal and demultiplexing of Oxford Nanopore reads |
| porechop_abi |
0.5.0 |
|
|
GPL3 |
X | X | | | Adapter inferrence and removal of Oxford Nanopore reads |
| poretools |
0.6.1a1 |
|
|
MIT |
X | X | | X | poretools: a toolkit for working with nanopore sequencing data from... |
| porfast |
0.8.0 |
|
|
MIT |
X | X | | | Extract ORFs from paired end Illumina reads (FASTQ). |
| portcullis |
1.2.4 |
|
|
GPL3 |
X | | | | Splice junction analysis and filtering from BAM files |
| poseidon-trident |
1.6.2.1 |
|
|
MIT |
X | X | | | A tool (trident) to work with modular genotype databases formatted... |
| poseidon-xerxes |
1.0.1.1 |
|
|
MIT |
X | X | | | A tool (xerxes) to analyse genotype databases formatted using Poseidon. |
| postmaster |
0.1.0 |
|
|
BSD |
X | | | | Postmaster is a tool for annotating transcriptome alignments with... |
| potrace |
1.11 |
|
|
GPL |
X | X | | | A tool for tracing a bitmap, which means, transforming a bitmap into a... |
| pourrna |
1.2.0 |
|
|
GPLv2 |
X | X | | | Compute local minima and respective transition rates of an RNA energy landscape. |
| pout2mzid |
0.3.03 |
|
|
|
X | | | | Adds percolator statistics to mzIdentML files that were used as input... |
| pp |
1.6.5 |
|
|
BSD |
X | X | | X | Parallel and distributed programming for Python |
| pp-sketchlib |
1.1.0 |
|
|
Apache-2.0 |
X | X | | | Library of sketching functions used by PopPUNK |
| ppanggolin |
2.2.1 |
doc |
|
CeCiLL |
X | X | | | PPanGGOLiN: Depicting microbial species diversity via a Partitioned... |
| ppanini |
0.7.4 |
|
|
MIT |
X | X | | X | PPANINI: Prioritization and Prediction of functional Annotations for... |
| pplacer |
1.1.alpha19 |
|
dev |
GPL-3.0 |
X | X | | | Pplacer places query sequences on a fixed reference phylogenetic tree... |
| pprodigal |
1.0.1 |
|
dev |
MIT |
| | | X | PProdigal - Parallelized gene prediction based on Prodigal. |
| ppx |
1.4.4 |
doc |
dev |
MIT |
| | | X | A Python interface to proteomics data repositories |
| prank |
170427 |
doc |
dev |
GPL-3.0-or-later |
X | X | | | PRANK is a probabilistic multiple alignment program for DNA, codon and... |
| predex |
0.9.3 |
|
|
MIT |
| | | X | Prepare expression data for dgeAnalysis - LUMC. |
| predicthaplo |
2.1.4 |
|
|
GPLv3 |
X | X | | | This software aims at reconstructing haplotypes from next-generation... |
| predictosaurus |
0.2.10 |
|
dev |
MIT |
X | X | | | Predictosaurus is a command-line tool designed for uncertainty-aware... |
| preface |
0.1.2 |
|
|
GPLv3 |
| | | X | PREFACE -- PREdict FetAl ComponEnt |
| prefersim |
1.0 |
|
|
GPL3 |
X | X | | | PReFerSim is an ANSI C program that performs forward simulations under... |
| prequal |
1.02 |
|
|
GNU |
X | X | | | a pre-alignment quality filter for comparative sequence analyses |
| preseq |
3.2.0 |
doc |
|
GPL-3.0-or-later |
X | X | | | predicting library complexity and genome coverage in high-throughput sequencing |
| president |
0.6.8 |
|
|
MIT |
| | | X | Calculate pairwise nucleotide identity with respect to a reference sequence. |
| presto |
0.7.4 |
doc |
dev |
AGPL-3.0-or-later |
X | X | | X | A bioinformatics toolkit for processing high-throughput lymphocyte... |
| prestor |
07f9c7caeb60 |
|
|
Creative |
X | X | | | A prototype package for generating quality control plots from pRESTO output. |
| pretext-suite |
0.0.2 |
|
|
MIT |
| | | X | Meta-package for Pretext Hi-C contact map tools. |
| pretextgraph |
0.0.8 |
|
|
MIT |
X | X | | | Embeds bedgraph data into Pretext contact maps. |
| pretextmap |
0.1.9 |
|
|
MIT |
X | X | | | Paired REad TEXTure Mapper. Converts SAM formatted read pairs into... |
| pretextsnapshot |
0.0.4 |
|
|
MIT |
X | X | | | Commandline image generator for Pretext Hi-C genome contact maps. |
| primalbedtools |
0.6.2 |
|
|
MPL-2.0 |
| | | X | A collection of tools for working with primer.bed files |
| primalscheme |
1.4.1 |
|
|
GPL-3 |
| | | X | primalscheme is a tool for designing primer panels for multiplex PCR |
| primedrpa |
1.0.3 |
|
|
GPL3 |
| | | X | RPA primer & probe design tool. |
| primer3 |
2.6.1 |
|
|
GPLv2 |
X | X | | | Design PCR primers from DNA sequence. From mispriming libraries to... |
| primer3-py |
2.0.3 |
doc |
|
GPL-2.0-only |
X | X | | | Python bindings for Primer3 |
| primerclip |
0.3.8 |
|
|
Copyright |
X | | | | Swift Accel-Amplicon primer trimming tool for fast alignment-based... |
| primerforge |
1.5.3 |
doc |
dev |
Apache-2.0 |
| | | X | primerForge: software to identify primers that can be used to... |
| primerprospector |
1.0.1 |
|
|
GPL |
X | X | | | Primer Prospector is a pipeline of programs to design and analyze PCR primers. |
| primers |
0.5.10 |
doc |
|
MIT |
| | | X | This is a small, straightforward tool for creating PCR primers. Its... |
| prince |
2.3 |
|
|
MIT |
| | | X | PRINCE estimates Variable Number Tandem Repeats (VNTR) copy number from... |
| prinseq |
0.20.4 |
|
|
GPLv3 |
X | X | | X | PRINSEQ can be used to filter, reformat, or trim your genomic and... |
| prinseq-plus-plus |
1.2.4 |
doc |
dev |
GNU |
X | X | | | PRINSEQ++ - Multi-threaded C++ sequence cleaning |
| probabilistic2020 |
1.2.3 |
|
|
Apache-2-0 |
X | | | | Simulates somatic mutations, and calls statistically significant... |
| probamconvert |
1.0.2 |
|
|
Apache |
X | | | X | proBAMconvert is a conversion tool to convert common peptide... |
| probcons |
1.12 |
|
|
Public |
X | X | | | PROBCONS is a probabilistic consistency-based multiple sequence alignment |
| probconsrna |
1.10 |
|
|
Public |
X | X | | | PROBCONSRNA is an experimental version of PROBCONS for nucleotide sequences |
| probeit |
2.2 |
|
|
AGPL-3.0 |
X | X | | | Probeit: a probe designer for detecting and genotyping pathogen!!! |
| proda |
1.0 |
|
|
Public |
X | X | | | ProDA - Multiple alignment of protein sequences with repeated and... |
| prodigal |
2.6.3 |
|
dev |
GPL |
X | X | | | Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a... |
| prodigal-gv |
2.11.0 |
|
|
GPL-3.0-only |
X | X | | | A fork of Prodigal meant to improve gene calling for giant viruses |
| profile_dists |
1.0.3 |
|
dev |
Apache-2.0 |
| | | X | Profile Dists: Rapid calcualtion of allele profile distances and... |
| progressivemauve |
snapshot_2015_02_13 |
|
|
GNU |
X | | | | progressiveMauve computes multiple genome alignment with gene gain,... |
| prokaryote |
2.4.4 |
|
dev |
GNU |
| | | X | CellProfiler's Java dependencies |
| prokbert |
0.0.46 |
doc |
dev |
MIT |
| | | X | ProkBERT is a genomic language model specifically designed for... |
| prokka |
1.14.6 |
|
dev |
GPL-3.0-only |
X | X | | X | Rapid annotation of prokaryotic genomes |
| proksee |
1.0.0a6 |
|
|
Apache |
| | | X | Proksee is a suite of command line tools for performing assembly,... |
| promotercalculator |
1.2.4 |
|
dev |
GPL-3.0-or-later |
| | | X | Promoter-Calculator (Barrick Lab Fork) |
| pronto |
2.6.0 |
doc |
dev |
MIT |
X | X | | X | Python frontend to ontologies. |
| proot |
5.1.0 |
|
|
GPL-2.0 |
X | | | | chroot, mount --bind, and binfmt_misc without privilege/setup |
| proovframe |
0.9.7 |
|
dev |
MIT |
| | | X | frame-shift correction for long read (meta)genomics |
| prophane |
6.2.6 |
|
|
MIT |
| | | X | Annotate your metaproteomic search results |
| prophasm |
0.1.1 |
|
|
MIT |
X | X | | | ProPhasm – ProPhyle Assembler. Compressing k-mer sets via assembling contigs. |
| prophex |
0.1.1 |
|
|
MIT |
X | X | | | The ProPhex k-mer index. |
| prophyle |
0.3.3.2 |
|
|
MIT |
X | X | | | ProPhyle is an accurate, resource-frugal and deterministic... |
| propy3 |
1.1.1 |
|
dev |
GPLv2 |
| | | X | Python library for calculating various protein descriptors from protein... |
| prosampler |
1.5 |
|
|
GPLv3 |
X | X | | | An ultra-fast motif finding program in large ChIP-seq datasets. |
| prosic |
2.1.2 |
|
|
GPLv3 |
X | X | | | A highly sensitive and accurate Bayesian caller for somatic insertions... |
| prosolo |
0.6.1 |
|
|
GPLv3 |
X | X | | | A highly sensitive and accurate Bayesian caller for variants in single... |
| prot-scriber |
0.1.6 |
|
|
GPL-3.0-only |
X | X | | | Assigns short human readable descriptions (HRD) to query biological... |
| proteinortho |
6.3.4 |
doc |
dev |
GPL-3.0-only |
X | X | | | Proteinortho is a tool to detect orthologous genes within different species. |
| proteomiqon-alignmentbasedquantification |
0.0.2 |
doc |
dev |
MIT |
| | | X | Given an MS run in the mzLite or mzml format and a list of a list of... |
| proteomiqon-alignmentbasedquantstatistics |
0.0.3 |
doc |
dev |
MIT |
| | | X | The tool ProteomIQon.AlignmentBasedQuantStatistics scores peptide ion... |
| proteomiqon-joinquantpepionswithproteins |
0.0.2 |
doc |
dev |
MIT |
| | | X | The tool JoinQuantPepIonsWithProteins combines results from... |
| proteomiqon-labeledproteinquantification |
0.0.3 |
doc |
dev |
MIT |
| | | X | The tool LabeledProteinQuantification combines the results from... |
| proteomiqon-labelfreeproteinquantification |
0.0.3 |
doc |
dev |
MIT |
| | | X | The tool LabelFreeProteinQuantification estimates protein abundances... |
| proteomiqon-mzmltomzlite |
0.0.8 |
doc |
dev |
MIT |
| | | X | The tool MzMLToMzLite allows to convert mzML files to mzLite files. |
| proteomiqon-peptidedb |
0.0.7 |
doc |
dev |
MIT |
| | | X | The tool ProteomIQon.PeptideDB creates a peptide database in the SQLite format. |
| proteomiqon-peptidespectrummatching |
0.0.7 |
doc |
dev |
MIT |
| | | X | Given raw an MS run in the mzLite format, this tool iterates across all... |
| proteomiqon-proteininference |
0.0.7 |
doc |
dev |
MIT |
| | | X | MS-based shotgun proteomics estimates protein abundances using a proxy:... |
| proteomiqon-psmbasedquantification |
0.0.9 |
doc |
dev |
MIT |
| | | X | The quantification tool was designed to allow label-free quantification... |
| proteomiqon-psmstatistics |
0.0.8 |
doc |
dev |
MIT |
| | | X | The PSMStatistics tool utilizes semi supervised machine learning... |
| proteowizard |
3_0_9992 |
|
|
Apache |
X | | | | Tools for dealing with mass spectrometry files (e.g., mzML, mzXML,... |
| protgraph |
0.3.11 |
|
|
BSD-3-Clause |
| | | X | ProtGraph, a graph generator for proteins. |
| protk |
1.4.4a |
|
|
MIT |
X | | | | protk (Proteomics toolkit) |
| protmapper |
0.0.29 |
doc |
dev |
BSD-2-Clause |
| | | X | Map protein sites to human reference sequence. |
| protrac |
2.4.2 |
|
|
CC |
X | X | | X | piRNA detection |
| provean |
1.1.5 |
|
|
GPL-3 |
X | X | | | PROVEAN (Protein Variation Effect Analyzer) is a software tool which... |
| prscs |
1.1.0 |
|
|
MIT |
| | | X | PRS-CS is a Python based command line tool that infers posterior SNP... |
| prymer |
3.0.2 |
doc |
dev |
MIT |
| | | X | Python Primer Design Library |
| psap |
1.0.7 |
|
|
MIT |
| | | X | CLI interface for the PSAP classifier. PSAP implements a RandomForest... |
| psascan |
0.1.0 |
|
|
MIT |
X | | | | A parallel external memory suffix array construction algorithm |
| psass |
3.1.0 |
|
|
GPL3 |
X | X | | | Comparison of pooled-sequencing data for two populations |
| psdm |
0.3.0 |
|
|
MIT |
X | X | | | Compute a pairwise SNP distance matrix from one or two alignment(s) |
| pseqsid |
1.0.2 |
|
|
MIT |
X | X | | | Calculates pairwise sequence identity, similarity and normalized... |
| pseudo-it |
3.1.1 |
doc |
dev |
GNU |
| | | X | Reference-based genome assembly with iterative mapping |
| psiclass |
1.0.3 |
|
|
GPL-3.0-only |
X | X | | | Simultaneous multi-sample transcript assembler for RNA-seq data |
| psims |
1.3.5 |
doc |
dev |
Apache-2.0 |
| | | X | Writers and controlled vocabulary manager for PSI-MS's mzML and... |
| psirc |
1.0.0 |
doc |
dev |
MIT |
X | X | | | Full-length linear and circular transcript isoform reconstruction and... |
| psm-utils |
1.4.0 |
doc |
dev |
Apache-2.0 |
| | | X | Common utilities for parsing and handling peptide-spectrum matches and... |
| psm_fragments |
1.0.3 |
|
|
MIT |
| | | X | PSM validation against ion fragmentation |
| psmc |
0.6.5 |
|
|
MIT |
X | X | | | This software package infers population size history from a diploid... |
| pstools |
0.2a3 |
|
|
MIT |
X | | | | Toolkit for fully phased sequences |
| pstrain |
1.0.3 |
|
|
MIT |
X | X | | | An Iterative Microbial Strains Profiling Algorithm for Shotgun... |
| psytrans |
2.0.0 |
|
|
GPLv3 |
| | | X | psytrans.py - Parasite & Symbiont Transcriptome Separation |
| ptgaul |
1.0.5 |
|
|
MIT |
| | | X | Plastid Genome Assembly Using long-read data (ptGAUL) |
| ptools_bin |
0.0.7 |
|
|
MIT |
| | | X | Installation for ptools scripts. |
| ptrimmer |
1.4.0 |
|
dev |
GPL-3.0-or-later |
X | X | | | Used to trim off the primer sequence from mutiplex amplicon sequencing |
| pubchempy |
1.0.4 |
doc |
dev |
MIT |
| | | X | A simple Python wrapper around the PubChem PUG REST API. |
| pubmlst_client |
0.2.0 |
|
|
MIT |
| | | X | List and download schemes from pubMLST.org |
| pulchra |
3.06 |
|
|
MIT |
X | X | | | A tool for all-atom reconstruction and refinement of reduced protein models |
| pullseq |
1.0.2 |
|
|
MIT |
X | X | | | Utility program for extracting sequences from a fasta/fastq file. |
| pupmapper |
0.0.9 |
|
dev |
MIT |
| | | X | Tool & python package for calculating genome wide pileup mappability. |
| pureclip |
1.3.1 |
|
|
GPLv3 |
X | X | | | PureCLIP is a tool to detect protein-RNA interaction footprints from... |
| purge-dups-runner |
2019.12.20 |
|
|
MIT |
| | | X | High Performance Cluster (HPC) runner. |
| purge_dups |
1.2.6 |
doc |
dev |
MIT |
X | X | | | purge_dups is a package used to purge haplotigs and overlaps in an... |
| purge_haplotigs |
1.1.3 |
|
|
MIT |
X | X | | X | Pipeline to help with curating heterozygous diploid genome assemblies. |
| purple-bio |
0.4.2.5 |
|
|
GNU |
| | | X | Picking Unique Relevant Peptides for viraL Experiments |
| pvacseq |
4.0.10 |
doc |
|
NPOSL-3.0 |
X | X | | X | Personalized Variant Antigens by Cancer Sequencing (pVAC-Seq) |
| pvga |
0.1.2 |
|
|
MIT |
| | | X | PVGA is a powerful virus-focused assembler that does both assembly and... |
| pxblat |
1.2.1 |
doc |
dev |
OTHER |
X | X | | | PxBLAT: An Efficient and Ergonomics Python Binding Library for BLAT. |
| py-graphviz |
0.4.10 |
|
|
MIT |
X | X | | X | Simple Python interface for Graphviz |
| py2bit |
0.3.3 |
doc |
dev |
MIT |
X | X | | | A package for accessing 2bit files using lib2bit. |
| py_fasta_validator |
0.6 |
doc |
dev |
MIT |
X | X | | | Simply and quickly validate a fasta file. Invalid files return non-zero... |
| pyaavf |
0.1.0 |
|
|
Apache |
| | | X | An amino acid variant format parser for Python. |
| pyabpoa |
1.5.3 |
|
dev |
MIT |
X | X | | | pyabpoa: SIMD-based partial order alignment using adaptive band |
| pyalveo |
1.0.3 |
|
|
BSD |
X | X | | | A Python library for interfacing with the Alveo API |
| pyani |
0.2.13.1 |
doc |
dev |
MIT |
X | X | | X | pyani provides a package and script for calculation of genome-scale... |
| pyasn1-modules |
0.0.5 |
|
|
BSD |
X | X | | | a small but growing collection of ASN.1 data structures expressed in... |
| pyasp |
1.4.3 |
|
|
GPLv3+ |
X | X | | | A convenience wrapper for the ASP tools gringo, gringo4 and clasp. |
| pyasr |
0.6.1 |
|
|
BSD-3-Clause |
| | | X | Ancestral sequence reconstruction using Python. |
| pybamparser |
0.0.3 |
|
|
GNU |
X | X | | X | Tools for parsing BAM data |
| pybamtools |
0.0.4 |
|
|
GNU |
X | X | | X | Tools for working on BAM data |
| pybarrnap |
0.5.1 |
doc |
dev |
GPL-3.0-or-later |
| | | X | Python implementation of barrnap (Bacterial ribosomal RNA predictor). |
| pybbi |
0.4.1 |
|
|
MIT |
X | X | | | Python bindings to UCSC Big Binary (bigWig/bigBed) file library |
| pybda |
0.1.0 |
doc |
dev |
GNU |
| | | X | Big biological data analytics powered by Apache Spark |
| pybdei |
0.13 |
|
dev |
LGPL-2.1 |
X | X | | | Maximum likelihood estimation of Birth-Death Exposed-Infectious (BDEI)... |
| pybedgraph |
0.5.43 |
|
|
MIT |
X | X | | | A package for fast operations on 1-dimensional genomic signal tracks |
| pybedlite |
1.0.0 |
doc |
dev |
MIT |
X | X | | X | Lightweight python classes for interfacing with bed intervals |
| pybedtools |
0.11.0 |
doc |
dev |
MIT |
X | X | | | Wraps BEDTools for use in Python and adds many additional features. |
| pybel |
0.13.2 |
doc |
dev |
Apache-2.0 |
X | X | | X | PyBEL is a Python package for parsing and handling biological networks... |
| pybigtools |
0.2.4 |
doc |
dev |
MIT |
X | X | | | pybigtools: Python bindings to the Bigtools Rust library for... |
| pybigwig |
0.3.24 |
doc |
dev |
MIT |
X | X | | | A python extension written in C for quick access to bigWig files. |
| pybiolib |
1.2.567 |
|
dev |
MIT |
| | | X | BioLib Python Client |
| pybiomart |
0.2.0 |
doc |
dev |
MIT |
| | | X | A simple pythonic interface to biomart. |
| pybmtools |
0.1.3 |
|
|
MIT |
X | X | | | A python extension written in C for quick access to DNA methylation BM files. |
| pybwa |
1.4.7 |
doc |
dev |
MIT |
X | X | | | Pybwa is a python module that makes it easy to align sequence data. It... |
| pychopper |
2.7.10 |
|
|
Mozilla |
| | | X | A tool to identify, orient and rescue full length cDNA reads from nanopore data. |
| pycli |
2.0.3 |
|
|
MIT |
X | X | | X | Simple, object-oriented approach to Python CLI apps |
| pyclone |
0.13.1 |
|
|
custom |
| | | X | PyClone: A probabilistic model for inferring clonal population... |
| pyclone-vi |
0.1.6 |
|
dev |
GPL-3.0-or-later |
| | | X | A fast method for inferring clonal population structure |
| pycluster |
1.54 |
|
|
MIT |
X | X | | | Clustering module for Python |
| pycomo |
0.2.8 |
|
dev |
MIT |
| | | X | PyCoMo is a software package for generating and analysing... |
| pycoqc |
2.5.2 |
doc |
|
GNU |
X | X | | X | PycoQC computes metrics and generates interactive QC plots for Oxford... |
| pycov3 |
2.1.0 |
|
dev |
MIT |
| | | X | Generate cov3 files used in DEMIC |
| pycoverm |
0.6.2 |
|
|
GPL-3.0 |
X | X | | | Python bindings for CoverM |
| pycrac |
1.5.2 |
|
|
Apache-2.0 |
| | | X | Python NextGen sequencing data processing software |
| pycsg |
0.3.12 |
|
|
MIT |
X | X | | X | Python port of csg.js from Evan Wallace |
| pyctv_taxonomy |
0.25 |
|
dev |
MIT |
| | | X | pyctv_taxonomy: download and use the ICTV Virus Metadata Resource |
| pydamage |
1.0 |
|
dev |
GPL-3.0-or-later |
| | | X | Damage parameter estimation for ancient DNA. |
| pydbsnp |
2.0.2 |
|
|
MIT |
| | | X | Interface with dbSNP VCF data |
| pydemult |
0.6 |
doc |
dev |
MIT |
X | X | | X | Streamed and parallel demultiplexing of fastq files in python |
| pydeseq2 |
0.5.0 |
doc |
dev |
MIT |
| | | X | A python implementation of DESeq2. |
| pydmtools |
0.1.1 |
|
|
MIT |
X | X | | | A python extension written in C for quick access to DNA methylation DM files. |
| pydna |
5.2.0 |
|
|
BSD-3-Clause |
X | X | | X | Representing double stranded DNA and functions for simulating cloning... |
| pydna_repeatfinder |
0.2.9 |
doc |
dev |
MIT |
X | X | | | Search for direct and inverted repeats in DNA sequences. |
| pydnase |
0.3.0 |
doc |
|
MIT |
X | X | | | DNase-seq analysis library |
| pydownsampler |
1.0 |
|
|
MIT |
| | | X | A Python package for downsampling sequence alignment files |
| pydp |
0.2.4 |
|
|
GPL |
| | | X | PyDP is library for implementing Dirichlet Process mixture models (DPMM) |
| pydpi |
1.0 |
|
|
GPL |
| | | X | A powerful tool for chemoinformatics, bioinforamtics and chemogenomics study |
| pydustmasker |
1.0.0 |
|
|
MIT |
X | X | | | Python library for identification and masking of low-complexity regions... |
| pyeasyfuse |
2.0.3 |
doc |
dev |
GPL-3.0-only |
| | | X | EasyFuse is a pipeline to detect fusion transcripts from RNA-seq data... |
| pyega3 |
5.2.0 |
doc |
dev |
Apache-2.0 |
X | X | | X | EGA python client |
| pyensembl |
2.3.13 |
|
|
Apache-2.0 |
X | X | | X | Python interface to ensembl reference genome metadata |
| pyexcelerator |
0.6.4a |
|
|
BSD |
X | X | | | generating Excel 97+ files; importing Excel 95+ files; Excel files... |
| pyfaidx |
0.8.1.3 |
doc |
|
BSD |
X | X | | X | pyfaidx: efficient pythonic random access to fasta subsequences |
| pyfamsa |
0.5.3.post1 |
doc |
dev |
GPL-3.0-or-later |
X | X | | | Cython bindings and Python interface to FAMSA, an algorithm for... |
| pyfasta |
0.5.2 |
|
|
MIT |
X | X | | X | fast, memory-efficient, pythonic (and command-line) access to fasta... |
| pyfastani |
0.6.1 |
doc |
dev |
MIT |
X | X | | | Cython bindings and Python interface to FastANI, a method for fast... |
| pyfastaq |
3.17.0 |
|
|
GNU |
X | X | | X | Script to manipulate FASTA and FASTQ files, plus API for developers |
| pyfastg |
0.1.0 |
|
|
MIT |
| | | X | Minimal Python library for parsing SPAdes FASTG files |
| pyfastx |
2.2.0 |
|
|
MIT |
X | X | | | pyfastx is a python module for fast random access to sequences from... |
| pyfba |
2.62 |
doc |
dev |
MIT |
X | X | | | Python-based Flux Balance Analysis using the ModelSEED |
| pyfish |
1.0.3 |
|
|
GPL-3 |
| | | X | Plotting tool for evolutionary population dynamics. Creates a Fish... |
| pygcap |
1.2.6 |
|
dev |
MIT |
| | | X | Python package for probe-based gene cluster finding in large microbial... |
| pygenetic_code |
0.20.0 |
|
dev |
MIT |
X | X | | | Python code for translating sequences using different NCBI translation... |
| pygenometracks |
3.9 |
|
|
GPL3 |
X | X | | X | Standalone program and library to plot beautiful genome browser tracks. |
| pygenomeviz |
0.4.4 |
|
|
MIT |
| | | X | A genome visualization python package for comparative genomics |
| pygmes |
0.1.7 |
|
dev |
GNU |
| | | X | Run GeneMark-ES using pretrained models |
| pygraphviz |
1.3.1 |
|
|
BSD |
X | X | | | Python interface to Graphviz |
| pygresql |
5.0.1 |
|
|
Python |
X | X | | | Python PostgreSQL Interfaces |
| pygtftk |
1.6.2 |
|
|
MIT |
X | X | | | The gtftk suite providing facilities to manipulate genomic annotations... |
| pygvcf2coverage |
0.2 |
|
|
MIT |
| | | X | Python tool to extra coverage from gVCF files. |
| pyhalcyon |
0.1.1 |
doc |
dev |
GPLv3 |
| | | X | Halcyon: an accurate basecaller exploiting an encoder-decoder model... |
| pyham |
1.1.11 |
|
|
MIT |
| | | X | A tool to analyse Hierarchical Orthologous Groups (HOGs) |
| pyhashxx |
0.1.3 |
|
|
BSD |
X | X | | | Python wrapper for xxHash algorithm |
| pyhmmer |
0.11.0 |
doc |
dev |
MIT |
X | X | | | Cython bindings and Python interface to HMMER3. |
| pyhmmsearch |
2024.10.20 |
doc |
dev |
MIT |
| | | X | Fast implementation of HMMSEARCH optimized for high-memory systems... |
| pyimagingmspec |
0.1.4 |
|
|
Apache |
X | X | | X | Python library for processing imaging mass spectrometry data |
| pyimzml |
1.5.1 |
|
|
Apache-2.0 |
X | X | | X | Parser for conversion of imzML 1.1.0 files |
| pyjaspar |
3.0.0 |
doc |
|
GPL-3.0-or-later |
| | | X | pyJASPAR: a serverless interface to Biopython to access different... |
| pyjess |
0.4.1 |
doc |
dev |
MIT |
X | X | | | Cython bindings and Python interface to JESS, a 3D template matching software. |
| pykofamsearch |
2024.10.20 |
|
dev |
MIT |
| | | X | Fast implementation of HMMSEARCH optimized for high-memory systems... |
| pylca |
1.0.0 |
|
|
MIT |
| | | X | Lowest common ancestor (LCA) algorithm implementation in python |
| pylibseq |
0.2.3 |
|
|
GPL-3.0-or-later |
X | X | | | A Python interface to libsequence |
| pyliftover |
0.4.1 |
|
|
MIT |
X | X | | X | Pure-python implementation of UCSC ``liftOver`` genome coordinate conversion. |
| pylipid |
1.5.14 |
|
|
MIT |
| | | X | PyLipID - A Python Library For Lipid Interaction Analysis |
| pyloh |
1.4.3 |
|
|
GPLv2 |
X | X | | X | Deconvolving tumor purity and ploidy by integrating copy number... |
| pylprotpredictor |
1.0.2 |
|
|
Apache |
| | | X | A tool to predict PYL proteins |
| pymethylation_utils |
0.5.3 |
|
|
MIT |
| | | X | Python wrapper for the methylation_utils Rust binary |
| pymisc-utils |
0.2.11 |
|
|
MIT |
X | | | X | Utility library for rp-bp |
| pymix |
0.8 |
|
|
GPL2 |
X | X | | | Python mixture package |
| pymlst |
2.1.6 |
|
|
GNU |
| | | X | python Mlst Local Search Tool |
| pymochi |
1.1 |
|
dev |
MIT |
| | | X | Neural networks to quantify energies, energetic couplings, epistasis... |
| pymot |
13.09.2016 |
|
|
All |
X | X | | X | This is a python implementation which determines the MOTP and MOTA... |
| pymsaviz |
0.5.0 |
doc |
dev |
MIT |
| | | X | MSA visualization python package for sequence analysis |
| pymummer |
0.11.0 |
|
|
GNU |
X | X | | X | Wrapper for MUMmer |
| pymvpa |
2.6.5 |
|
dev |
perl_5 |
X | X | | | PyMVPA -- Multivariate Pattern Analysis in Python |
| pymzml |
2.5.11 |
|
dev |
MIT |
X | X | | X | High-throughput mzML parsing. |
| pynacl |
0.3.0 |
|
|
Apache |
X | X | | | Python binding to the Networking and Cryptography (NaCl) library |
| pynast |
1.2.2 |
|
|
BSD |
X | X | | X | The Python Nearest Alignment Space Termination tool |
| pynnotator |
2.0 |
|
|
BSD |
| | | X | A Python Annotation Framework for VCFs using multiple tools. |
| pynteny |
1.0.0 |
doc |
dev |
Apache-2.0 |
X | X | | | Multiple HMM - search via synteny structures in Python |
| pyomero-upload |
5.6.2_2.2.0 |
|
|
MIT |
| | | X | Client library offering helper methods to upload data to an OMERO server. |
| pyomo |
4.1.10527 |
|
|
BSD |
X | | | | None |
| pyopal |
0.7.1 |
doc |
dev |
MIT |
X | X | | | Cython bindings and Python interface to Opal, a SIMD-accelerated... |
| pyopenms |
3.3.0 |
|
|
BSD |
X | X | | | python bindings for OpenMS, an open-source software C++ library for... |
| pyopt |
1.2.0 |
|
|
LGPLv3 |
X | | | | None |
| pypairs |
3.2.3 |
doc |
|
BSD |
| | | X | A python scRNA-Seq classifier |
| pypeflow |
2.2.0 |
|
|
BSD-3-Clause-Clear |
X | X | | X | Light weight and reusable make / flow data process library written in Python |
| pypgatk |
0.0.24 |
doc |
dev |
Apache |
| | | X | The Pypgatk framework and library provides a set of tools to perform... |
| pypgx |
0.25.0 |
doc |
dev |
MIT |
| | | X | A Python package for pharmacogenomics research |
| pypints |
1.1.15 |
|
dev |
GPL-3.0-only |
| | | X | Peak Identifier for Nascent Transcripts Starts (PINTS) |
| pypiper |
0.8 |
|
dev |
BSD-2-Clause |
X | X | | X | Pypiper is a lightweight python toolkit that helps you write slick... |
| pyplink |
1.3.7 |
|
|
MIT |
| | | X | Python module to read binary Plink files. |
| pypolca |
0.3.1 |
|
|
MIT |
| | | X | Standalone Python re-implementation of the POLCA polisher from MaSuRCA |
| pypore |
0.0.6.dev20180 |
|
|
Apache |
X | X | | | Pythonic/Cythonic Nanopore Translocation Analysis |
| pyprophet |
2.2.5 |
|
|
BSD |
X | X | | | Python reimplementation of mProphet peak scoring |
| pyqi |
0.3.2 |
|
|
BSD |
X | X | | | pyqi: expose your interface |
| pyquant-ms |
0.2.4 |
|
|
MIT |
X | X | | | A framework for the analysis of quantitative mass spectrometry data |
| pyquery |
1.2.9 |
|
|
BSD |
X | X | | | A jquery-like library for python |
| pyrad |
3.0.66 |
|
|
GPLv3 |
X | X | | X | Assembly and analysis of RADseq data sets |
| pyranges |
0.1.2 |
doc |
dev |
MIT |
X | X | | X | Performant Pythonic GenomicRanges |
| pyrle |
0.0.40 |
|
|
MIT |
X | X | | | Genomic Rle-objects for Python |
| pyrodigal |
3.6.3.post1 |
doc |
dev |
GPL-3.0-or-later |
X | X | | | Python bindings to Prodigal, an ORF finder for microbial sequences. |
| pyrodigal-gv |
0.3.2 |
|
|
GPL-3.0-or-later |
| | | X | A Pyrodigal extension to predict genes in giant viruses and viruses... |
| pyroe |
0.9.3 |
|
|
BSD-3-Clause |
| | | X | A python toolkit to aid with scRNA-seq analysis workflows using alevin-fry |
| pyrovelocity |
0.1.0 |
doc |
|
Affero |
| | | X | Probabilistic RNA velocity for cell fate uncertainty estimation |
| pyrpipe |
0.0.5 |
doc |
|
MIT |
| | | X | pyrpipe is a lightweight python package for RNA-Seq workflows. |
| pysais |
1.1.0 |
|
|
MIT |
X | X | | | Suffix array computation with induced sorting algorithm. |
| pysam |
0.23.0 |
|
|
MIT |
X | X | | | Pysam is a Python module for reading and manipulating SAM/BAM/VCF/BCF... |
| pysamstats |
1.1.2 |
|
|
MIT |
X | X | | | Calculate read mapping stats from SAM/BAM/CRAM |
| pyscaf |
0.12a4 |
|
|
GPLv3 |
X | X | | X | Genome assembly scaffolding using information from paired-end/mate-pair... |
| pyscenic |
0.12.1 |
doc |
dev |
GPL-3.0-or-later |
| | | X | Python implementation of the SCENIC pipeline for transcription factor... |
| pyseer |
1.3.12 |
|
|
Apache-2.0 |
X | X | | X | Sequence Element Enrichment Analysis (SEER), python implementation |
| pyseq-align |
1.0.2 |
|
dev |
MIT |
X | X | | | Python interface for the seq-align C library |
| pysftp |
0.2.9 |
|
|
BSD |
X | X | | | A friendly face on SFTP |
| pyskani |
0.1.3 |
doc |
|
MIT |
X | | | | PyO3 bindings and Python interface to skani, a method for fast fast... |
| pyslim |
0.401 |
doc |
dev |
MIT |
| | | X | Manipulate tree sequences produced by SLiM. |
| pyslow5 |
1.3.0 |
|
dev |
Apache-2.0 |
X | X | | | slow5lib Python binding |
| pysnptools |
0.3.13 |
|
|
Apache |
X | X | | | Python library for reading and manipulating genetic data |
| pyspoa |
0.2.1 |
doc |
dev |
MIT |
X | X | | | Python binding to spoa library. |
| pysradb |
2.2.2 |
doc |
dev |
BSD-3-Clause |
X | X | | X | Python package for retrieving metadata and downloading datasets from SRA/ENA/GEO |
| pysvg |
0.2.2 |
|
|
BSD |
X | X | | | Python SVG Library |
| pysvmlight |
0.4 |
|
|
UNKNOWN |
X | X | | | Interface to Thorsten Joachims' SVM-Light |
| pytabix |
0.1 |
|
|
MIT |
X | X | | | Fast random access to sorted files compressed with bgzip and indexed by tabix. |
| pytaxonkit |
0.9.1 |
|
dev |
BSD-3-Clause |
| | | X | Python bindings for the TaxonKit library. |
| pyteomics |
4.7.5 |
|
|
Apache-2.0 |
X | X | | X | A framework for proteomics data analysis. |
| pytest-marks |
0.4 |
|
|
GNU |
X | X | | | set marks on py.test test methods |
| pytest-timeout |
1.0.0 |
|
|
MIT |
X | | | | py.test plugin to abort hanging tests |
| pytest-workflow |
1.2.0 |
doc |
|
GNU |
| | | X | A pytest plugin for configuring workflow/pipeline tests using YAML files |
| pythomics |
0.4.1 |
|
|
GPL3 |
X | X | | X | A multi-omic python package |
| python-bioext |
0.21.9 |
|
|
GPL-3.0-only |
X | X | | | A few handy bioinformatics tools not already in BioPython |
| python-bioformats |
4.0.7 |
|
|
GNU |
| | | X | Read and write life sciences file formats |
| python-chado |
2.3.9 |
|
|
MIT |
X | X | | X | A Python library for interacting with Chado database. |
| python-cluster |
1.4.1.post3 |
|
|
LGPL-2.1 |
X | X | | X | python-cluster is a "simple" package that allows to create... |
| python-codon-tables |
0.1.11 |
|
|
NIST-PD |
| | | X | Codon Usage Tables for Python, from kazusa.or.jp |
| python-consensuscore |
1.1.1 |
|
|
BSD-3-Clause-Clear |
X | X | | | PacBio Quiver Consensus library for RSII data |
| python-consensuscore2 |
3.4.1 |
|
|
BSD-3-Clause-Clear |
X | X | | | PacBio Arrow Consensus library for Sequel data |
| python-crypt4gh |
1.7 |
doc |
dev |
Apache-2.0 |
| | | X | GA4GH cryptographic tools |
| python-edlib |
1.3.9.post1 |
doc |
dev |
MIT |
X | X | | | Lightweight, super fast C/C++ (& Python) library for sequence... |
| python-eel |
1.0 |
|
|
GPL |
X | X | | | Tool for finding evolutionarily conserved mammalian enhancer elements. |
| python-fakemp |
0.9.1 |
|
|
GPL-3 |
X | X | | X | Fake multiprocessing pool objects |
| python-goenrichment |
1.0.3 |
|
|
PUBLIC-DOMAIN |
| | | X | GO enrichment analysis from a list of gene names using a precomputed database |
| python-hivclustering |
1.8.0 |
|
|
MIT |
X | X | | X | A Python 3 library that makes inferences on HIV-1 transmission networks. |
| python-hppy |
0.9.9 |
|
|
GPL-3 |
X | X | | X | An intuitive HyPhy interface for Python |
| python-htsget |
0.2.6 |
|
|
Apache |
| | | X | Python API and command line interface for the GA4GH htsget API. |
| python-hyphy-python |
0.1.12 |
|
dev |
MIT |
X | X | | | HyPhy package interface library |
| python-intervaltree |
3.1.0 |
|
|
Apache |
| | | X | Faster than intervaltree_bio |
| python-levenshtein |
0.12.0 |
|
|
GPL |
X | X | | | Python extension for computing string edit distances and similarities. |
| python-libsbml |
5.18.0 |
|
|
LGPL |
X | X | | | LibSBML Python API. |
| python-mailund-newick |
1.3 |
|
|
GNU |
X | X | | | Another python module to read and write the Newick format |
| python-monovar |
0.1 |
|
|
MIT |
| | | X | single cell joint genotyper, patched version |
| python-msgpack |
0.6.1 |
|
|
Apache |
X | X | | | It's like JSON. But fast and small. |
| python-newick |
1.9.0 |
|
|
Apache-2.0 |
X | X | | X | A python module to read and write the Newick format |
| python-nextflow |
0.8 |
|
|
MIT |
| | | X | Python module to run Nextflow pipelines |
| python-omero |
5.7.1 |
|
|
GPL |
X | X | | X | Client library offering helper methods to access an OMERO server. |
| python-rnacentral |
1.0.0 |
|
|
BSD |
| | | X | This tool exploits the RNAcentral public APIs to automatically retrieve... |
| python-sortedcontainers |
2.4.0 |
|
|
Apache |
| | | X | sorted collections library, written in pure-Python, and fast as C-extensions |
| python-tripal |
3.2.1 |
|
|
MIT |
X | X | | X | Tripal API library |
| python-weblogo |
3.4 |
|
|
Public |
X | X | | | Tool for creating sequence logos from biological sequence alignments |
| python_circos |
0.2.0 |
|
|
GPL-3.0 |
| | | X | Circos plots for python |
| pythoncyc |
2.0.2 |
|
dev |
MIT |
| | | X | A Python interface to Pathway Tools, 2019 update |
| pythonnet |
2.3.0 |
|
|
MIT |
X | X | | | .Net and Mono integration for Python |
| pythonpy |
0.4.11 |
|
|
Unknown |
X | X | | X | the swiss army knife of the command line |
| pytransaln |
0.2.1 |
|
|
MIT |
| | | X | Translation-guided nucleotide alignment for coding sequences |
| pytrf |
1.4.1 |
|
|
MIT |
X | X | | | a fast Python package for finding tandem repeat sequences |
| pytriangle |
1.0.9 |
|
|
MIT |
X | X | | | A python interface to the 2D triangulation program TRIANGLE |
| pytrimal |
0.8.0 |
doc |
dev |
GPL-3.0-or-later |
X | X | | | Cython bindings and Python interface to trimAl, a tool for automated... |
| pytximport |
0.11.0 |
doc |
dev |
GPL-3.0-only |
| | | X | pytximport - gene count estimation from transcript-level quantification |
| pyutilib |
5.1.3556 |
|
|
BSD |
X | | | | None |
| pyvcf |
0.6.8 |
|
|
BSD |
X | X | | | A Variant Call Format reader for Python |
| pyvcf3 |
1.0.3 |
doc |
|
MIT |
| | | X | A Variant Call Format reader for Python |
| pyvolve |
0.9.0 |
|
|
FreeBSD |
X | X | | X | Pyvolve is an open-source Python module for simulating sequences along... |
| pywdl |
1.0.22 |
|
|
Apache |
X | X | | X | A Python implementation of a WDL parser and language bindings. |
| pywfa |
0.5.1 |
|
|
MIT |
X | X | | | A python wrapper for wavefront alignment using WFA2-lib |
| pywgsim |
0.5.2 |
|
|
MIT |
X | X | | | pywgsim |
| pyx |
0.14.1 |
|
|
GNU |
X | X | | | Python package for the generation of PostScript, PDF, and SVG files |
| qax |
0.9.6 |
|
|
GPL-3.0-only |
X | X | | | Extract data, metadata, bibliography and provenance from Qiime2 artifacts |
| qcat |
1.1.0 |
|
|
Mozilla |
| | | X | Qcat is Python command-line tool for demultiplexing Oxford Nanopore... |
| qcli |
0.1.1 |
|
|
GPL |
X | X | | X | qcli |
| qcumber |
2.0.4 |
|
|
LGPL3 |
X | X | | | Quality control, quality trimming, adapter removal and sequence content... |
| qfilt |
0.0.1 |
|
|
MIT |
X | X | | | Filter sequencing data using some simple heuristics |
| qgrs-cpp |
1.0 |
|
|
MIT |
X | X | | | C++ implementation of QGRS mapping. |
| qhery |
0.1.2 |
|
|
GPL-3.0-only |
| | | X | Identification of mutations in SARS-CoV-2 associated with resistance to... |
| qiime |
1.9.1 |
|
|
GNU |
X | X | | X | Quantitative Insights Into Microbial Ecology |
| qiime-default-reference |
0.1.3 |
|
|
CC |
X | X | | X | Default reference data files for use with QIIME. |
| qiimetomaaslin |
1.1.0 |
|
|
Unknown |
X | X | | | Data munging script to change text Qiime OTU tables to pcl-formatted,... |
| qimba |
0.4.0 |
|
|
MIT |
| | | X | Toolkit for metabarcoding analyses |
| qiskit-xyz2pdb |
0.1.2 |
|
|
MIT |
| | | X | qiskit-xyz2pdb |
| qorts |
1.3.6 |
|
|
Public |
X | X | | X | QoRTs toolkit for analysis, quality control, and data management of... |
| qsignature |
0.1pre |
|
|
GPLv3 |
X | X | | X | qsignature is a simple and highly effective method for detecting... |
| qtip |
1.6.2 |
|
|
MIT |
X | X | | | A tandem simulation approach for accurately predicting read alignment... |
| qtlseq |
2.2.9 |
|
dev |
GPL-3.0-or-later |
| | | X | QTL-seq: pipeline to identify causative mutations responsible for a phenotype. |
| quake |
0.3.5 |
|
|
Artistic-2.0 |
X | X | | | Quake is a package to correct substitution sequencing errors in... |
| qualimap |
2.3 |
|
|
GPL-2.0-or-later |
X | X | | X | Quality control of alignment sequencing data and its derivatives like... |
| quantiprot |
0.2.5 |
|
|
MIT |
| | | X | Quantiprot is a Python package for quantitative analysis of protein sequences |
| quantms-rescoring |
0.0.5 |
|
dev |
Apache |
| | | X | PSM rescoring python package with scripts and helpers for the quantms workflow |
| quantms-utils |
0.0.20 |
doc |
dev |
MIT |
| | | X | Python package with scripts and helpers for the quantms workflow. |
| quantpi |
1.0.0 |
|
|
GPL-3.0-only |
| | | X | A general profiling system focus on robust microbiome research |
| quantwiz-iq |
2.0 |
|
|
GPL |
| | | X | QuantWiz-IQ is a tool for reporter based MS/MS quantitation using iTRAQ... |
| quasildr |
0.2.2 |
|
|
BSD |
| | | X | Quasilinear data representations for single-cell omics data analysis. |
| quasirecomb |
1.2 |
|
|
GNU |
| | | X | Software of Inference of Quasispecies subjected to Recombination |
| quasitools |
0.7.0 |
|
|
Apache |
X | X | | X | Quasitools is a collection of tools for analysing Viral Quasispecies |
| quast |
5.3.0 |
doc |
dev |
Custom |
X | X | | X | Quality Assessment Tool for Genome Assemblies. |
| quatradis |
1.3.3 |
|
dev |
GPL-3.0-only |
X | X | | X | A set of tools to analyse the output from TraDIS analyses |
| query_phenomizer |
1.2.1 |
|
|
MIT |
X | X | | X | Tool for query and parsing the phenomizer tool |
| querynator |
0.6.0 |
doc |
dev |
MIT |
| | | X | Python package to query cancer variant databases |
| quickbam |
1.0.0 |
|
|
BSD |
X | | | | Parallel BAM file access API for high throughput sequence analysis informatics |
| quickdeconvolution |
1.2 |
|
|
GPL3 |
X | X | | | Deconvolves linked-reads sequencing data |
| quickmerge |
0.3 |
|
|
GPL-3 |
X | X | | | Quickmerge uses a simple concept to improve contiguity of genome... |
| quicksect |
0.2.2 |
|
|
MIT |
X | X | | | A cythonized, extended version of the interval search tree in bx |
| quicksnp |
1.0.1 |
|
|
GPL-3 |
| | | X | A python script to quickly build a Neighbor Joining tree using only a... |
| quicktree |
2.5 |
|
dev |
Apache-2.0 |
X | X | | | Fast implementation of the neighbour-joining phylogenetic inference method. |
| quip |
1.1.8 |
|
|
Custom |
X | X | | | Aggressive compression of FASTQ and SAM/BAM files. |
| quorum |
1.1.1 |
|
|
GPLv3 |
X | X | | | QuorUM (Quality Optimized Reads from the University of Maryland) is an... |
| quota_anchor |
0.0.1rc |
|
dev |
MIT |
| | | X | Strand and WGD aware syntenic gene identification |
| r-abdiv |
0.2.0 |
|
|
MIT |
| | | X | Alpha and Beta Diversity Measures |
| r-abind |
1.4.3 |
|
|
LGPL |
X | X | | | Combine multidimensional arrays into a single array. This is a... |
| r-acidbase |
0.7.3 |
|
dev |
AGPL-3.0 |
| | | X | Low-level base functions imported by Acid Genomics packages. |
| r-acidcli |
0.3.0 |
|
dev |
AGPL-3.0 |
| | | X | Interative R command line interface toolkit for Acid Genomics packages. |
| r-acidexperiment |
0.5.4 |
|
dev |
AGPL-3.0 |
| | | X | Toolkit to extend the functionality of SummarizedExperiment. |
| r-acidgenerics |
0.7.8 |
|
dev |
AGPL-3.0 |
| | | X | S4 generic functions for Acid Genomics packages. |
| r-acidgenomes |
0.7.2 |
|
dev |
AGPL-3.0 |
| | | X | Toolkit for downloading and processing genome annotations. |
| r-acidgsea |
0.9.0 |
|
dev |
AGPL-3.0 |
| | | X | Parameterized fast gene set enrichment analysis. |
| r-acidmarkdown |
0.3.0 |
|
dev |
AGPL-3.0 |
| | | X | Toolkit for extending the functionality of R Markdown. |
| r-acidplots |
0.7.3 |
|
dev |
AGPL-3.0 |
| | | X | Functions for plotting genomic data. |
| r-acidplyr |
0.5.4 |
|
dev |
AGPL-3.0 |
| | | X | A grammar of S4 class data manipulation. |
| r-acidsinglecell |
0.4.2 |
|
dev |
AGPL-3.0 |
| | | X | Toolkit for single-cell RNA-seq analysis that extends the functionality... |
| r-ada |
2.0_5 |
|
|
GPL |
X | X | | | Performs discrete, real, and gentle boost under both exponential and ... |
| r-ade4 |
1.7_2 |
|
|
GPL |
X | X | | | Multivariate data analysis and graphical display. |
| r-adegenet |
2.1.1 |
|
|
GPL |
X | X | | | Toolset for the exploration of genetic and genomic data. Adegenet... |
| r-adephylo |
1.1_11 |
|
|
GPL |
X | X | | | Multivariate tools to analyze comparative data, i.e. a phylogeny and... |
| r-agricolae |
1.2_4 |
|
|
GPL |
X | X | | | Original idea was presented in the thesis "A statistical analysis... |
| r-ahocorasicktrie |
0.1.0 |
|
|
Apache |
X | | | | Aho-Corasick is an optimal algorithm for finding many keywords in a... |
| r-airr |
1.2.0 |
|
|
CC |
| | | X | Schema definitions and read, write and validation tools for data ... |
| r-alakazam |
1.2.1 |
|
|
AGPL-3 |
X | X | | | Provides methods for high-throughput adaptive immune receptor... |
| r-algdesign |
1.1_7.3 |
|
|
GPL |
X | X | | | Algorithmic experimental designs. Calculates exact and approximate... |
| r-amap |
0.8_14 |
|
|
GPL |
X | X | | | Tools for Clustering and Principal Component Analysis (With robust... |
| r-ampliconduo |
1.1 |
|
|
GPL |
X | X | | | Increasingly powerful techniques for high-throughput sequencing open... |
| r-ampvis |
1.27.0 |
|
|
AGPL-3 |
X | X | | | A package to visualise amplicon data |
| r-ampvis2 |
2.8.9 |
|
|
AGPL-3.0-only |
| | | X | Tools for visualising amplicon data |
| r-anndata |
0.7.5.6 |
|
dev |
MIT |
| | | X | A 'reticulate' wrapper for the Python package... |
| r-annotables |
0.2.0 |
|
|
GPL-3 |
X | X | | X | Provides tables for converting and annotating Ensembl Gene IDs. |
| r-aod |
1.3 |
|
|
GPL |
X | X | | | This package provides a set of functions to analyse overdispersed... |
| r-aptreeshape |
1.5_0 |
|
|
GPL |
X | X | | | Simulation and analysis of phylogenetic tree topologies using... |
| r-archr |
1.0.3 |
doc |
dev |
MIT |
X | X | | | This package is designed to streamline scATAC analyses in R. |
| r-argparse |
1.0.1 |
|
|
GPL |
X | X | | | A command line parser to be used with Rscript to write "#!"... |
| r-argparser |
0.4 |
|
|
GPL |
X | X | | | Cross-platform command-line argument parser written purely in R with no... |
| r-argumentcheck |
0.10.2 |
|
|
GPL-3 |
X | X | | | The typical process of checking arguments in functions is iterative. ... |
| r-aroma.affymetrix |
3.2.2 |
|
|
LGPL-2.1-or-later |
X | X | | X | A cross-platform R framework that facilitates processing of any number... |
| r-aroma.apd |
0.6.0 |
|
|
LGPL |
X | X | | | DEPRECATED. Do not start building new projects based on this package.... |
| r-aroma.core |
3.3.1 |
|
dev |
LGPL-2.1-or-later |
X | X | | X | Core methods and classes used by higher-level 'aroma.*'... |
| r-ash |
1.0_15 |
|
|
GPL |
X | X | | | David Scott's ASH routines ported from S-PLUS to R. |
| r-asics |
1.0.1 |
|
|
GPL |
X | X | | | With a set of pure metabolite spectra, ASICS quantifies metabolites... |
| r-autospill |
0.2.0 |
|
dev |
MIT |
| | | X | AutoSpill algorithm for calculating spillover coefficients to... |
| r-azimuth |
0.5.0 |
|
|
GPL-3.0-only |
X | X | | | Azimuth is a Shiny app demonstrating a query-reference mapping... |
| r-base64 |
1.1 |
|
|
GPL |
X | X | | | Base 64 encoder/decoder |
| r-basejump |
0.18.0 |
|
dev |
AGPL-3.0 |
X | X | | X | Base functions for bioinformatics and R package development. |
| r-batch |
1.1_4 |
|
|
GPL |
X | X | | | Functions to allow you to easily pass command-line arguments into R,... |
| r-batchjobs |
1.6 |
|
|
BSD_2_clause |
X | X | | | Provides Map, Reduce and Filter variants to generate jobs on batch... |
| r-bayesprism |
0 |
|
|
GPL-3 |
X | X | | | BayesPrism: Bayesian cell type and gene expression deconvolution |
| r-bbmisc |
1.11 |
|
|
BSD_3_clause |
X | X | | | Miscellaneous helper functions for and from B. Bischl and some other... |
| r-bbmle |
1.0.18 |
|
|
GPL-2 |
X | X | | | Methods and functions for fitting maximum likelihood models in R. This... |
| r-bc3net |
1.0.4 |
|
|
GPL |
| | | X | Implementation of the BC3NET algorithm for gene regulatory network... |
| r-bcbiobase |
0.9.0 |
|
dev |
GPL-3.0 |
X | X | | X | Base functions and generics for bcbio R packages. |
| r-bcbiornaseq |
0.6.2 |
|
dev |
AGPL-3.0 |
X | X | | X | R package for bcbio RNA-seq analysis. |
| r-bcbiosinglecell |
0.7.1 |
|
dev |
MIT |
| | | X | R package for bcbio single-cell RNA-seq analysis. |
| r-beanplot |
1.2 |
|
|
GPL-2 |
X | X | | | Plots univariate comparison graphs, an alternative to... |
| r-bedr |
1.0.4 |
|
|
GPL-2 |
X | X | | | Genomic regions processing using open-source command line tools such as... |
| r-bedtoolsr |
2.30.0.2 |
|
|
MIT |
| | | X | R package wrapping bedtools |
| r-beyondcell |
1.3.3 |
|
|
GPL-3 |
| | | X | Tool for the Analysis of tumour therapeutic heterogeneity in single-cell RNA-seq |
| r-bh |
1.60.0_2 |
|
|
BSL-1.0 |
X | X | | | Boost provides free peer-reviewed portable C++ source libraries. A... |
| r-biasedurn |
1.07 |
|
|
GPL-3 |
X | X | | | Statistical models of biased sampling in the form of univariate and... |
| r-biganalytics |
1.1.14 |
|
|
LGPL-3 |
X | | | | Extend the 'bigmemory' package with various analytics.... |
| r-biglm |
0.9_1 |
|
|
GPL |
X | | | | Regression for data too large to fit in memory |
| r-bigmemory |
4.5.19 |
|
|
LGPL-3 |
X | X | | | Create, store, access, and manipulate massive matrices. Matrices are... |
| r-bigmemory.sri |
0.1.3 |
|
|
LGPL-3 |
X | X | | | This package provides a shared resource interface for the bigmemory and... |
| r-bio3d |
2.3_3 |
|
|
GPL |
X | X | | | Utilities to process, organize and explore protein structure, sequence... |
| r-biodb |
1.2.2 |
|
|
AGPL-3.0 |
X | X | | | An R package for connecting to chemical and biological databases. |
| r-biom |
0.3.12 |
|
|
GPL-2 |
X | X | | | This is an R package for interfacing with the BIOM format. |
| r-biomark |
0.4.5 |
|
|
GPL |
X | X | | | Variable selection methods are provided for several classification... |
| r-biomartr |
1.0.7 |
|
|
GPL-2.0-only |
| | | X | Perform large scale genomic data retrieval and functional annotation... |
| r-bioverbs |
0.2.13 |
|
dev |
MIT |
X | X | | X | S4 generic functions for bioinformatics. |
| r-bipartite |
2.11 |
|
|
GPL |
X | X | | | Functions to visualise webs and calculate a series of indices commonly... |
| r-bisquerna |
1.0.5 |
|
|
GPL-3.0-only |
| | | X | Provides tools to accurately estimate cell type abundances from... |
| r-bit |
1.1_12 |
|
|
GPL-2 |
X | X | | | bitmapped vectors of booleans (no NAs), coercion from and to logicals,... |
| r-bit64 |
0.9_5 |
|
|
GPL-2 |
X | X | | | Package 'bit64' provides serializable S3 atomic 64bit (signed)... |
| r-blockfest |
1.6 |
|
|
GPL-2 |
X | X | | | An R implementation of an extension of the 'BayeScan' software... |
| r-blockmodeling |
0.1.8 |
|
|
GPL |
X | X | | | The package is primarly ment as an implementation of Generalized... |
| r-bma |
3.18.6 |
|
|
GPL |
X | X | | | Package for Bayesian model averaging and variable selection for linear... |
| r-breakaway |
4.7.9 |
|
|
GPL-2 |
X | X | | X | Understanding the drivers of microbial diversity is an important... |
| r-brio |
0.3.17 |
|
dev |
MIT |
X | X | | X | Biological R input/output. |
| r-bseqsc |
1.0 |
|
|
GPL-2 |
| | | X | Companion package to: A single-cell transcriptomic map of the human and... |
| r-buencolors |
0.5.6 |
|
dev |
MIT |
| | | X | R utility package for color mapping and plot aesthetics. |
| r-bulkanalyser |
1.1.0 |
|
|
GPL-2.0-only |
| | | X | Given an expression matrix from a bulk sequencing experiment,... |
| r-calder2 |
0.7 |
|
|
MIT |
| | | X | CALDER is a Hi-C analysis tool for the analysis of hierarchical... |
| r-calibrate |
1.7.2 |
|
|
GPL-2 |
X | X | | | Package for drawing calibrated scales with tick marks on... |
| r-canopy |
1.3.0 |
|
|
GPL-2 |
X | X | | | A statistical framework and computational procedure for identifying the... |
| r-car |
2.1_4 |
|
|
GPL |
X | X | | | Functions and Datasets to Accompany J. Fox and S. Weisberg, An R... |
| r-caroline |
0.7.6 |
|
|
Artistic-2.0 |
X | X | | | The caroline R library contains dozens of functions useful for:... |
| r-cate |
1.1.1 |
|
|
GPL-2 |
X | X | | X | Provides several methods for factor analysis in high dimension (both... |
| r-catools |
1.17.1 |
|
|
GPL-3 |
X | X | | | Contains several basic utility functions including: moving (rolling,... |
| r-ccqtl |
0.0.1_beta.2 |
|
|
GPL3 |
X | X | | | CCQTL is a wrapper around the R/qtl2 (Broman et al, Genetics 2019... |
| r-ccube |
1.0_beta.1 |
|
|
GPL-3 |
X | X | | | R package for clustering and estimating cancer cell fractions (CCF) of... |
| r-cdseq |
0 |
|
|
GPL-3 |
X | X | | | Estimate cell-type-specific gene expression profiles and... |
| r-cellassign |
0.99.2 |
|
|
Apache-2.0 |
X | X | | X | Automated, probabilistic assignment of cell types in scRNA-seq data |
| r-cellosaurus |
0.8.2 |
|
dev |
AGPL-3.0 |
| | | X | Cellosaurus identifier mapping toolkit. |
| r-cghflasso |
0.2_1 |
|
|
GPL |
X | X | | | Spatial smoothing and hot spot detection using the fused lasso regression |
| r-cghseg |
1.0.5 |
|
|
GPL |
| | | X | Dedicated to the analysis of CGH (Comparative Genomic Hybridization)... |
| r-changepoint |
2.2.2 |
|
|
GPL |
X | X | | | Implements various mainstream and specialised changepoint methods for... |
| r-chbutils |
0.1_2017_10_26 |
|
|
MIT |
X | X | | X | Useful utility functions used at the Harvard Chan School Bioinformatics core |
| r-checkmate |
1.8.2 |
|
|
BSD_3_clause |
X | X | | | Tests and assertions to perform frequent argument checks. A substantial... |
| r-checkpoint |
0.4.0 |
|
|
GPL-2 |
X | X | | | The goal of checkpoint is to solve the problem of package... |
| r-chord |
2.03 |
|
|
GPL-3.0-only |
| | | X | Predict HRD using somatic mutations contexts |
| r-chromium |
0.3.0 |
|
dev |
AGPL-3.0 |
| | | X | Toolkit for 10X Genomics Chromium single cell data. |
| r-chromvarmotifs |
0.2.0 |
|
|
MIT |
| | | X | Stores several motifs as PWMatrixList objects for use in R with... |
| r-cimpl |
1.1 |
|
|
GPL-3 |
X | X | | | An analysis package for multi sample insertional mutagenesis data... |
| r-circlize |
0.3.3 |
|
|
GPL |
X | X | | | Circular layout is an efficient way for the visualization of huge ... |
| r-circrnafull |
1.0.0 |
|
|
unknown |
| | | X | An R package for reconstruction of full length circRNA sequence using... |
| r-classdiscovery |
3.4.5 |
|
|
Apache-2.0 |
X | X | | X | Defines the classes used for "class discovery" problems in the... |
| r-cleangeostreamr |
1.0.0 |
|
|
GPL-3.0 |
| | | X | Automatic curation of spatially annotated data. |
| r-clinfun |
1.0.15 |
|
|
GPL-2 |
X | X | | | Utilities to make your clinical collaborations easier if not fun. It... |
| r-clvalid |
0.6_6 |
|
|
LGPL-3 |
| | | X | Statistical and biological validation of clustering results. |
| r-cnogpro |
1.1 |
|
|
GPL-2 |
X | X | | | Methods for assigning copy number states and breakpoints in... |
| r-cobrar |
0.1.1 |
doc |
dev |
GPL-3.0-or-later |
X | X | | | COnstraint-based Reconstruction and Analysis (COBRA) of metabolic networks in R |
| r-codedepends |
0.6.6 |
|
|
GPL-3 |
| | | X | Tools for analyzing R expressions or blocks of code and determining the... |
| r-coenocliner |
0.2_2 |
|
|
GPL-2 |
X | X | | | Simulate species occurrence and abundances (counts) along gradients. |
| r-coloc |
5.1.0.1 |
|
|
GPL |
X | X | | X | Performs the colocalisation tests described in Plagnol et al (2009)... |
| r-combinat |
0.0_8 |
|
|
GPL-2 |
X | X | | | routines for combinatorics |
| r-compquadform |
1.4.1 |
|
|
GPL |
X | X | | | Computes the distribution function of quadratic forms in normal... |
| r-compute.es |
0.2_4 |
|
|
GPL-2 |
X | X | | | This package contains several functions for calculating the most widely... |
| r-conos |
1.5.2 |
|
|
GPL-3.0-only |
X | X | | | Wires together large collections of single-cell RNA-seq datasets, which... |
| r-consensustme |
0.0.1.9000 |
|
|
GPL-3 |
| | | X | ConsensusTME is a consensus based approach to generating cancer... |
| r-corbi |
0.4_2 |
|
|
GPL |
X | X | | | Provides a bundle of basic and fundamental bioinformatics tools, such... |
| r-corncob |
0.4.1 |
|
|
GPL-2.0-or-later |
| | | X | Statistical modeling for correlated count data using the beta-binomial... |
| r-corpcor |
1.6.8 |
|
|
GPL |
X | X | | | Efficient Estimation of Covariance and (Partial) Correlation |
| r-corrplot |
0.77 |
|
|
GPL |
X | X | | | The corrplot package is a graphical display of a correlation matrix,... |
| r-cp4p |
0.3.6 |
|
|
GPL-3 |
| | | X | Functions to check whether a vector of p-values respects the... |
| r-crbhits |
0.0.7 |
|
|
MIT |
X | X | | | CRBHits: From Conditional Reciprocal Best Hits to Codon Alignments and... |
| r-crisprcleanr |
3.0.0 |
|
|
MIT |
| | | X | Analysis of CRISPR functional genomics, remove false positive due to CNVs. |
| r-crmn |
0.0.21 |
|
|
GPL-3 |
| | | X | Implements the Cross-contribution Compensating Multiple standard... |
| r-cssam |
1.4 |
|
|
LGPL |
X | X | | | Cell-type specific differential expression of a microarray experiment... |
| r-d3heatmap |
0.6.1.1 |
|
|
GPL-3 |
X | X | | | Create interactive heat maps that are usable from the R console, in the... |
| r-dartr |
2.9.7 |
|
|
GPL-3.0-or-later |
X | | | X | Functions are provided that facilitate the import and analysis of SNP... |
| r-data.table |
1.11.6 |
|
|
MPL-2.0 |
X | X | | | Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins,... |
| r-dbchip |
1.1.6 |
|
|
GPL |
X | | | | ChIP-seq differential binding |
| r-ddir |
0.0.3 |
|
|
GPL2 |
| | | X | An R package to access to Omics Discovery Index API |
| r-ddrtree |
0.1.5 |
|
|
Artistic |
X | | | | Provides an implementation of the framework of reversed graph embedding... |
| r-deconcell |
0.1.0 |
|
dev |
GPL-3.0-or-later |
| | | X | DeconCell is an statitsical framework for generating cell proportions... |
| r-deconstructsigs |
1.9.0 |
|
|
GPL |
X | X | | X | Takes sample information in the form of the fraction of mutations in... |
| r-delaporte |
3.0.0 |
|
|
GPL |
X | X | | | Provides probability mass, distribution, quantile, random-variate... |
| r-deldir |
0.1_12 |
|
|
GPL |
X | X | | | Calculates the Delaunay triangulation and the Dirichlet or Voronoi... |
| r-dendextend |
1.1.2 |
|
|
GPL-2 |
X | X | | | Offers a set of functions for extending dendrogram objects in R,... |
| r-densityclust |
0.2.1 |
|
|
GPL |
X | | | | An implementation of the clustering algorithm described by Alex... |
| r-deoptimr |
1.0_8 |
|
|
GPL |
X | X | | | Differential Evolution (DE) stochastic algorithms for global... |
| r-deseqanalysis |
0.7.1 |
|
dev |
AGPL-3.0 |
| | | X | Toolkit for performing differential expression with DESeq2. |
| r-dgeclustering |
0.1.0 |
|
|
MIT |
X | X | | | DGEclustering is an R package for multidimensional clustering of... |
| r-diagram |
1.6.3 |
|
|
GPL |
X | X | | | Visualises simple graphs (networks) based on a transition matrix,... |
| r-diffcorr |
0.4.4 |
|
|
GPL3 |
| | | X | A method for identifying pattern changes between 2 experimental... |
| r-digest |
0.6.12 |
|
|
GPL |
X | X | | | Implementation of a function 'digest()' for the creation of... |
| r-dimsum |
1.3.2 |
|
dev |
MIT |
| | | X | An error model and pipeline for analyzing deep mutational scanning... |
| r-dinamic.duo |
1.0.2 |
|
|
GPL-3.0-only |
| | | X | In tumor tissue, underlying genomic instability can lead to DNA copy... |
| r-diptest |
0.75_7 |
|
|
GPL |
X | X | | | Compute Hartigan's dip test statistic for unimodality /... |
| r-disco |
0.6 |
|
|
GPL |
| | | X | Concordance and discordance of homologous gene regulation allows... |
| r-discriminer |
0.1_29 |
|
|
GPL-3 |
X | X | | | Functions for Discriminant Analysis and Classification purposes... |
| r-disprose |
0.1.6 |
|
|
GPL-3.0-only |
| | | X | Set of tools for molecular probes selection and design of a microarray,... |
| r-dnet |
1.1.7 |
|
|
GPL-2 |
| | | X | The focus of the dnet by Fang and Gough (2014)... |
| r-docopt |
0.4.3.3 |
|
|
MIT |
X | X | | | Define a command-line interface by just giving it a description in the... |
| r-dorng |
1.6 |
|
|
GPL |
X | X | | | This package provides functions to perform reproducible parallel... |
| r-downloader |
0.0.4 |
|
|
GPL-2 |
X | X | | | Provides a wrapper for the download.file function, making it possible... |
| r-dowser |
1.2.0 |
|
|
AGPL-3 |
| | | X | Provides a set of functions for inferring, visualizing, and analyzing B... |
| r-dpeak |
2.0.1 |
|
|
GPL |
X | X | | | This package provides functions for fitting dPeak, a statistical... |
| r-dplyr |
0.5.0 |
|
|
MIT |
X | X | | | A fast, consistent tool for working with data frame like objects, both... |
| r-drc |
3.0_1 |
|
|
GPL-2 |
X | X | | | Analysis of dose-response data is made available through a suite of... |
| r-dsb |
1.0.4 |
|
|
CC0 |
| | | X | Normalizing and denoising protein expression data from droplet-based... |
| r-dt |
0.2 |
|
|
GPL-3 |
X | X | | | Data objects in R can be rendered as HTML tables using the JavaScript... |
| r-dunn.test |
1.3.1 |
|
|
GPL-2 |
X | X | | | Computes Dunn's test (1964) for stochastic dominance and reports... |
| r-dwls |
1.0 |
|
|
GPL-2 |
| | | X | Deconvolution of bulk mRNA data using single-cell RNAseq to provide... |
| r-dynamictreecut |
1.63_1 |
|
|
GPL |
X | X | | | Contains methods for detection of clusters in hierarchical clustering... |
| r-e1071 |
1.6_8 |
|
|
GPL-2 |
X | X | | | Functions for latent class analysis, short time Fourier transform,... |
| r-eacon |
0.3.6 |
|
|
MIT |
| | | X | Easy Copy Number. EaCoN aims to be an all-packed in, user-friendly... |
| r-easydifferentialgenecoexpression |
1.4 |
|
|
GPL-3.0-only |
| | | X | A function that reads in the GEO code of a list of probesets or gene... |
| r-easylift |
0.2.1 |
|
dev |
MIT |
| | | X | A convenience package for converting between popular mouse & human builds. |
| r-ebimetagenomics |
0.6 |
|
|
LGPL-3 |
X | X | | | Functions for querying the EBI Metagenomics Portal... |
| r-ecodist |
2.0.1 |
|
|
GPL |
X | X | | | Dissimilarity-based analysis functions including ordination and Mantel... |
| r-eggnog |
0.3.0 |
|
dev |
AGPL-3.0 |
| | | X | EggNOG database annotations. |
| r-ellipse |
0.3_8 |
|
|
GPL |
X | X | | | This package contains various routines for drawing ellipses and... |
| r-emdbook |
1.3.9 |
|
|
GPL |
X | X | | | Auxiliary functions and data sets for "Ecological Models and... |
| r-empiricalfdr.deseq2 |
1.0.3 |
|
|
GPL-3 |
X | X | | X | Auxiliary functions for the DESeq2 package to simulate read counts... |
| r-enchantr |
0.1.3 |
|
|
AGPL-3 |
| | | X | Analysis of immune repertoires. QC and reports for the analysis of... |
| r-enrichr |
1.0 |
|
|
GPL |
| | | X | Provides an R interface to all 'Enrichr' databases, a web-based... |
| r-epic |
1.1.7 |
|
|
other |
X | X | | X | Estimate the Proportion of Immune and Cancer cells from bulk gene... |
| r-epitrace |
0.0.1.3 |
|
dev |
GPL-3.0-or-later |
| | | X | Inference of cell age and phylogeny from single cell ATAC data. |
| r-erah |
2.0.1 |
|
|
GPL-2.0-or-later |
X | X | | | Automated compound deconvolution, alignment across samples, and... |
| r-exactranktests |
0.8_29 |
|
|
GPL-2|GPL-3 |
X | X | | | Computes exact conditional p-values and quantiles using an... |
| r-exomedepth |
1.1.16 |
|
|
GPL-3 |
X | X | | | Calls copy number variants (CNVs) from targeted sequence data,... |
| r-extrafont |
0.17 |
|
|
GPL-2 |
X | X | | | Tools to using fonts other than the standard PostScript fonts. This... |
| r-extrafontdb |
1.0 |
|
|
GPL-2 |
X | X | | | Package for holding the database for the extrafont package |
| r-eztune |
3.1.1 |
|
|
GPL-3 |
| | | X | Contains two functions that are intended to make tuning supervised... |
| r-facets |
0.6.2 |
|
|
GPL |
X | X | | | Cellular Fraction and Copy Numbers from Tumor Sequencing |
| r-factominer |
1.38 |
|
|
GPL |
X | X | | | Exploratory data analysis methods to summarize, visualize and describe... |
| r-fail |
1.3 |
|
|
BSD_3_clause |
X | X | | | More comfortable interface to work with R data or source files in a... |
| r-fastbaps |
1.0.8 |
|
|
MIT |
X | X | | X | A fast approximation to a Dirichlet Process Mixture model (DPM) for... |
| r-fastcluster |
1.1.20 |
|
|
FreeBSD |
X | X | | | This is a two-in-one package which provides interfaces to both R and... |
| r-fastica |
1.2_0 |
|
|
GPL |
X | X | | | Implementation of FastICA algorithm to perform Independent Component... |
| r-fastmatch |
1.1_0 |
|
|
GPL-2 |
X | X | | | Package providing a fast match() replacement for cases that require... |
| r-fastqcr |
0.1.2 |
|
|
GPL-2 |
X | X | | | 'FASTQC' is the most widely used tool for evaluating the... |
| r-fateid |
0.1.8 |
|
|
GPL-3 |
X | | | X | Application of 'FateID' allows computation and visualization of... |
| r-fda |
2.4.4 |
|
|
GPL |
X | X | | | These functions were developed to support functional data analysis as... |
| r-ff |
2.2_13 |
|
|
GPL-2 |
X | | | | The ff package provides data structures that are stored on disk but... |
| r-fftwtools |
0.9.7 |
|
|
GPL |
X | X | | | Provides a wrapper for several FFTW functions. This package provides... |
| r-fgwas |
0.3.6 |
|
|
GNU |
X | X | | X | GWAS tools for longitudinal genetic traits based on fGWAS statistical model. |
| r-fields |
8.10 |
|
|
GPL |
X | X | | | For curve, surface and function fitting with an emphasis on splines,... |
| r-findpython |
1.0.1 |
|
|
MIT |
X | X | | | Package designed to find an acceptable python binary. |
| r-firebrowser |
1.1.35 |
|
dev |
MIT |
| | | X | An R client for broads firehose pipeline, providing TCGA data sets. |
| r-fitdistrplus |
1.0_6 |
|
|
GPL |
X | X | | | Extends the fitdistr function (of the MASS package) with several... |
| r-flashclust |
1.01_2 |
|
|
GPL |
X | X | | | Fast implementation of hierarchical clustering |
| r-flexclust |
1.3_4 |
|
|
GPL-2 |
X | X | | | The main function kcca implements a general framework for k-centroids... |
| r-flexmix |
2.3_14 |
|
|
GPL |
X | X | | | A general framework for finite mixtures of regression models using the... |
| r-flowr |
0.9.10 |
|
|
MIT |
X | X | | | This framework allows you to design and implement complex pipelines,... |
| r-fmsb |
0.6.3 |
|
|
GPL |
X | X | | X | Several utility functions for the book entitled "Practices of... |
| r-fnn |
1.1 |
|
|
GPL |
X | X | | | Cover-tree and kd-tree fast k-nearest neighbor search algorithms and... |
| r-fpc |
2.1_10 |
|
|
GPL |
X | X | | | Various methods for clustering and cluster validation. Fixed point... |
| r-freerange |
0.2.8 |
|
dev |
MIT |
X | X | | X | Generate and manipulate genomic ranges. |
| r-funr |
0.2.0 |
|
|
MIT |
X | X | | | A small utility which wraps Rscript and provides access to all R... |
| r-funrar |
1.2.2 |
|
|
GPL |
X | X | | | Computes functional rarity indices as proposed by Violle et al. (2017)... |
| r-futile.logger |
1.4.1 |
|
|
LGPL-3 |
X | X | | | Provides a simple yet powerful logging utility. Based loosely on log4j,... |
| r-futile.options |
1.0.0 |
|
|
LGPL-3 |
X | X | | | A scoped options management framework |
| r-future |
1.2.0 |
|
|
LGPL |
X | X | | | A Future API for R is provided. In programming, a future is an... |
| r-gam |
1.14_4 |
|
|
GPL-2 |
X | X | | | Functions for fitting and working with generalized additive models, as... |
| r-gamlss |
5.0_0 |
|
|
GPL-2 |
X | X | | | Functions for fitting, displaying and checking GAMLSS Models. |
| r-gamlss.data |
5.0_0 |
|
|
GPL-2 |
X | X | | | Data for GAMLSS models. |
| r-gamlss.dist |
5.0_0 |
|
|
GPL-2 |
X | X | | | The different distributions used for the response variables in GAMLSS modelling. |
| r-gap |
1.2.1 |
|
|
GPL |
X | X | | | It is designed as an integrated package for genetic data analysis of... |
| r-garnett |
0.2.8 |
|
dev |
MIT |
| | | X | Bioconda-installable version of Garnett cell classification tool. |
| r-gbm |
2.1.3 |
|
|
GPL |
X | X | | | An implementation of extensions to Freund and Schapire's AdaBoost... |
| r-gchromvar |
0.3.2 |
|
dev |
MIT |
| | | X | R package for computing cell-type specific GWAS enrichments from... |
| r-gdtools |
0.1.4 |
|
|
GPL-3 |
X | X | | | Useful tools for writing vector graphics devices. |
| r-geiger |
2.0.6.2 |
|
|
GPL |
X | X | | | Methods for fitting macroevolutionary models to phylogenetic trees. |
| r-genabel |
1.8_0 |
|
|
GPL |
X | X | | | A package for genome-wide association analysis between quantitative or... |
| r-genabel.data |
1.0.0 |
|
|
GPL |
X | X | | | GenABEL.data package consists of a data set used by GenABEL functions |
| r-geneexpressionfromgeo |
0.9 |
|
|
GPL-3.0-only |
| | | X | A function that reads in the GEO code of a gene expression dataset,... |
| r-genemodel |
1.1.0 |
|
|
GPL-2 |
X | X | | | Using simple input, this package creates plots of gene models. Users... |
| r-genenet |
1.2.13 |
|
|
GPL |
X | X | | | Analyzes gene expression (time series) data with focus on the inference... |
| r-genometricorr |
1.1.17 |
|
|
Artistic-2.0 |
X | X | | | Genometric Correlation (GenometriCorr) is an R package for spatial... |
| r-genomictools |
0.2.9.7 |
|
|
GPL-2 |
X | X | | | A loose collection of tools for the analysis of expression and genotype... |
| r-genomictools.filehandler |
0.1.5.9 |
|
|
GPL-2 |
| | | X | A collection of I/O tools for handling the most commonly used genomic... |
| r-geoaxe |
0.1.0 |
|
|
MIT |
X | X | | | Split 'geospatial' objects into pieces. Includes support for... |
| r-geomap |
2.3_8 |
|
|
GPL |
X | X | | | Set of routines for making Map Projections (forward and inverse),... |
| r-george |
1.0.1 |
|
|
GPL |
X | | | | geoRge, a computational tool for stable isotope labelling detection in... |
| r-getoptlong |
0.1.0 |
|
|
GPL |
X | X | | | This is yet another command-line argument parser which wraps the ... |
| r-ggally |
1.3.0 |
|
|
GPL |
X | X | | | The R package 'ggplot2' is a plotting system based on the... |
| r-ggalt |
0.4.0 |
|
|
AGPL |
X | X | | | A compendium of new geometries, coordinate systems, statistical ... |
| r-gganatogram |
0.0.1 |
|
dev |
GPL-2.0-only |
| | | X | Create anatogram images for different organisms |
| r-ggbiplot |
0.55 |
|
|
GPL-2 |
X | X | | | A biplot based on ggplot2 |
| r-ggcoverage |
0.7.1 |
|
|
MIT |
| | | X | The goal of 'ggcoverage' is to simplify the process of... |
| r-ggdendro |
0.1_17 |
|
|
GPL-2 |
X | X | | | This is a set of tools for dendrograms and tree plots using... |
| r-ggmsa |
1.0.2 |
|
|
Artistic-2.0 |
| | | X | Supports visualizing multiple sequence alignment of DNA and protein... |
| r-ggplot2 |
2.2.1 |
|
|
GPLv2 |
X | X | | | A system for 'declaratively' creating graphics, based on... |
| r-ggrasp |
1.0 |
|
|
GPL-2 |
X | X | | | Given a group of genomes and their relationship with each other, the... |
| r-ggrepel |
0.6.5 |
|
|
GPL-2 |
X | X | | | Provides text and label geoms for 'ggplot2' that help to avoid... |
| r-ggsignif |
0.4.0 |
|
|
GPL-3 |
X | X | | | Enrich your 'ggplots' with group-wise comparisons. This package... |
| r-giant |
1.2 |
|
|
Artistic-2.0 |
X | X | | | Toolbox for various enrichment analysis methods and quantification of... |
| r-gkmsvm |
0.83.0 |
|
|
GPL-2.0-or-later |
X | X | | | Imports the 'gkmSVM' v2.0 functionalities into R... |
| r-globaloptions |
0.0.8 |
|
|
GPL |
X | X | | | It provides more controls on the option values such as validation and... |
| r-globals |
0.7.1 |
|
|
LGPL |
X | X | | | Identifies global ("unknown") objects in R expressions by code... |
| r-gmd |
0.3.3 |
|
|
GPL |
X | X | | | GMD is a package for non-parametric distance measurement between two... |
| r-gmodels |
2.16.2 |
|
|
GPL-2 |
X | X | | | Various R programming tools for model fitting. |
| r-gmwt |
1.2 |
|
|
GPL-2.0-only |
X | X | | | Generalized Mann-Whitney type tests based on probabilistic indices and... |
| r-goalie |
0.7.7 |
|
dev |
AGPL-3 |
X | X | | X | Assertive check functions for defensive R programming. |
| r-goeveg |
0.4.2 |
|
|
GPL |
X | X | | | A collection of functions useful in (vegetation) community analyses and... |
| r-googlevis |
0.5.10 |
|
|
GPL |
X | X | | | R interface to Google Charts API, allowing users to create interactive... |
| r-gpca |
1.0 |
|
|
GPL |
X | X | | | This package implements guided principal components analysis for the... |
| r-gplots |
2.17.0 |
|
|
GPL-2 |
X | | | | Various R programming tools for plotting data, including: - calculating... |
| r-gprofiler |
0.6.1 |
|
|
GPL |
X | X | | | Functional enrichment analysis, gene identifier conversion and mapping... |
| r-gpseq |
0.5 |
|
|
GPL-2 |
X | X | | | Some functions for modeling sequence read counts as a generalized... |
| r-grain |
1.4.5 |
|
|
GPL-2.0-or-later |
X | X | | | Probability propagation in graphical independence networks, also known... |
| r-grbase |
2.0.3 |
|
|
GPL-2.0-or-later |
X | X | | | The 'gRbase' package provides graphical modelling features used... |
| r-grimport |
0.9_0 |
|
|
GPL |
X | X | | | Functions for converting, importing, and drawing PostScript pictures... |
| r-gsalib |
2.1 |
|
|
MIT |
X | X | | | This package contains utility functions used by the Genome Analysis... |
| r-gsmoothr |
0.1.7 |
|
|
LGPL |
X | X | | | Tools rewritten in C for various smoothing tasks |
| r-gsubfn |
0.6_6 |
|
|
GPL |
X | X | | | gsubfn is like gsub but can take a replacement function or certain... |
| r-guilds |
1.3 |
|
|
GPL-2 |
X | X | | | A collection of sampling formulas for the unified neutral model of... |
| r-gwasexacthw |
1.01 |
|
|
GPL-3 |
X | X | | | This package contains a function to do exact Hardy-Weinburg testing... |
| r-gwpcr |
1.0.4 |
|
|
AGPLv3 |
X | X | | | Implements the necessary distributions and parameter estimation... |
| r-haplo.stats |
1.7.7 |
|
|
GPL |
X | X | | | Routines for the analysis of indirectly measured haplotypes. The... |
| r-hardyweinberg |
1.6.3 |
|
|
GPL |
X | X | | | Contains tools for exploring Hardy-Weinberg equilibrium (Hardy, 1908; ... |
| r-harmony |
0.1 |
|
dev |
GPL-3.0-only |
X | X | | | Fast, sensitive and accurate integration of single-cell data with Harmony |
| r-hdrcde |
3.1 |
|
|
GPL |
X | X | | | Computation of highest density regions in one and two dimensions,... |
| r-hemdag |
2.7.4 |
doc |
dev |
GPL-3.0-or-later |
X | X | | | a collection of Hierarchical Ensemble Methods (HEMs) for Directed... |
| r-hgvsparser |
0.1.0 |
doc |
dev |
GPL-3.0-only |
| | | X | hgvsParseR |
| r-hierfstat |
0.04_22 |
|
|
GPL |
X | X | | | Allows the estimation of hierarchical F-statistics from haploid or... |
| r-histonehmm |
1.8 |
|
dev |
GPL |
X | X | | | histoneHMM is a software to analyse ChIP-seq data of histone... |
| r-htmltools |
0.3 |
|
|
GPL |
X | X | | | Tools for HTML generation and output. |
| r-htmlwidgets |
0.5 |
|
|
MIT |
X | | | | A framework for creating HTML widgets that render in various contexts... |
| r-htscluster |
2.0.11 |
|
|
GPL |
| | | X | A Poisson mixture model is implemented to cluster genes from high-... |
| r-htssip |
1.4.1 |
|
|
GPL-2 |
X | X | | X | Functions for analyzing high throughput sequencing stable isotope... |
| r-hwriter |
1.3.2 |
|
|
LGPL-2.1 |
X | X | | | Easy-to-use and versatile functions to output R objects in HTML format |
| r-ic10 |
2.0.2 |
|
|
GPL-3.0-or-later |
X | X | | X | Implementation of the classifier described in the paper... |
| r-ic10trainingdata |
1.0.1 |
|
|
GPL-3 |
X | X | | | Training datasets for iC10; which implements the classifier described... |
| r-ichorcna |
0.5.1 |
|
|
GPL-3.0-only |
X | X | | X | Estimating tumor fraction in cell-free DNA from ultra-low-pass whole... |
| r-icluster |
2.1.0 |
|
|
GPL |
X | X | | | Integrative clustering of multiple genomic data types using a joint... |
| r-idpmisc |
1.1.17 |
|
|
GPL |
X | X | | | The IDPmisc package contains different high-level graphics functions... |
| r-idr |
1.2 |
|
|
GPL |
X | X | | | This is a package for estimating the copula mixture model and plotting... |
| r-immucellaimouse |
1.0 |
|
|
GPL |
| | | X | ImmuCellAI-mouse is a tool to estimate the abundance of 36 immune cells... |
| r-immunedeconv |
2.1.2 |
|
|
BSD_3_clause |
| | | X | collection of methods for immune cell deconvolution of bulk RNA-seq samples. |
| r-imp4p |
0.7 |
|
|
GPL-3 |
X | X | | | Functions to analyse missing value mechanisms and to impute data sets... |
| r-imputelcmd |
2.1 |
|
|
GPL-2.0-or-later |
| | | X | The package contains a collection of functions for left-censored... |
| r-inline |
0.3.14 |
|
|
LGPL |
X | X | | | Functionality to dynamically define R functions and S4 methods with... |
| r-inlinedocs |
2013.9.3 |
|
|
GPL-2 |
X | X | | | Generates Rd files from R source code with comments. The main features... |
| r-intego |
2.0 |
|
|
GPL3 |
X | X | | | An unsupervised gene clustering algorithm based on the integration of... |
| r-interpretmsspectrum |
1.3.3 |
|
|
GPL-3.0-only |
| | | X | Annotate and interpret deconvoluted mass spectra (mass*intensity pairs)... |
| r-intlim |
1.1.0 |
|
|
GPL-2.0-only |
| | | X | Integration of Omics Data Using Linear Modeling |
| r-ipo |
1.7.5 |
|
|
GPL |
X | X | | | The outcome of XCMS data processing strongly depends on the parameter... |
| r-isogene |
1.0_24 |
|
|
GPL-3 |
| | | X | Offers framework for testing for monotonic relationship between gene... |
| r-isva |
1.9 |
|
|
GPL-2 |
| | | X | Independent Surrogate Variable Analysis is an algorithm for feature... |
| r-itertools |
0.1_3 |
|
|
GPL-2 |
X | X | | | Various tools for creating iterators, many patterned after functions in... |
| r-jackstraw |
1.3.17 |
|
|
GPL-2.0-only |
| | | X | Test for association between the observed data and their systematic... |
| r-jetset |
3.4.0 |
|
|
Artistic-2.0 |
| | | X | On Affymetrix gene expression microarrays, a single gene may be... |
| r-jpeg |
0.1.8 |
|
|
GPL-2 |
X | X | | | None |
| r-jsonlite |
0.9.19 |
|
|
MIT |
X | X | | | A fast JSON parser and generator optimized for statistical data and the... |
| r-kaos |
0.1.0 |
|
|
GPL |
X | X | | | Sequences encoding by using the chaos game representation. Löchel et... |
| r-kernlab |
0.9_25 |
|
|
GPL |
X | X | | | Kernel-based machine learning methods for classification, regression,... |
| r-kinship2 |
1.6.4 |
|
|
GPL |
X | X | | X | Routines to handle family data with a pedigree object. The initial... |
| r-klar |
0.6_12 |
|
|
GPL-2 |
X | X | | | Miscellaneous functions for classification and visualization developed... |
| r-km.ci |
0.5_2 |
|
|
GPL-2|GPL-3 |
X | X | | | Computes various confidence intervals for the Kaplan-Meier estimator,... |
| r-kmsurv |
0.1_5 |
|
|
GPL |
X | X | | | Data sets and functions for Klein and Moeschberger (1997),... |
| r-knitr |
1.12.3 |
|
|
GPL-2 |
X | X | | | Provides a general-purpose tool for dynamic report generation in R... |
| r-knitrbootstrap |
1.0.0 |
|
|
MIT |
X | X | | | A framework to create Bootstrap 3 HTML reports from knitr Rmarkdown. |
| r-kriging |
1.1 |
|
|
GPL-2 |
X | X | | | Simple and highly optimized ordinary kriging algorithm to plot geographical data |
| r-ks |
1.10.6 |
|
|
GPL-2 |
X | X | | | Kernel smoothers for univariate and multivariate data, including... |
| r-lambda.r |
1.1.7 |
|
|
LGPL-3 |
X | X | | | A language extension to efficiently write functional programs in R.... |
| r-ldrtools |
0.2_1 |
|
|
GPL |
X | X | | | Linear dimension reduction subspaces can be uniquely defined using... |
| r-ldweaver |
1.5.1 |
|
|
GPL-3.0-or-later |
X | X | | | Perform genomewide epistasis analysis by evaluating the LD structure in... |
| r-leapp |
1.3 |
|
|
GPL-2.0-or-later |
X | X | | X | These functions take a gene expression value matrix, a primary... |
| r-leaps |
2.9 |
|
|
GPL-2|GPL-3 |
X | X | | | Regression subset selection including exhaustive search |
| r-learnbayes |
2.15 |
|
|
GPL |
X | X | | | LearnBayes contains a collection of functions helpful in learning the... |
| r-leidenbase |
0.1.31 |
|
|
GPL-2.0-only, |
X | X | | | An R to C interface that runs the Leiden community detection algorithm... |
| r-liger |
2.1.0 |
doc |
dev |
GPL-3.0-or-later |
X | X | | | Uses an extension of nonnegative matrix factorization to identify... |
| r-linxreport |
1.0.0 |
|
|
MIT |
| | | X | LINX Result Reporter |
| r-lipidomer |
0.1.2 |
|
|
GPL-3.0-only |
| | | X | Create lipidome-wide heatmaps of statistics with the... |
| r-lisi |
1.0 |
|
|
GPL-3 |
X | X | | X | A method to assess how well mixed cells with different labels are in... |
| r-listenv |
0.6.0 |
|
|
LGPL |
X | X | | | List environments are environments that have list-like properties. For... |
| r-lme4qtl |
0.1.10 |
|
|
GPL |
X | X | | | Linear mixed models (lme4) with flexible covariance structure for qtl... |
| r-lncpipereporter |
0.1.1 |
|
|
GPL-2 |
X | X | | | Automatically Aggregating and Summarizing lncRNA Analysis Results for... |
| r-locfdr |
1.1_8 |
|
|
GPL-2 |
X | | | | Computation of local false discovery rates. |
| r-locfit |
1.5_9.1 |
|
|
GPL |
X | X | | | Local regression, likelihood and density estimation. |
| r-locuszoomr |
0.3.8 |
|
|
GPL-3 |
| | | X | Publication-ready regional gene locus plots similar to those produced... |
| r-logging |
0.7_103 |
|
|
GPL |
X | X | | | logging is a pure R package that implements the ubiquitous log4j package. |
| r-longitudinal |
1.1.12 |
|
|
GPL |
X | X | | | Contains general data structures and functions for longitudinal data... |
| r-loom |
0.2.0.2 |
|
|
GPL-3 |
X | X | | X | An interface for the single-cell RNAseq-oriented loom format. Loom... |
| r-loomr |
0.2.0_beta |
|
|
GPL-3 |
| | | X | An interface for the single-cell RNAseq-oriented loom format. Loom... |
| r-loose.rock |
1.0.13 |
|
|
GPL |
| | | X | Collection of functions to improve work-flow in survival analysis and... |
| r-lsd |
3.0 |
|
|
Unlimited |
X | X | | | Create lots of colorful plots in a plethora of variations (try the LSD... |
| r-lymphclon |
1.3.0 |
|
|
LGPL-2 |
| | | X | We provide a clonality score estimator that takes full advantage of the... |
| r-magrittr |
1.5 |
|
|
MIT |
X | X | | | Provides a mechanism for chaining commands with a new forward-pipe... |
| r-maldiquant |
1.18 |
|
|
GPL |
X | X | | | A complete analysis pipeline for matrix-assisted laser... |
| r-maldiquantforeign |
0.12 |
|
|
GPL |
X | X | | X | Functions for reading (tab, csv, Bruker fid, Ciphergen XML, mzXML,... |
| r-maldirppa |
1.0.1 |
|
|
GPL |
X | X | | | Provides methods for quality control and robust pre-processing and... |
| r-mams |
1.0.1 |
doc |
dev |
MIT |
| | | X | R package for Matrix and Analysis Metadata Standards. |
| r-matlab |
1.0.2 |
|
|
Artistic-2.0 |
X | X | | | Emulate MATLAB code using R. |
| r-matrixeqtl |
2.1.1 |
|
|
LGPL-3 |
X | X | | | Matrix eQTL is designed for fast eQTL analysis on large datasets.... |
| r-matrixstats |
0.51.0 |
|
|
Artistic-2.0 |
X | X | | | High-performing functions operating on rows and columns of matrices,... |
| r-maxlik |
1.3_4 |
|
|
GPL |
X | | | | Functions for Maximum Likelihood (ML) estimation and non-linear... |
| r-mba |
0.0_8 |
|
|
GPL |
X | X | | | Scattered data interpolation with Multilevel B-Splines |
| r-mclust |
5.2 |
|
|
GPL |
X | X | | | Normal Mixture Modelling fitted via EM algorithm for Model-Based... |
| r-mcpcounter |
1.1.0 |
|
|
GPL-3 |
X | X | | X | Estimating tissue-infiltrating immune and other stromal subpopulations... |
| r-merge-kallisto |
0.6 |
|
|
Apache |
| | | X | merge_kallisto |
| r-mess |
0.5.5 |
|
|
GPL-2 |
X | X | | | A mixed collection of useful and semi-useful diverse statistical... |
| r-metablastr |
0.3.2 |
|
|
GPL-2.0-or-later |
X | X | | | The metablastr package harnesses the power of BLAST by providing... |
| r-metaboanalyst |
2.0.0 |
|
|
GPL-3 |
| | | X | MetaboAnalystR 2.0 contains the R functions and libraries underlying... |
| r-metacoder |
0.3.8 |
doc |
|
GPL-2 |
X | X | | | A set of tools for parsing, manipulating, and graphing data classified... |
| r-metadig |
0.2.1 |
|
|
Apache-2.0 |
| | | X | A set of utility methods for authoring MetaDIG checks in R. |
| r-metalonda |
1.1.8 |
|
|
MIT |
X | X | | X | Identify time intervals of differentially abundant metagenomics... |
| r-metama |
3.1.3 |
|
|
GPL |
X | X | | X | Combines either p-values or modified effect sizes from different... |
| r-metap |
1.4 |
|
|
GPL-2 |
| | | X | The canonical way to perform meta-analysis involves using effect sizes.... |
| r-metarnaseq |
1.0.2 |
|
|
GPL |
X | X | | | Implementation of two p-value combination techniques (inverse normal... |
| r-metstat |
1.0 |
|
|
Apache |
X | X | | | A diverse collection of metabolomics related statistical tools. |
| r-mfassignr |
1.1.2 |
|
|
GPL-3.0-or-later |
| | | X | The MFAssignR package was designed for multi-element molecular formula... |
| r-mgsz |
1.0 |
|
|
GPL |
| | | X | Performs gene set analysis based on GSZ scoring function and asymptotic... |
| r-micropan |
1.2 |
|
|
GPL-2 |
X | X | | | A collection of functions for computations and visualizations of... |
| r-microseq |
1.2 |
|
|
GPL-2 |
X | X | | | Basic functions for microbial sequence data analysis. |
| r-millefy |
0.1.9 |
|
|
MIT |
| | | X | Millefy: Genome browser-like visualization of single-cell RNA-seq dataset. |
| r-minems2 |
0.9.3 |
|
|
GPL-3.0 |
X | X | | | Mine MS-MS spectra using a frequent usbgraph mining approach. |
| r-minionqc |
1.4.2 |
|
|
MIT |
X | X | | X | Quality control for MinION sequencing data |
| r-minpack.lm |
1.2_1 |
|
|
GPL-3 |
X | | | | The nls.lm function provides an R interface to lmder and lmdif from the... |
| r-misc3d |
0.8_4 |
|
|
GPL |
X | X | | | A collection of miscellaneous 3d plots, including isosurfaces. |
| r-misctools |
0.6_22 |
|
|
GPL |
X | | | | Miscellaneous small tools and utilities. Many of them facilitate the... |
| r-misha |
4.1.0 |
|
|
GPL-2 |
X | X | | | Toolkit for analysis of genomic data |
| r-missforest |
1.4 |
|
|
GPL |
X | X | | | The function 'missForest' in this package is used to impute... |
| r-mitools |
2.3 |
|
|
GPL-2 |
X | X | | | Tools to perform analyses and combine results from multiple-imputation datasets. |
| r-mixedcca |
1.5.2 |
|
|
GPL-3.0-only |
X | X | | | Semi-parametric approach for sparse canonical correlation analysis |
| r-mixkernel |
0.9 |
|
|
GPL |
X | X | | X | Kernel-based methods are powerful methods for integrating ... |
| r-mixomics |
6.3.1 |
|
|
GPL |
X | X | | | Multivariate methods are well suited to large omics data sets where the... |
| r-mixtools |
1.1.0 |
|
|
GPL |
X | X | | | Analyzes finite mixture models for various parametric and... |
| r-mkmisc |
1.9 |
|
|
LGPL-3.0-only |
| | | X | Contains several functions for statistical data analysis; e.g. for... |
| r-mlgt |
0.16 |
|
|
GPL |
X | X | | | Processing and analysis of high throughput (Roche 454) sequences... |
| r-mmcpcounter |
1.1.0 |
|
|
GPL-3 |
| | | X | Murine version of MCP-counter, a tool to estimate the immune and... |
| r-mmgenome |
0.7.1 |
|
|
AGPL-3 |
X | X | | | Tools for extracting individual genomes from metagenomes |
| r-mmod |
1.3.3 |
|
|
MIT |
X | X | | | Provides functions for measuring population divergence from genotypic data. |
| r-momf |
0 |
|
|
GPL-2 |
X | X | | | The package can fit single RNA-seq data set(SOMF) and multiple RNA-seq... |
| r-momr |
1.1 |
|
|
Artistic-2.0 |
X | X | | | 'MetaOMineR' suite is a set of R packages that offers many... |
| r-monocle3 |
1.3.1 |
|
dev |
MIT |
X | X | | X | An analysis toolkit for single-cell RNA-seq. |
| r-motifbinner |
2.0.0 |
|
|
GPL3 |
X | X | | | MotifBinner processes high-throughput sequencing data of an RNA virus... |
| r-mqtl |
1.0 |
|
|
GPL |
X | X | | | mQTL provides a complete QTL analysis pipeline for metabolomic data. ... |
| r-msm |
1.6.7 |
|
|
GPL |
X | X | | | Functions for fitting continuous-time Markov and hidden Markov... |
| r-mspbwt |
0.1.0 |
doc |
dev |
GPL-3.0-only |
X | X | | | Multi Symbol Positional Burrows Wheeler Transform |
| r-msqrob |
0.7.7 |
|
|
GPL |
X | | | X | Robust statistical inference for quantitative LC-MS proteomics. |
| r-multicool |
0.1_10 |
|
|
GPL-2 |
X | X | | | A set of tools to permute multisets without loops or hash tables and to... |
| r-multitaper |
1.0.11 |
|
|
GPL-2|GPL-3 |
X | X | | | Implements multitaper spectral analysis using discrete prolate... |
| r-music |
0.2.0 |
|
|
GPL-3 |
| | | X | Companion package to: A bulk tissue deconvolution method with... |
| r-mutationalpatterns |
0.2b |
|
|
MIT |
X | X | | | R package for extracting and visualizing mutational patterns in base... |
| r-mutoss |
0.1_12 |
|
|
GPL |
X | X | | X | Designed to ease the application and comparison of multiple hypothesis... |
| r-mutsigextractor |
1.29 |
|
|
GPL-3.0-only |
| | | X | Extract mutational signatures from VCF files |
| r-mvr |
1.33.0 |
|
|
GPL |
X | X | | | This is a non-parametric method for joint adaptive mean-variance... |
| r-mytai |
0.9.3 |
|
|
GPL-2.0-or-later |
X | X | | | Investigate the evolution of biological processes by capturing... |
| r-nabor |
0.5.0 |
|
|
BSD |
X | X | | X | An R wrapper for 'libnabo', an exact or approximate k nearest... |
| r-nam |
1.6.4 |
|
|
GPL-3 |
X | X | | | Designed for association studies in nested association mapping (NAM)... |
| r-nanopore |
0.2.9 |
|
dev |
MPL-2.0 |
X | X | | | R methods, associated with Nanopore tutorials, for analysis and... |
| r-nanostringnorm |
1.2.1.1 |
|
|
GPL-2.0-only |
X | X | | X | A set of tools for normalizing, diagnostics and visualization of... |
| r-nastiseq |
1.0 |
|
|
GPL-2.0 |
X | X | | | Pairs of RNA molecules transcribed from partially or entirely... |
| r-nbpseq |
0.3.1 |
|
|
GPL-2.0-only |
X | X | | | Negative Binomial (NB) models for two-group comparisons and regression... |
| r-ncbit |
2013.03.29 |
|
|
GPL |
X | X | | | making NCBI taxonomic data locally available and searchable as an R object |
| r-netcomi |
1.1.0 |
|
|
GPL-3.0-only |
| | | X | Network Construction and Comparison for Microbiome Data |
| r-ngsplot |
2.63 |
|
|
GPL-2.0 |
X | X | | X | Quick mining and visualization of NGS data by integrating genomic databases |
| r-ngsplotdb-hg19 |
3.00 |
|
|
GPL-2.0 |
X | X | | | HG19 genome database for NGSplot |
| r-ngsplotdb-hg38 |
3.00 |
|
|
GPL-2.0 |
X | X | | X | HG19 genome database for NGSplot |
| r-ngsplotdb-mm10 |
3.00 |
|
|
GPL-2.0 |
X | X | | X | MM10 genome database for NGSplot |
| r-nhmmfdr |
1.0.6 |
|
|
GPL |
X | | | | The NHMMfdr package implements the non-homogeneous Hidden Markov Model... |
| r-nleqslv |
3.2 |
|
|
GPL |
X | X | | | Solve a system of nonlinear equations using a Broyden or a Newton... |
| r-nodiv |
1.3.0 |
|
|
MIT |
X | X | | | An implementation of the nodiv algorithm, see Borregaard, M.K., Rahbek,... |
| r-noisyr |
1.0.0 |
|
|
GPL-2.0-only |
| | | X | Quantifies and removes technical noise from high-throughput sequencing... |
| r-nor1mix |
1.2_1 |
|
|
GPL |
X | X | | | Onedimensional Normal Mixture Models Classes, for, e.g., density... |
| r-nozzle.r1 |
1.1_1 |
|
|
LGPL-2 |
X | X | | | The Nozzle package provides an API to generate HTML reports with... |
| r-oai |
0.2.2 |
|
|
MIT |
X | X | | | A general purpose client to work with any 'OAI-PMH' (Open... |
| r-oncopharmadb |
1.9.2 |
|
dev |
MIT |
| | | X | Targeted and non-targeted anticancer drugs and drug regimens |
| r-ontologyplot |
1.7 |
|
|
GPL-2.0-or-later |
| | | X | Functions for visualising sets of ontological terms using the... |
| r-openxlsx |
4.0.17 |
|
|
GPL-3 |
X | X | | | Simplifies the creation of Excel .xlsx files by providing a high level... |
| r-optparse |
1.3.2 |
|
|
GPL |
X | X | | | A command line parser inspired by Python's 'optparse'... |
| r-ore |
1.3.0 |
|
|
BSD_3_clause |
X | X | | | Provides an alternative to R's built-in functionality for handling... |
| r-orqa |
0.2.1 |
|
|
GPL |
X | X | | | Assess repeatability, accuracy and corss-platform agreement of... |
| r-outliers |
0.14 |
|
|
GPL |
X | X | | | A collection of some tests commonly used for identifying outliers. |
| r-pack |
0.1_1 |
|
|
GPL-3 |
X | X | | | Functions to easily convert data to binary formats other... |
| r-pairadise |
1.0.0 |
|
|
MIT |
| | | X | PAIRADISE - Paired Replicate Analysis of Differential Splicing Events |
| r-pamr |
1.55 |
|
|
GPL-2 |
X | X | | | Some functions for sample classification in microarrays |
| r-panther |
0.5.0 |
|
dev |
AGPL-3.0 |
| | | X | PANTHER database annotations. |
| r-params |
0.4 |
|
|
GPL-2 |
X | X | | | An interface to simplify organizing parameters used in a package, using... |
| r-pathfindr |
2.4.2 |
doc |
dev |
MIT |
| | | X | Enrichment analysis enables researchers to uncover mechanisms... |
| r-pathosurveilr |
0.3.0 |
|
|
MIT |
| | | X | Utilities for interacting with the pathogensurveillance pipeline. |
| r-pathwaytmb |
0.1.3 |
|
|
GPL-2.0-or-later |
| | | X | A systematic bioinformatics tool to develop a new pathway-based gene... |
| r-patpro |
1.1.0 |
|
|
GPL-3 |
X | X | | | Quickly and easily visualize longitudinal microbiome profiles using... |
| r-pcalg |
2.6_12 |
|
|
GPL-2 |
X | X | | | Functions for causal structure learning and causal inference using... |
| r-pcapp |
1.9_60 |
|
|
GPL |
X | X | | | Robust PCA by Projection Pursuit |
| r-pctgcdata |
0.3.0 |
|
|
GPL |
X | X | | X | Provides GC percentage of a 1 kilobase window at a genomic position for... |
| r-peer |
1.3 |
|
|
GPL |
X | | | | PEER is a collection of Bayesian approaches to infer hidden... |
| r-pegas |
0.11 |
|
|
GPL |
X | X | | | Functions for reading, writing, plotting, analysing, and manipulating... |
| r-penalized |
0.9.47 |
|
|
GPL-2 |
X | X | | | Fitting possibly high dimensional penalized regression models. The... |
| r-perfmeas |
1.2.5 |
|
|
GPL-2.0-or-later |
X | X | | | Package that implements different performance measures for... |
| r-permute |
0.8_4 |
|
|
GPL-2 |
X | X | | | A set of restricted permutation designs for freely exchangeable, line... |
| r-phangorn |
2.4.0 |
|
|
GPL |
X | X | | | Package contains methods for estimation of phylogenetic trees and... |
| r-pheatmap |
1.0.8 |
|
|
GPL-2 |
X | X | | | Implementation of heatmaps that offers more control over dimensions and... |
| r-phewas |
0.99.6 |
|
|
GPL-3 |
X | X | | | Phenome Wide Association Studies (PheWAS) - Functions to perform... |
| r-phonr |
1.0_3 |
|
|
GPL-3 |
X | X | | | Tools for phoneticians and phonologists, including functions for... |
| r-phyext2 |
0.0.4 |
|
|
GPL-3 |
X | X | | X | Based on (but not identical to) the no-longer-maintained package... |
| r-phylobase |
0.8.6 |
|
|
GPL |
X | X | | | Provides a base S4 class for comparative methods, incorporating one or... |
| r-phylomeasures |
2.1 |
|
|
GPL-3 |
X | X | | | Given a phylogenetic tree T and an assemblage S of species represented... |
| r-phylosignal |
1.2.1 |
|
|
GPL-3 |
X | X | | | A collection of tools to explore the phylogenetic signal in univariate... |
| r-phytools |
0.6_99 |
|
|
GPL |
X | X | | X | Phylogenetic tools for comparative biology |
| r-pinfsc50 |
1.1.0 |
|
|
GPL |
X | X | | | Genomic data for the plant pathogen "Phytophthora infestans."... |
| r-pipette |
0.15.2 |
|
dev |
AGPL-3.0 |
| | | X | Pipette biological data in and out of R. |
| r-plasmidprofiler |
0.1.6 |
|
|
Apache |
X | X | | | Contains functions developed to combine the results of querying a... |
| r-plotly |
4.5.6 |
|
|
MIT |
X | X | | | Easily translate ggplot2 graphs to an interactive web-based version... |
| r-plotrix |
3.6_4 |
|
|
GPL |
X | X | | | Lots of plots, various labeling, axis and color scaling functions. |
| r-plsgenomics |
1.5_2 |
|
|
GPL |
| | | X | Routines for PLS-based genomic analyses, implementing PLS methods for... |
| r-pma |
1.2.1 |
|
|
GPL |
X | X | | | Performs Penalized Multivariate Analysis: a penalized matrix... |
| r-pmcmr |
4.1 |
|
|
GPL |
X | X | | | The Kruskal and Wallis one-way analysis of variance by ranks or van... |
| r-png |
0.1.7 |
|
|
GPL-2 |
X | X | | | This package provides an easy and simple way to read, write and display... |
| r-polynom |
1.3_8 |
|
|
GPL-2 |
X | X | | | A collection of functions to implement a class for univariate... |
| r-polysat |
1.7_4 |
|
|
GPL |
X | X | | | A collection of tools to handle microsatellite data of any ploidy (and... |
| r-popgenome |
2.7.2 |
|
|
GPL-3 |
X | X | | | Provides efficient tools for population genomics data analysis, able to... |
| r-popgenreport |
3.0.4 |
|
|
GPL |
X | X | | X | Provides beginner friendly framework to analyse population genetic... |
| r-pophelper |
2.3.1 |
|
|
GPL-3 |
X | X | | X | A set of useful functions for processing admixture proportion files... |
| r-poppr |
2.8.5 |
|
|
GPL |
X | X | | | An R package for genetic analysis of populations with mixed... |
| r-pore |
0.24 |
|
|
BSD |
X | X | | | An R package to enable organisation and visualisation of nanopore... |
| r-prabclus |
2.2_6 |
|
|
GPL |
X | X | | | Distance-based parametric bootstrap tests for clustering with spatial... |
| r-pracma |
1.8.8 |
|
|
GPL |
X | X | | | Functions from numerical analysis and linear algebra, numerical... |
| r-precrec |
0.9.1 |
|
|
GPL-3 |
X | X | | | Accurate calculations and visualization of precision-recall and ROC... |
| r-preseqr |
2.0.0 |
|
|
GPL-3 |
X | X | | | Estimating the number of species represented r or more times in a random sample. |
| r-presto |
1.0.0 |
doc |
|
GPL-3.0-only |
X | X | | | Scalable implementation of the Wilcoxon rank sum test and auROC... |
| r-prestor |
0.0.5 |
|
|
Creative |
| | | X | A prototype package for generating quality control plots from pRESTO output. |
| r-prettyunits |
1.0.2 |
|
|
MIT |
X | X | | | Pretty, human readable formatting of quantities. Time intervals:... |
| r-probmetab |
1.1 |
|
|
GPL |
X | X | | | Provides probability ranking to candidate compounds assigned to masses,... |
| r-progress |
1.0.2 |
|
|
MIT |
X | X | | | Terminal progress bars. They are configurable, may include percentage,... |
| r-proj4 |
1.0_8 |
|
|
GPL-2 |
X | X | | | A simple interface to lat/long projection and datum transformation of... |
| r-propcis |
0.3_0 |
|
|
GPL |
X | X | | | Computes two-sample confidence intervals for single, paired and... |
| r-proteus-bartongroup |
0.2.16 |
|
|
MIT |
| | | X | R package for analysing proteomics data |
| r-proxy |
0.4_16 |
|
|
GPL-2 |
X | X | | | Provides an extensible framework for the efficient calculation of auto-... |
| r-prroc |
1.1 |
|
|
GPL-3 |
X | X | | | Computes the areas under the precision-recall (PR) and ROC curve for... |
| r-pscbs |
0.67.0 |
|
|
GPL-2.0-or-later |
X | X | | X | Segmentation of allele-specific DNA copy number data and detection of... |
| r-pscl |
1.4.9 |
|
|
GPL-2 |
X | X | | | Bayesian analysis of item-response theory (IRT) models, roll call... |
| r-psminer |
0.2.0 |
|
|
MIT |
| | | X | Utilities for interacting with the pathogensurveillance pipeline. |
| r-pspecterlib |
1.1.0 |
|
|
BSD-2-Clause |
| | | X | Proteomics R package for matching peaks in digested and intact proteomics |
| r-psych |
1.5.8 |
|
|
GPL |
X | X | | | A general purpose toolbox for personality, psychometrics and... |
| r-ptw |
1.9_11 |
|
|
GPL |
X | X | | | Parametric Time Warping aligns patterns, i.e. it aims to put... |
| r-purbayes |
1.3 |
|
|
GPL-2 |
X | X | | | PurBayes is an MCMC-based algorithm that uses next-generation... |
| r-qiime2r |
0.99.20 |
|
|
MIT |
| | | X | Import qiime2 artifacts to R. |
| r-qiimer |
0.9.4 |
|
|
GPL |
X | X | | | Open QIIME output files in R, compute statistics, and create plots from... |
| r-qlcmatrix |
0.9.5 |
|
|
GPL-3 |
X | X | | | Extension of the functionality of the Matrix package for using sparse... |
| r-qorts |
1.3.6 |
|
|
Public |
X | X | | X | QoRTs toolkit for analysis, quality control, and data management of... |
| r-qpcr |
1.4_1 |
|
|
GPL |
X | | | | Model fitting, optimal model selection and calculation of various... |
| r-qqman |
0.1.4 |
|
|
GPL-3 |
X | X | | | Create Q-Q and manhattan plots for GWAS data from PLINK results. |
| r-qtl |
1.41_6 |
|
|
GPL-3 |
X | X | | | Analysis of experimental crosses to identify genes (called quantitative... |
| r-qtl2 |
0.22 |
|
|
GPL-3 |
X | X | | | R/qtl2 provides a set of tools to perform quantitative trait locus... |
| r-qtlseqr |
0.7.5.2 |
|
|
GPL |
X | X | | | QTLseqr is an R package for QTL mapping using NGS Bulk Segregant Analysis. |
| r-quilt |
2.0.1 |
doc |
dev |
GPL-3.0-only |
X | X | | | Rapid and accurate genotype imputation from low coverage short read,... |
| r-quorts |
1.3.0 |
|
|
Public |
X | X | | | The QoRTs software package is a fast, efficient, and portable... |
| r-r.cache |
0.12.0 |
|
|
LGPL |
X | X | | | Memoization can be used to speed up repetitive and computational... |
| r-r.devices |
2.15.1 |
|
|
LGPL |
X | X | | | Functions for creating plots and image files in a unified way... |
| r-r.filesets |
2.10.0 |
|
|
LGPL |
X | X | | | A file set refers to a set of files located in one or more directories... |
| r-r.huge |
0.9.0 |
|
|
LGPL |
X | X | | | DEPRECATED. Do not start building new projects based on this package.... |
| r-r.methodss3 |
1.7.1 |
|
|
LGPL |
X | X | | | Methods that simplify the setup of S3 generic functions and S3 methods.... |
| r-r.oo |
1.21.0 |
|
|
LGPL |
X | X | | | Methods and classes for object-oriented programming in R with or... |
| r-r.rsp |
0.30.0 |
|
|
LGPL |
X | X | | | The RSP markup language makes any text-based document come alive. RSP... |
| r-r.utils |
2.5.0 |
|
|
LGPL |
X | X | | | Utility functions useful when programming and developing R packages. |
| r-r0 |
1.2_6 |
|
|
GPL-2 |
| | | X | Estimation of R0 and Real-Time Reproduction Number from Epidemics. |
| r-r2html |
2.3.2 |
|
|
GPL |
X | X | | | Includes HTML function and methods to write in an HTML file. Thus,... |
| r-r4cker |
1.0 |
|
|
Unknown |
| | | X | Analysis of 4C-seq (circularized chromosome conformation capture) data |
| r-raceid |
0.1.3 |
|
|
GPL-3 |
X | | | X | Application of 'RaceID' allows inference of cell types and... |
| r-rainbow |
3.3 |
|
|
GPL |
X | X | | | Functions and data sets for functional data display and outlier detection. |
| r-ramclustr |
1.3.1 |
|
|
GPL-2.0-or-later |
| | | X | A feature clustering algorithm for non-targeted mass spectrometric... |
| r-rann |
2.5 |
|
|
GPL |
X | X | | | Finds the k nearest neighbours for every point in a given dataset in... |
| r-rapidr |
0.1.1 |
|
|
GPL-3 |
X | X | | X | Package to perform non-invasive fetal testing for aneuploidies using... |
| r-rappdirs |
0.3 |
|
|
MIT |
X | X | | | An easy way to determine which directories on the users computer you... |
| r-rbamtools |
2.16.11 |
|
|
Artistic-2.0 |
X | X | | | Provides an R interface to functions of the 'SAMtools'... |
| r-rbison |
0.6.0 |
|
|
MIT |
X | X | | | Interface to the 'USGS' 'BISON'... |
| r-rblast |
0.99.1 |
|
|
GPL3 |
X | X | | | Seamlessly interfaces the Basic Local Alignment Search Tool (BLAST) to... |
| r-rcircos |
1.2.0 |
|
|
GPL |
X | X | | | A simple and flexible way to generate Circos 2D track plot images for... |
| r-rcppgsl |
0.3.1 |
|
|
GPL-3 |
X | | | | None |
| r-rcppparallel |
4.3.20 |
|
|
GPL-2 |
X | X | | | High level functions for parallel programming with 'Rcpp'. For... |
| r-rcpptoml |
0.1.3 |
|
|
GPL |
X | X | | | The configuration format defined by 'TOML' (which expands to... |
| r-readbrukerflexdata |
1.8.5 |
|
|
GPL |
X | X | | | Reads data files acquired by Bruker Daltonics' matrix-assisted... |
| r-readmzxmldata |
2.8.1 |
|
|
GPL |
X | X | | | Functions for reading mass spectrometry data in mzXML format. |
| r-readr |
0.2.2 |
|
|
GPL |
X | X | | | Read flat/tabular text files from disk (or a connection). |
| r-rebird |
1.0.0 |
|
|
MIT |
X | X | | | A programmatic client for the eBird database, including functions for... |
| r-recetox-aplcms |
0.13.4 |
doc |
dev |
GPL-2.0-or-later |
| | | X | apLCMS is a software which generates a feature table from a batch of... |
| r-recetox-waveica |
0.2.0 |
|
|
MIT |
| | | X | Removal of batch effects for large-scale untargeted metabolomics data... |
| r-recetox-xmsannotator |
0.10.0 |
|
|
GPL2.0 |
| | | X | Annotate peak intensity table with compounds from the compounds... |
| r-redeemr |
1.0.0 |
doc |
dev |
MIT |
X | X | | | R package for Regulatory multi-omics with Deep Mitochondrial mutation profiling. |
| r-relaimpo |
2.2_2 |
|
|
GPL-2 |
X | X | | | relaimpo provides several metrics for assessing relative importance in... |
| r-relations |
0.6_6 |
|
|
GPL-2 |
X | X | | | Data structures and algorithms for k-ary relations with arbitrary... |
| r-remapenrich |
0.99.0 |
|
|
AGPL-3 |
| | | X | Bioinformatics tools to compute statistical enrichment of geonomic... |
| r-rematch2 |
2.0.1 |
|
|
MIT |
X | X | | | Wrappers on 'regexpr' and 'gregexpr' to return the... |
| r-rentrez |
1.1.0 |
|
|
MIT |
X | X | | | Provides an R interface to the NCBI's EUtils API allowing users to... |
| r-reshape |
0.8.6 |
|
|
MIT |
X | X | | | Flexibly restructure and aggregate data using just melt() and cast(). |
| r-restfulr |
0.0.15 |
|
|
Artistic-2.0 |
X | X | | | Models a RESTful service as if it were a nested R list. |
| r-rfoc |
3.3_3 |
|
|
GPL |
X | X | | | Graphics for statistics on a sphere, as applied to geological fault... |
| r-rgbif |
1.3.0 |
|
|
MIT |
X | X | | | A programmatic interface to the Web Service methods provided by the... |
| r-rgraphics |
2.0_14 |
|
|
GPL |
X | X | | | Data and Functions from the book R Graphics, Second Edition. There is a... |
| r-riborex |
2.4.0 |
|
|
GPL-3.0 |
X | X | | X | Riborex is a R package for identification of differential translation... |
| r-ridigbio |
0.3.5 |
|
|
MIT |
X | X | | | An interface to iDigBio's search API that allows downloading... |
| r-rismed |
2.1.7 |
|
|
GPL |
| | | X | A set of tools to extract bibliographic content from the National... |
| r-rjson |
0.2.15 |
|
|
GPL-2 |
X | | | | Converts R object into JSON objects and vice-versa |
| r-rlist |
0.4.6.1 |
|
|
MIT |
X | X | | | Provides a set of functions for data manipulation with list objects,... |
| r-rmarkdown |
0.9.5 |
|
|
GPL-3 |
X | X | | | Convert R Markdown documents into a variety of formats. |
| r-rmysql |
0.10.11 |
|
|
GPL-2 |
X | X | | | A 'DBI' interface to 'MySQL' / 'MariaDB' |
| r-rnexml |
2.4.0 |
|
|
BSD_3_clause |
X | X | | X | Provides access to phyloinformatic data in 'NeXML' format. The... |
| r-rniftyreg |
2.2.0 |
|
|
GPL-2 |
X | X | | | Provides an R interface to the NiftyReg image registration tools... |
| r-robustrankaggreg |
1.1 |
|
|
GPL-2 |
X | X | | | Methods for aggregating ranked lists, especially lists of genes. It... |
| r-rocr |
1.0_7 |
|
|
GPL |
X | X | | | ROC graphs, sensitivity/specificity curves, lift charts, and... |
| r-rphast |
1.6.9 |
|
|
BSD_3_clause |
X | X | | | Provides an R interface to the... |
| r-rphylip |
0.1_23 |
|
|
GPL |
X | X | | | Rphylip provides an R interface for the PHYLIP package. All users of... |
| r-rpmg |
2.2_1 |
|
|
GPL |
X | X | | | Really Poor Man's Graphical User Interface, used to create... |
| r-rrbgen |
0.0.6 |
doc |
dev |
GPL3 |
X | X | | | A lightweight limited functionality R bgen read/write library |
| r-rrcov |
1.3_11 |
|
|
GPL |
X | X | | | Robust Location and Scatter Estimation and Robust Multivariate Analysis... |
| r-rseis |
3.5_2 |
|
|
GPL |
X | X | | | Multiple interactive codes to view and analyze seismic data, via... |
| r-rsm |
2.7_4 |
|
|
GPL-2 |
X | X | | | Provides functions to generate response-surface designs, fit first- and... |
| r-rsnps |
0.3.0 |
|
|
MIT |
| | | X | A programmatic interface to various 'SNP' 'datasets' on... |
| r-rsolnp |
1.16 |
|
|
GPL |
X | X | | | General Non-linear Optimization Using Augmented Lagrange Multiplier Method. |
| r-rspectral |
1.0.0.10 |
|
|
GPL-2 |
X | X | | | Implements the network clustering algorithm described in Newman (2006)... |
| r-rtassel |
0.1.2019.07.25 |
|
|
GNU |
| | | X | R front-end for TASSEL |
| r-rtfbs |
0.3.15 |
|
|
BSD_3_clause |
X | X | | | Identifies and scores possible Transcription Factor Binding Sites and... |
| r-rtsne |
0.13 |
|
|
BSD |
X | X | | | An R wrapper around the fast T-distributed Stochastic Neighbor... |
| r-rttf2pt1 |
1.3.4 |
|
|
file |
X | X | | | Contains the program 'ttf2pt1', for use with the... |
| r-rubic |
1.0.3 |
|
|
Apache-2.0 |
X | X | | X | RUBIC detects recurrent copy number aberrations using copy number... |
| r-runit |
0.4.31 |
|
|
GPL-2 |
X | X | | | R functions implementing a standard Unit Testing framework, with... |
| r-rvertnet |
0.7.0 |
|
|
MIT |
X | X | | X | Retrieve, map and summarize data from the 'VertNet.org' ... |
| r-rwave |
2.4 |
|
|
GPL |
X | X | | | A set of R functions which provide an environment for the... |
| r-saccharis |
1.0.5 |
|
|
GPL-3.0-or-later |
| | | X | A rendering package for creating phylogenetic trees from SACCHARIS... |
| r-sads |
0.4.2 |
|
|
GPL-2 |
X | X | | | Maximum likelihood tools to fit and compare models of species abundance... |
| r-saige |
1.3.1 |
|
dev |
GPL-3.0-only |
X | X | | | SAIGE is an R package with Scalable and Accurate Implementation of... |
| r-samr |
3.0 |
|
|
LGPL |
X | X | | | Significance Analysis of Microarrays |
| r-sartools |
1.8.1 |
|
|
GPL-2 |
X | X | | X | Statistical Analysis of RNA-Seq data |
| r-sbpiper |
1.9.0 |
|
|
MIT |
X | X | | X | Provides an API for analysing repetitive parameter estimations and... |
| r-scales |
0.4.1 |
|
|
MIT |
X | X | | | Graphical scales map data to aesthetics, and provide methods for... |
| r-scatterplot3d |
0.3_36 |
|
|
GPL-2 |
X | X | | | Plots a three dimensional (3D) point cloud. |
| r-scavenge |
1.0.2 |
|
dev |
GPL-2.0-or-later |
| | | X | SCAVENGE (Single Cell Analysis of Variant Enrichment through Network... |
| r-scbio |
0.1.4 |
|
|
GPL-2 |
| | | X | Cellular population mapping (CPM) a deconvolution algorithm in which... |
| r-scdc |
0 |
|
|
MIT |
X | X | | | SCDC adopts an ENSEMBLE method to integrate deconvolution results from... |
| r-sceasy |
0.0.7 |
|
dev |
GPL3 |
| | | X | A package providing functions to convert between different single-cell... |
| r-scevan |
1.0.3 |
|
|
GPL-3.0-only |
| | | X | Single CEll Variational Aneuploidy aNalysis |
| r-scimpute |
0.0.8 |
|
|
GPL |
X | X | | X | scImpute is accurate and robust imputation of single-cell RNA sequencing data. |
| r-scoper |
1.2.1 |
|
|
AGPL-3.0-only |
X | X | | | Provides a computational framework for identification of B cell clones... |
| r-scopfunctions |
0 |
|
|
AGPL-3 |
X | X | | | An R package of functions for single cell -omics analysis. |
| r-scpred |
1.9.2 |
|
dev |
MIT |
| | | X | Bioconda-installable version of scPred cell type classification method. |
| r-scrm |
1.7.2_4 |
|
|
GPL |
X | X | | | A coalescent simulator that allows the rapid simulation of biological... |
| r-scroshi |
1.0.0.0 |
|
|
MIT |
| | | X | scROSHI: robust supervised hierarchical identification of single cells |
| r-seamless |
0.1.1 |
|
|
GPL-3 |
| | | X | Given a bulk transcriptomic (RNA-seq) sample of an Myeloid Leukemia... |
| r-segmented |
0.5_1.4 |
|
|
GPL |
X | X | | | Given a regression model, segmented `updates' the model by adding... |
| r-sendmailr |
1.2_1 |
|
|
GPL-2 |
X | X | | | Package contains a simple SMTP client which provides a portable... |
| r-seqinr |
3.4_5 |
|
|
GPL |
X | X | | | Exploratory data analysis and data visualization for biological... |
| r-seqmagick |
0.1.7 |
|
|
Artistic-2.0 |
| | | X | Supports reading and writing sequences for different formats (currently... |
| r-seqminer |
7.1 |
|
|
GPL |
X | X | | | Integrate sequencing data (Variant call format, e.g. VCF or BCF) or... |
| r-sequenza |
3.0.0 |
|
|
GPL-3 |
X | X | | X | Tools to analyze genomic sequencing data from paired normal-tumor... |
| r-sets |
1.0_16 |
|
|
GPL-2 |
X | X | | | Data structures and basic operations for ordinary sets, generalizations... |
| r-seurat |
3.0.2 |
|
dev |
GPL-3 |
X | X | | | A toolkit for quality control, analysis, and exploration of single cell... |
| r-seurat-data |
0.2.1 |
|
dev |
GPL-3.0-only |
X | X | | | Single cell RNA sequencing datasets can be large, consisting of... |
| r-seurat-disk |
0.0.0.9021 |
|
dev |
GPL-3.0-only |
X | X | | | The h5Seurat file format is specifically designed for the storage and... |
| r-seurat-scripts |
0.0.4 |
|
dev |
GPL-3 |
X | X | | X | A set of wrappers for individual components of the Seurat package.... |
| r-sew |
1.0.1 |
doc |
dev |
BSD3 |
X | X | | | SEW |
| r-sgtr |
1.1.4 |
|
|
GPL3 |
X | X | | | Visualize population genomics analyses results in R. |
| r-shaman |
2.0 |
|
|
GPL |
X | | | X | The shaman package - sampling HiC contact matrices for a-parametric... |
| r-shape |
1.4.2 |
|
|
GPL |
X | X | | | Functions for plotting graphical shapes such as ellipses, circles,... |
| r-shazam |
1.1.2 |
|
|
AGPL-3 |
X | X | | X | Provides a computational framework for analyzing mutations in... |
| r-shinyace |
0.2.1 |
|
|
MIT |
X | X | | | Ace editor bindings to enable a rich text editing environment within Shiny. |
| r-shinyngs |
2.2.0 |
|
|
AGPL-3.0 |
| | | X | Provides Shiny applications for various array and NGS applications.... |
| r-sigminer |
2.3.1 |
|
|
MIT |
X | X | | X | Genomic alterations including single nucleotide substitution, copy... |
| r-signac |
1.14.0 |
doc |
dev |
MIT |
X | X | | | A framework for the analysis and exploration of single-cell chromatin... |
| r-signal |
0.7_6 |
|
|
GPL-2 |
X | X | | | A set of signal processing functions originally written for... |
| r-sigqc |
0.1.24 |
|
|
GPL-3.0-or-later |
X | X | | X | Provides gene signature quality control metrics in publication ready... |
| r-sigtree |
1.10.6 |
|
|
GPL-3 |
X | X | | | Provides tools to identify and visualize branches in a phylogenetic... |
| r-singlecellnet |
0.4.1 |
|
|
MIT |
| | | X | SingleCellNet enables the classifcation of single cell RNA-Seq data... |
| r-skellam |
0.2.0 |
|
|
GPL |
X | X | | | Densities and Sampling for the Skellam Distribution |
| r-sleuth |
0.30.1 |
|
dev |
GPLv3 |
X | X | | X | Tools for investigating RNA-Seq. |
| r-smartsva |
0.1.3 |
|
|
GPL-3 |
X | X | | | Introduces a fast and efficient Surrogate Variable Analysis algorithm... |
| r-smvar |
1.3.3 |
|
|
GPL |
X | X | | | Implements the structural model for variances in order to detect... |
| r-snow |
0.4_1 |
|
|
GPL |
X | X | | | Support for simple parallel computing in R. |
| r-snowfall |
1.84_6.1 |
|
|
GPL |
X | X | | | Usability wrapper around snow for easier development of parallel R... |
| r-snpassoc |
1.9_2 |
|
|
GPL |
X | X | | | This package carries out most common analysis when performing whole... |
| r-soap-nmr |
0.1.0.20170207 |
|
|
GPL2 |
X | X | | | R package for 1H-NMR data pre-treatment |
| r-solarius |
0.3.0.2 |
|
|
GPL |
X | X | | | SOLAR is the standard software program to perform linkage and... |
| r-som |
0.3_5.1 |
|
|
GPL |
X | X | | | Self-Organizing Map (with application in gene clustering). |
| r-spacexr |
2.2.1 |
|
|
GPL-3.0-only |
| | | X | Cell type identification and cell type-specific differential expression... |
| r-spam |
1.4_0 |
|
|
LGPL-2 |
X | X | | | Set of functions for sparse matrix algebra. Differences with... |
| r-sparql |
1.16 |
|
|
GPL-3 |
X | X | | | Use SPARQL to pose SELECT or UPDATE queries to an end-point. |
| r-spdep |
0.6_8 |
|
|
GPL |
X | X | | | A collection of functions to create spatial weights matrix objects from... |
| r-speaq |
2.7.0 |
|
|
Apache-2.0 |
X | X | | X | Makes Nuclear Magnetic Resonance spectroscopy (NMR spectroscopy) data... |
| r-speedglm |
0.3_1 |
|
|
GPL |
X | X | | | Fitting linear models and generalized linear models to large data sets... |
| r-spieceasi |
1.1.1 |
|
|
GPL-2.0-or-later |
X | X | | X | Estimate networks from the precision matrix of compositional microbial... |
| r-splancs |
2.01_38 |
|
|
GPL |
X | X | | | The Splancs package was written as an enhancement to S-Plus for display... |
| r-splitstackshape |
1.4.2 |
|
|
GPL-3 |
X | X | | | Online data collection tools like Google Forms often export... |
| r-spocc |
0.9.0 |
|
|
MIT |
X | X | | | A programmatic interface to many species occurrence data sources,... |
| r-spp |
1.16.0 |
|
|
GPL-2.0-only |
X | X | | | Analysis of ChIP-seq and other functional sequencing data [Kharchenko... |
| r-spring |
1.0.4 |
|
|
GPL-3.0-only |
| | | X | Semi-Parametric Rank-based approach for INference in Graphical model (SPRING) |
| r-sqldf |
0.4_10 |
|
|
GPL-2 |
X | X | | | Description: Manipulate R data frames using SQL. |
| r-stampp |
1.5.1 |
|
|
GPL-3 |
X | X | | X | Allows users to calculate pairwise Nei's Genetic Distances (Nei... |
| r-statmod |
1.4.29 |
|
|
GPL-2 |
X | X | | | A collection of algorithms and functions to aid statistical modeling.... |
| r-statvisual |
1.2.1 |
|
|
GPL |
| | | X | Visualization functions in the applications of translational medicine... |
| r-stitch |
1.7.3 |
doc |
dev |
GPL-3.0-only |
X | X | | | STITCH - Sequencing To Imputation Through Constructing Haplotypes. |
| r-stringr |
1.1.0 |
|
|
GPL-2 |
X | X | | | A consistent, simple and easy to use set of wrappers around the... |
| r-structssi |
1.1.1 |
|
|
GPL-2 |
X | X | | X | Performs multiple testing corrections that take specific structure of... |
| r-survey |
3.31_5 |
|
|
GPL-2 |
X | X | | | Summary statistics, two-sample tests, rank tests, generalised linear... |
| r-svdialogs |
0.9_57 |
|
|
GPL-2 |
X | X | | | Rapidly construct dialog boxes for your GUI, including an automatic... |
| r-svgui |
0.9_55 |
|
|
GPL-2 |
X | X | | | Functions to manage GUIs from R |
| r-swamp |
1.5.1 |
|
|
GPL |
X | X | | X | Collection of functions to connect the structure of the data with the... |
| r-syntactic |
0.7.1 |
|
dev |
AGPL-3 |
X | X | | X | Make syntactically valid names out of character vectors. |
| r-tailfindr |
1.4 |
|
|
AGPL-3.0 |
X | X | | | An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA... |
| r-taxa |
0.3.2 |
|
|
MIT |
X | X | | | Provides taxonomic classes for groupings of taxonomic names without... |
| r-taxonomizr |
0.7.1 |
|
|
GPL |
X | X | | | Functions for assigning taxonomy to NCBI accession numbers and taxon... |
| r-tcga2stat |
1.2 |
|
|
GPL-2 |
X | X | | X | Automatically downloads and processes TCGA genomics and clinical data... |
| r-tcr |
2.3.2 |
|
|
Apache |
X | X | | | Platform for the advanced analysis of T cell receptor and... |
| r-testthat |
1.0.2 |
|
|
MIT |
X | X | | | A unit testing system designed to be fun, flexible and easy to set up. |
| r-tfmpvalue |
0.0.6 |
|
|
GPL-2 |
X | X | | | In putative Transcription Factor Binding Sites (TFBSs) identification... |
| r-tftargets |
1.3 |
|
|
CC0 |
| | | X | Human transcription factor target genes. |
| r-tibble |
1.2 |
|
|
MIT |
X | X | | | Provides a 'tbl_df' class that offers better checking and... |
| r-tidygenomics |
0.1.2 |
|
|
GPL-3 |
X | X | | | Handle genomic data within data frames just as you would with... |
| r-tidyheatmap |
1.11.6 |
doc |
dev |
GPL-3.0-only |
| | | X | This is a tidy implementation for heatmap. At the moment it is based... |
| r-tiff |
0.1.5 |
|
|
GPL-2 |
X | | | | This package provides an easy and simple way to read, write and display... |
| r-tigger |
0.4.0 |
|
|
CC |
| | | X | Infers the V genotype of an individual from immunoglobulin (Ig)... |
| r-tinyarray |
2.4.3 |
|
|
MIT |
| | | X | Gene Expression Omnibus(GEO) and The Cancer Genome Atlas(TCGA) are... |
| r-tmae |
1.0.4 |
|
|
MIT |
X | X | | X | Tests and visualizations for mono-allelicly expressed variants. |
| r-traminer |
2.0_9 |
|
|
GPL |
X | X | | | Toolbox for the manipulation, description and rendering of sequences,... |
| r-transformer |
0.2.12 |
|
dev |
MIT |
X | X | | X | Additional S3 and S4 coercion methods for easy interconversion between... |
| r-transphylo |
1.4.0 |
|
|
GPL2 |
X | X | | | Reconstruction of transmission trees using genomic data |
| r-treesim |
2.4 |
|
|
GPL-2 |
X | X | | | Simulation methods for phylogenetic trees where (i) all tips are... |
| r-trimcluster |
0.1_2 |
|
|
GPL |
X | X | | | Trimmed k-means clustering. |
| r-truncnorm |
1.0_7 |
|
|
GPL-2 |
X | X | | | r/d/p/q functions for the truncated normal distribution |
| r-tsne |
0.1_3 |
|
|
GPL |
X | X | | | A "pure R" implementation of the t-SNE algorithm. |
| r-tximport |
0.0.15 |
|
|
GPL |
X | X | | | None |
| r-txrevise |
2.0 |
|
|
Apache |
| | | X | Construct custom transcript annotations for Salmon and kallisto |
| r-ukbrapr |
0.3.2 |
|
dev |
GPL-3.0-only |
| | | X | R functions to use in the UK Biobank Research Analysis Platform (RAP) |
| r-umi4c |
0.0.1 |
|
|
GPL |
X | | | X | Process UMI-4C data from scratch to produce nice plots. |
| r-umianalyzer |
1.0.0 |
|
|
GPL-3.0-only |
| | | X | Tools for analyzing sequencing data containing unique molecular... |
| r-upsetr |
1.0.3 |
|
|
MIT |
X | X | | | Creates visualizations of intersecting sets using a novel matrix... |
| r-vcfr |
1.8.0 |
|
|
GPL |
X | X | | | Facilitates easy manipulation of variant call format (VCF) data.... |
| r-vegan |
2.3_4 |
|
|
GPL-2 |
X | X | | | Ordination methods, diversity analysis and other functions for... |
| r-velocyto.r |
0.6 |
|
|
GPL-3 |
X | X | | | RNA velocity estimation in R |
| r-venn |
1.2 |
|
|
GPL |
X | X | | | Draws and displays Venn diagrams up to 7 sets, and any Boolean union of... |
| r-venndiagram |
1.6.16 |
|
|
GPL-2 |
X | X | | | A set of functions to generate high-resolution Venn and Euler plots.... |
| r-virfinder |
1.1 |
|
|
USC-RL |
X | X | | | VirFinder: a novel k-mer based tool for identifying viral sequences... |
| r-viridis |
0.3.1 |
|
|
MIT |
X | X | | | Port of the new 'matplotlib' color maps ('viridis' -... |
| r-viscorvar |
0.9 |
|
|
GPL3 |
| | | X | Overlaying of Correlation Circles and Network of Correlated Variables |
| r-vision |
2.0.0 |
|
|
MIT |
X | X | | | A high-throughput and unbiased module for interpreting scRNA-seq data. |
| r-wasabi |
1.0.1 |
|
|
BSD-3-clause |
X | X | | X | Prepare Sailfish and Salmon output for downstream analysis |
| r-waveslim |
1.7.5 |
|
|
BSD_3_clause |
X | X | | | Basic wavelet routines for time series (1D), image (2D) and array (3D)... |
| r-wgcna |
1.73 |
|
|
GPL-3.0-or-later |
X | X | | | Functions necessary to perform Weighted Correlation Network Analysis on... |
| r-whopgenome |
0.9.7 |
|
|
GPL |
X | X | | | Provides very fast access to whole genome, population scale variation... |
| r-wicket |
0.4.0 |
|
|
MIT |
X | X | | | Utilities to generate bounding boxes from 'WKT' (Well-Known... |
| r-workflowscriptscommon |
0.0.8 |
|
dev |
GPL-3.0-or-later |
| | | X | Common functions for making R function wapper scripts. Functions in R... |
| r-wormbase |
0.5.0 |
|
dev |
AGPL-3.0 |
| | | X | Fetch Caenorhabditis elegans genome annotations from WormBase. |
| r-wrassp |
0.1.4 |
|
|
GPL |
X | X | | | A wrapper around Michel Scheffers's libassp (Advanced Speech Signal... |
| r-writexls |
4.0.0 |
|
|
GPL |
X | X | | | Cross-platform Perl based R function to create Excel 2003 (XLS) and... |
| r-xcell |
1.3 |
|
|
GPL-3 |
X | X | | | Estimate immune cell proportions from gene expression data |
| r-xgr |
1.1.7 |
|
|
GPL-2 |
| | | X | The central goal of XGR by Fang et al. (2016)... |
| r-xmlrpc |
0.2_4 |
|
|
BSD |
X | X | | | A simple implementation of XML-RPC for R. |
| r-xnomial |
1.0.4 |
|
|
GPL-2|GPL-3 |
X | X | | | Tests whether a set of counts fit a given expected ratio. For example,... |
| r-yaml |
2.1.13 |
|
|
BSD_3_clause |
X | X | | | This package implements the libyaml YAML 1.1 parser and emitter... |
| r-zerone |
1.0 |
|
dev |
GPL-3 |
X | X | | | Zerone discretizes several ChIP-seq replicates simultaneously and... |
| r2r |
1.0.6 |
|
|
GPL-2 |
X | X | | | software to speed depiction of aesthetic consensus RNA secondary structures |
| ra |
0.9 |
|
|
GPL3 |
X | X | | | Ra is short for RNA Assembler and it is a C++ implementation of an... |
| ra-integrate |
0.1 |
|
|
GPL3 |
X | | | | None |
| rabbitqcplus |
2.3.0 |
|
|
MIT |
X | | | | RabbitQCPlus is an efficient quality control tool for sequencing data |
| rabbitsketch |
0.1.1 |
|
|
GPL-3.0-or-later |
X | | | | RabbitSketch is a highly optimized sketching library that exploits the... |
| rabbittclust |
2.3.0 |
|
|
https://github. |
X | | | | RabbitTClust enables fast clustering analysis of millions bacteria... |
| rabies |
0.5.1 |
|
|
GPL-2.0 |
| | | X | RABIES: Rodent Automated Bold Improvement of EPI Sequences. |
| rabix-bunny |
1.0.4 |
|
|
Apache |
X | X | | X | Open-source development kit for the Common Workflow Language from Seven... |
| racon |
1.5.0 |
doc |
dev |
MIT |
X | X | | | Ultrafast consensus module for raw de novo genome assembly of long... |
| rad_haplotyper |
1.1.9 |
|
|
Perl |
X | X | | | A program for building SNP haplotypes from RAD sequencing data |
| radiant |
1.1.5 |
|
|
GPL-3.0-or-later |
X | X | | | Annotate proteomes with protein domains |
| radiantkit |
0.1.0 |
|
|
MIT |
| | | X | Radiantkit is a Python package containing tools for full-stack image... |
| radsex |
1.2.0 |
|
|
GPL3 |
X | X | | | The radsex software is part of RADSex, a computational workflow for the... |
| radtk |
0.2.0 |
|
|
BSD-3-Clause |
X | X | | | A collection of tools for working with RAD files. |
| ragout |
2.3 |
|
|
GPLv3 |
X | X | | | Chromosome-level scaffolding using multiple references |
| ragtag |
2.1.0 |
doc |
dev |
MIT |
| | | X | Fast reference-guided genome assembly scaffolding |
| rainbow |
2.0.4 |
|
|
GNU |
X | X | | | Efficient tool for clustering and assembling short reads, especially for RAD |
| raiss |
4.0.1 |
|
|
MIT |
| | | X | SNP summary statistics imputation package |
| rambo-k |
1.21 |
|
|
GNU |
X | X | | X | a reference-based tool for rapid and sensitive extraction of one... |
| randfold |
2.0.1 |
|
|
GNU |
X | X | | | Minimum free energy of folding randomization test software |
| rapclust |
0.1.2 |
|
|
BSD |
X | X | | X | Accurate, Fast and Lightweight Clustering of de novo Transcriptomes... |
| rapgreen |
1.0 |
doc |
|
GPLv3 |
| | | X | Manipulate and annotate phylogenetic trees |
| rapid |
1.0 |
|
|
GPL2 |
X | X | | X | Read Alignment, Analysis, and Differential Pipeline (RAPID) is a set of... |
| rapidnj |
2.3.2 |
|
dev |
GPL-2-only |
X | X | | | RapidNJ is an algorithmic engineered implementation of canonical... |
| rapidshapes |
2.1.0 |
|
|
GPL-3.0-or-later |
X | X | | | RapidShapes computes a thermodynamic matcher (TDM), using a runtime... |
| rapifilt |
1.0 |
|
|
GPL-3.0 |
X | | | | RAPIFILT:RAPId FILTer is a quality control of DNA sequences |
| rapmap |
0.6.0 |
|
|
GPL |
X | X | | | Rapid sensitive and accurate read mapping via quasi-mapping |
| rappas |
1.22 |
|
|
GPL3 |
| | | X | RAPPAS (Rapid Alignment-free Phylogenetic PLacement via Ancestral... |
| rapsearch |
2.24 |
|
|
GNU |
X | | | | RAPSearch2 is a tool for fast protein similarity searches. |
| raptor |
3.0.1 |
doc |
dev |
BSD-3-Clause |
X | | | | Raptor: A fast and space-efficient pre-filter for querying very large... |
| rascaf |
20161129 |
|
|
GPL2 |
X | X | | | Scaffolding with RNA-seq read alignment |
| rasusa |
2.1.0 |
|
|
MIT |
X | X | | | Randomly subsample sequencing reads or alignments |
| ratatosk |
0.9.0 |
doc |
dev |
BSD-2-Clause |
X | | | | Hybrid error correction of long reads using colored de Bruijn graphs. |
| ratt |
1.0.3 |
|
|
GPL3 |
| | | X | Rapid Annotation Transfer Tool |
| raven-assembler |
1.8.3 |
doc |
dev |
MIT |
X | X | | | Raven is an assembler for raw reads generated by the third generation... |
| rawtools |
2.0.4 |
|
|
Apache |
| | | X | RawTools is an open-source and freely available package designed to... |
| raxml |
8.2.13 |
|
|
GPL |
X | X | | | Phylogenetics - Randomized Axelerated Maximum Likelihood. |
| raxml-ng |
1.2.2 |
|
|
AGPL-3 |
X | X | | | RAxML Next Generation: faster, easier-to-use and more flexible |
| ray |
2.3.1 |
|
|
GPL3 |
X | X | | | Parallel genome assemblies for parallel DNA sequencing |
| razers3 |
3.5.8 |
|
dev |
GPL-3.0-only |
X | X | | | RazerS 3 - Faster, fully sensitive read mapping |
| rbpbench |
1.0.2 |
|
|
MIT |
| | | X | Evaluate CLIP-seq and other genomic region data using a comprehensive... |
| rcorrector |
1.0.7 |
|
|
GPL-3.0-only |
X | X | | | Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction... |
| rcsbsearch |
0.2.3 |
doc |
dev |
BSD |
| | | X | Access the RCSB Search API |
| rcx-tk |
0.1.0 |
|
|
MIT |
| | | X | This package adjusts and cleans the metadata file provided by a user. |
| rd-analyzer |
1.01 |
|
|
GPL-3 |
| | | X | In silico region of difference (RD) analysis of Mycobacterium... |
| rdeval |
0.0.5 |
doc |
dev |
MIT |
X | X | | | A general purpose, multithreaded read analysis and manipulation tool. |
| rdfextras |
0.4 |
|
|
BSD |
X | X | | | RDFExtras provide tools, extra stores and such for RDFLib. |
| rdflib |
4.2.2 |
|
|
BSD |
X | X | | | RDFLib is a pure Python package work working with RDF |
| rdflib-jsonld |
0.4 |
|
|
BSD |
X | X | | | rdflib extension adding JSON-LD parser and serializer |
| rdkit |
2016.03.3 |
|
|
BSD |
X | | | | None |
| rdock |
2013.1 |
|
|
LGPLv3 |
X | | | | A Fast, Versatile and Open Source Program for Docking Ligands to... |
| rdp-readseq |
2.0.2 |
|
|
GPL |
X | X | | X | Java based common sequence file format reader and sequence file manipulation. |
| rdp_classifier |
2.14 |
|
|
GPL-2.0-only |
X | X | | X | Naive Bayesian classifier that can rapidly and accurately provide... |
| rdptools |
2.0.3 |
|
|
Creative |
X | X | | X | Metaproject for RDP Tools |
| read-it-and-keep |
0.3.0 |
|
|
MIT |
X | X | | | Read contamination removal |
| read2tree |
0.1.5 |
|
|
MIT |
| | | X | Building phylogenetic trees directly from sequencing reads |
| readfq |
2015.08.30 |
|
|
MIT |
X | X | | | A high-speed tool to calculate reads number and total base count in... |
| reads2graph |
1.0.0 |
|
|
BSD-3-Clause |
X | | | | reads2graph is an efficient tool for constructing edit-distance-based... |
| readseq |
2.1.30 |
|
|
PUBLIC |
X | X | | X | Read & reformat biosequences, Java command-line version |
| readucks |
0.0.3 |
|
|
GPL-3.0 |
| | | X | Readucks: a simple demultiplexer for nanopore reads |
| reago |
1.1 |
|
|
MIT |
X | X | | | An assembly tool for 16S ribosomal RNA recovery from metagenomic data |
| real |
1.0 |
|
|
file |
X | X | | | REad ALigner for Next-Generation sequencing reads. |
| realphy |
1.13 |
|
|
No |
| | | X | The Reference sequence Alignment based Phylogeny |
| reaper |
16.098 |
|
|
GPL3 |
X | X | | | Tool for demultiplexing, trimming and filtering sequencing data. |
| rebaler |
0.2.0 |
|
|
GPL-3.0 |
X | X | | X | Reference-based long read assemblies of bacterial genomes |
| rebar |
0.2.1 |
|
|
Apache-2.0 |
X | X | | | Genomic recombination detection using mutational barcodes. |
| recalladapters |
9.0.0 |
|
|
BSD-3-Clause-Clear |
X | | | | recalladapters - A tool to recall adapters for PacBio data |
| recentrifuge |
1.15.1 |
doc |
dev |
AGPL-3.0-or-later |
| | | X | Robust comparative analysis and contamination removal for metagenomics. |
| recgraph |
1.0.0 |
|
|
MIT |
X | X | | | Optimal sequence-to-graph alignment with recombinations |
| recognizer |
1.11.1 |
doc |
dev |
BSD-3-Clause |
| | | X | A tool for domain based annotation with the COG database |
| recon |
1.08 |
|
|
GPL2 |
X | X | | | The RECON package performs de novo identification and classification of... |
| recontig |
1.5.0 |
|
|
MIT |
X | X | | | recontig is a D program and python package that provides fast... |
| recycler |
0.7 |
|
|
BSD-3-Clause |
X | X | | X | Recycler is a tool designed for extracting circular sequences from de... |
| red |
2018.09.10 |
|
|
Custom |
X | X | | | Red (RepeatsDetector): an intelligent, rapid, accurate tool for... |
| reduce |
4.14 |
doc |
dev |
BSD-4-Clause-UC |
X | X | | | Reduce - tool for adding and correcting hydrogens in PDB files |
| redundans |
2.01 |
|
|
GPL-3.0-or-later |
X | | | | Redundans is a pipeline that assists an assembly of... |
| referee |
1.2 |
|
|
GPL-3.0-only |
| | | X | Quality scoring for reference genomes |
| referenceseeker |
1.8.0 |
|
dev |
GPLv3 |
| | | X | Rapid determination of appropriate reference genomes. |
| reffinder |
0.81 |
|
|
GPLv3, |
X | X | | | refFinder: Fast Lightweighttool for extracting nucleotides from... |
| refgenconf |
0.12.2 |
|
|
BSD-2-Clause |
| | | X | A standardized configuration object for reference genome assemblies |
| refgenie |
0.12.1 |
|
|
BSD-2-Clause |
| | | X | Refgenie creates a standardized folder structure for reference genome... |
| refgenieserver |
0.7.0 |
|
|
BSD-2-Clause |
| | | X | This server provides both a web interface and a RESTful API. Users may... |
| refinem |
0.1.2 |
doc |
dev |
GPL3 |
| | | X | A toolbox for improving population genomes. |
| reframed |
1.5.3 |
|
dev |
Apache-2.0 |
| | | X | Metabolic modeling package. |
| refseq_masher |
0.1.2 |
doc |
dev |
Apache |
X | X | | X | refseq_masher finds what NCBI RefSeq genomes match or are contained... |
| regenie |
4.1 |
doc |
dev |
MIT |
X | X | | | Regenie is a C++ program for whole genome regression modelling of large... |
| regex |
2016.06.24 |
|
|
Python |
X | X | | | Alternative regular expression module, to replace re. |
| regional |
1.1.2 |
|
|
MIT |
| | | X | simple manipulation and display of spatial regions in python |
| regtools |
1.0.0 |
|
|
MIT |
X | X | | | Tools that integrate DNA-seq and RNA-seq data to help interpret... |
| relecov-tools |
1.3.0 |
|
|
GPL-3.0-or-later |
| | | X | Tools for managing and processing of relecov data. |
| relion |
5.0.0 |
doc |
dev |
GPL-2.0-or-later |
X | X | | | Image-processing software for cryo-electron microscopy. |
| relocate2 |
2.0.1 |
|
|
unknown |
X | X | | X | a high resolution transposable element insertion sites mapping tool for... |
| remurna |
1.0 |
|
|
|
X | | | | Measurement of Single-Nucleotide Polymorphism-induced Changes of RNA... |
| rename |
1.601 |
|
|
GNU |
X | X | | X | Perl-powered file rename script with many helpful built-ins |
| renano |
1.3 |
|
|
MIT |
X | X | | | RENANO is a FASTQ lossless reference-based compression algorithm... |
| reneo |
0.5.0 |
doc |
dev |
MIT |
| | | X | Reneo: Unraveling Viral Genomes from Metagenomes |
| renet2 |
1.2 |
|
|
BSD-3-Clause |
| | | X | RENET2: High-Performance Full-text Gene-Disease Relation Extraction... |
| repaq |
0.3.0 |
|
|
MIT |
X | X | | | A fast lossless FASTQ compressor with ultra-high compression ratio |
| reparation_blast |
1.0.9 |
|
|
GPL3 |
X | | | X | A pipeline that detects novel open reading frames with ribseq data for bacteria. |
| repdenovo |
0.0.1 |
|
|
MIT |
X | X | | | REPdenovo is designed for constructing repeats directly from sequence reads. |
| repeatmasker |
4.1.7p1 |
doc |
dev |
Open |
X | X | | X | RepeatMasker is a program that screens DNA sequences for interspersed... |
| repeatmodeler |
2.0.6 |
doc |
dev |
Open |
X | X | | X | RepeatModeler is a de-novo repeat family identification and modeling package. |
| repeatscout |
1.0.7 |
doc |
dev |
CC0 |
X | X | | | De novo identification of repeat families in large genomes. |
| repenrich |
1.2 |
|
|
Custom |
X | X | | X | RepEnrich is a method to estimate repetitive element enrichment using... |
| repic |
1.0.0 |
doc |
dev |
BSD-3-Clause |
| | | X | REPIC - an ensemble learning approach to cryo-EM particle picking. |
| replidec |
0.3.1.1 |
|
|
MIT |
| | | X | Replication Cycle Decipher for Phages |
| reportfunk |
1.0.1 |
|
|
GPL-3.0 |
| | | X | Central set of functions generally useful for civet, llama and any... |
| represent |
1.5.1 |
|
|
MIT |
X | X | | X | Create __repr__ automatically or declaratively. |
| req |
1.3.190304ac |
|
|
GPLv3 |
| | | X | Estimating the rate of elementary quartets (REQ) of each internal... |
| requests-cache |
0.4.10 |
|
|
BSD |
X | X | | | Persistent cache for requests library |
| requests-mock |
1.0.0 |
|
|
Apache |
X | X | | | Mock out responses from the requests package |
| requests-toolbelt |
0.5.0 |
|
|
Apache |
X | X | | | A toolbelt of useful classes and functions to be used with python-requests |
| rerconverge |
0.3.0 |
|
|
GPL-3 |
X | X | | | RERconverge is a set of software written in R that estimates the... |
| reseek |
2.4 |
doc |
dev |
GPL-3.0-only |
X | X | | | Protein structure alignment and search algorithm. |
| reseq |
1.1 |
|
|
MIT |
X | | | | ReSeq Illumina/BGI simulator |
| resfinder |
4.6.0 |
doc |
dev |
Apache-2.0 |
| | | X | ResFinder identifies acquired antimicrobial resistance genes in total... |
| resistify |
1.1.5 |
doc |
dev |
GPL-3.0-or-later |
| | | X | A resistance gene annotation tool. |
| resmico |
1.2.2 |
doc |
dev |
MIT |
X | X | | | Increasing the quality of metagenome-assembled genomes with deep learning |
| retry_decorator |
1.1.1 |
|
|
MIT |
X | X | | X | Retry Decorator |
| revbayes |
1.2.5 |
doc |
dev |
GPL-3.0-or-later |
X | X | | | Bayesian Phylogenetic Inference Using Graphical Models and an... |
| reveal |
0.1 |
|
|
MIT |
X | X | | | Graph based multi genome aligner |
| reviewer |
0.2.7 |
|
|
GPL-3.0 |
X | X | | | A tool for visualizing alignments of reads in regions containing tandem repeats |
| revoluzer |
0.1.8 |
|
|
GPL-3.0-or-later |
X | | | | Genome rearrangement analysis tools |
| revtrans |
1.4 |
|
|
GPLv2 |
X | X | | X | revtrans - performs a reverse translation of a peptide alignment. |
| rfmix |
2.03.r0.9505bfa |
|
|
Free |
X | X | | | RFMix implements a fast discriminative approach to modeling ancestry... |
| rfplasmid |
0.0.18 |
|
|
GNU |
| | | X | RFPlasmid predicts plasmid contigs from assemblies using single copy... |
| rgccacmd |
3.0.3 |
doc |
|
GPL-2.0-or-later |
| | | X | Multiblock data analysis concerns the analysis of several sets of... |
| rgi |
6.0.3 |
|
|
https://card.mc |
X | X | | X | This tool provides a preliminary annotation of your DNA sequence(s)... |
| rgt |
1.0.2 |
doc |
dev |
GPL-3.0-or-later |
X | X | | | Toolkit to perform regulatory genomics data analysis |
| rhocall |
0.5.1 |
doc |
dev |
GPLv3 |
X | X | | | Call regions of homozygosity and make tentative UPD calls. |
| rhotermpredict |
3.4 |
|
dev |
AGPL-3.0-or-later |
| | | X | RhoTermPredict (Barrick Lab Fork) |
| riassigner |
0.4.1 |
|
dev |
MIT |
| | | X | GC-MS retention index calculation |
| riblast |
1.2.0 |
|
|
MIT |
X | X | | | RIblast is ultrafast RNA-RNA interaction prediction software. |
| ribocode |
1.2.15 |
|
|
MIT |
X | X | | X | A package for detecting the actively translated ORFs using... |
| ribocutter |
0.1.1 |
|
|
MIT |
| | | X | Design oligos to produce sgRNAs for abundant sequences in a fastq file |
| ribodetector |
0.3.1 |
|
|
GPL-3.0-or-later |
| | | X | Accurate and rapid RiboRNA sequences Detector based on deep learning |
| ribodiff |
0.2.2 |
|
|
GPL |
X | X | | X | RiboDiff is a statistical tool that detects the protein translational... |
| ribolands |
0.6.1 |
|
|
MIT |
| | | X | Energy landscapes and folding kinetics of nucleic acids |
| riboloco |
0.3.9 |
|
|
MIT |
| | | X | Riboseq analysis |
| ribominer |
0.2.3.2 |
|
|
GPLv3.0 |
| | | X | A python toolset for mining multi-dimensional features of the... |
| riboplot |
0.3.1 |
|
|
GNU |
X | X | | | Plot read counts of RiboSeq data from BAM format alignment files |
| riboraptor |
0.2.2 |
doc |
dev |
BSD |
X | X | | X | Python package to analyse ribosome profiling data |
| riborex |
2.4.0 |
|
|
GPL-3 |
X | X | | X | Riborex is a R package for identification of differential translation... |
| riboseed |
0.4.90 |
|
dev |
MIT |
X | X | | X | riboSeed: assemble across rDNA regions |
| riboseq-rust |
1.2 |
|
|
GPL-3.0 |
X | | | | Ribo-seq Unit Step Transformation. Tools to characterise the... |
| riboseqc |
1.1 |
|
|
GPL-3 |
| | | X | Read length specific QC of Ribo-seq data |
| ribotaper |
1.3.1 |
|
|
GPL |
X | | | | RiboTaper is a new analysis pipeline for Ribosome Profiling (Ribo-seq)... |
| ribotin |
1.4 |
|
|
MIT |
X | | | | Ribosomal DNA assembly tool |
| ribotish |
0.2.7 |
|
|
GPL-3.0-or-later |
X | | | X | Ribo TIS Hunter (Ribo-TISH) identifies translation activities using... |
| ribotools |
1.0.4 |
doc |
|
MIT |
| | | X | Ribo-seq analysis tools associated with the Rp-Bp package and more |
| ribotricer |
1.4.0 |
|
|
GNU |
X | X | | X | Python package to detect translating ORF from Ribo-seq data |
| ribowaltz |
2.0 |
|
|
MIT |
| | | X | Calculation of optimal P-site offsets, diagnostic analysis and visual... |
| rich-msa |
0.1.0 |
|
|
MIT |
| | | X | A Rich renderable for viewing Multiple Sequence Alignments in the terminal. |
| rilseq |
0.82 |
|
|
MIT |
| | | X | Processing RILSeq experiments results |
| ripcal |
2.0 |
|
|
GPL-3.0-or-later |
| | | X | RIPCAL is used for the bioinformatic analysis of repeat-induced point... |
| ripser |
1.0.1 |
|
dev |
MIT |
X | X | | | Ripser: efficient computation of Vietoris–Rips persistence barcodes. |
| rjchallis-assembly-stats |
17.02 |
|
|
MIT |
| | | X | Assembly metric visualisations to facilitate rapid assessment and... |
| rkp |
0.1.0 |
doc |
dev |
GNU |
| | | X | Relative K-mer Project |
| rlpipes |
0.9.4 |
|
|
MIT |
| | | X | A standardized R-loop-mapping pipeline |
| rmap |
2.1 |
|
|
GNU |
X | X | | | rmap is a short reads mapper for next-generation sequencing data |
| rmath4 |
4.3.1 |
|
|
GPL-2.0 |
X | X | | | standalone Rmath library from R |
| rmats |
4.3.0 |
|
|
Free |
X | X | | | MATS is a computational tool to detect differential alternative... |
| rmats-long |
1.0.0 |
|
|
Free |
| | | X | rMATS-long is an integrated computational workflow for long-read RNA-seq data |
| rmats2sashimiplot |
3.0.0 |
|
|
GNU |
X | X | | X | rmats2sashimiplot |
| rmblast |
2.14.1 |
doc |
|
OSL-2.1 |
X | X | | | RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST+ suite. |
| rmetl |
1.0.4 |
|
|
MIT |
| | | X | rMETL is a realignment-based Mobile Element insertion detection Tool... |
| rmlst_api |
0.1.6 |
|
|
MIT |
| | | X | API to perform rMLST on PubMLST.org |
| rna-cd |
0.2.0 |
doc |
dev |
GNU |
| | | X | RNA contamination detector |
| rna-seqc |
2.4.2 |
doc |
dev |
BSD-3-Clause |
X | X | | X | Fast, efficient RNA-Seq metrics for quality control and process optimization. |
| rnaalishapes |
2.5.0 |
|
|
GPL-3.0-or-later |
X | X | | | RNAalishapes is a tool for secondary structure prediction, using shape... |
| rnabloom |
2.0.1 |
doc |
dev |
GPL-3.0 |
| | | X | Java tool for RNA-seq assembly |
| rnablueprint |
1.3.2 |
|
|
GPL3 |
X | X | | | The RNAblueprint library solves the problem of uniformly sampling... |
| rnabob |
2.2.1 |
|
|
|
X | X | | | fast RNA motif searching |
| rnabridge-align |
1.0.1 |
|
|
BSD-3-Clause |
X | X | | | A tool to construct the alignments of entire fragments given the... |
| rnabridge-denovo |
1.0.1 |
|
|
BSD-3-Clause |
X | X | | | A tool to construct the alignments of entire fragments given the... |
| rnachipintegrator |
3.0.0 |
doc |
dev |
Artistic |
X | X | | X | Analyse genes against peak data, and vice versa |
| rnaclust |
1.3 |
|
|
GPL-2.0 |
X | X | | | A tool for clustering of RNAs based on their secondary structures using LocARNA |
| rnacode |
0.3 |
|
|
unknown |
X | | | | RNAcode - Analyze the protein coding potential in multiple sequence... |
| rnahybrid |
2.1.2 |
|
|
GPL-2 |
X | X | | | RNAhybrid is a tool for finding the minimum free energy hybridization... |
| rnalien |
1.8.0 |
|
|
GPL-3 |
X | | | X | A tool for unsupervised construction of RNA family models |
| rnalyze |
1.0.1 |
doc |
dev |
MIT |
| | | X | A comprehensive pipeline for RNA-Seq data analysis. |
| rnamining |
1.0.4 |
|
|
MIT |
| | | X | Package to predict potential coding of RNA sequences provided in fasta format |
| rnanorm |
2.2.0 |
|
|
Apache-2.0 |
| | | X | Common RNA-seq normalization methods |
| rnaprot |
0.5 |
|
|
MIT |
| | | X | Modelling RBP binding preferences to predict RPB binding sites |
| rnaquast |
2.3.0 |
|
dev |
GPL-2.0-or-later |
X | X | | | rnaQUAST is a tool for evaluating RNA-Seq assemblies using reference... |
| rnaredprint |
0.3 |
|
|
GPL |
X | X | | | Tree-decomposition based dynamic programming algorithm for multiple... |
| rnasamba |
0.2.5 |
|
|
GPL-3 |
X | X | | X | A tool for computing the coding potential of RNA transcript sequences... |
| rnashapes |
3.4.0 |
|
|
GPL-3.0-or-later |
X | X | | | RNAshape abstraction maps structures to a tree-like domain of shapes,... |
| rnasketch |
1.5 |
|
|
GPL3 |
X | | | X | RNAsketch Library for designing RNA molecules. Glue between... |
| rnasnp |
1.2 |
|
|
RTH |
X | X | | | Efficient detection of local RNA secondary structure changes induced by SNPs. |
| rnastructure |
6.4 |
|
|
GPL-2.0-only |
X | X | | | RNAstructure is a complete package for RNA and DNA secondary structure ... |
| rnavirhost |
1.0.5 |
|
|
MIT |
| | | X | RNAVirHost: a machine learning-based method for predicting hosts of RNA... |
| rnaz |
2.1.1 |
|
|
MIT-like |
X | | | | predicting structural noncoding RNAs |
| rnftools |
0.3.1.3 |
|
|
MIT |
X | X | | | RNF framework for NGS: simulation of reads, evaluation of mappers,... |
| roadies |
0.1.4 |
doc |
|
MIT |
X | X | | | Reference-free Orthology-free Alignment-free DIscordance aware... |
| roary |
3.13.0 |
|
|
GPL-3.0 |
X | X | | | Rapid large-scale prokaryote pan genome analysis |
| roary2fripan.py |
0.1 |
|
|
GPLv2 |
X | X | | X | Formats Roary output for viewing in FriPan |
| robust-bias-aware |
0.0.1 |
|
|
GPL-3.0-or-later |
| | | X | Robust bias aware. |
| rock |
2.0 |
|
|
AGPL-3.0 |
X | X | | | ROCK - Reducing Over-Covering K-mers |
| rodeo |
2.3.3 |
|
|
AGPL |
| | | X | RODEO evaluates one or many genes, characterizing a gene neighborhood... |
| roguenarok |
1.0.1 |
|
|
GPL-2.0-or-later |
X | X | | | Phylogenetics - algorithm for the identification of rogue taxa in a tree set. |
| rop |
1.1.2 |
|
|
GPL-3.0 |
X | | | | The Read Origin Protocol (ROP) is a computational protocol that aims to... |
| ropebwt2 |
r187 |
|
|
MIT |
X | X | | | Incremental construction of FM-index for DNA sequences |
| ropebwt3 |
3.9 |
doc |
dev |
MIT |
X | X | | | Constructs the FM-index of a large DNA sequence set and searches for... |
| roprofile |
1.4.5 |
|
|
GPLv3 |
X | X | | | Generation of pan-genome profile files using Roary output. |
| roprofile.py |
1.4.5 |
|
|
GPLv3 |
X | X | | | Generation of pan-genome profile files using Roary output. |
| rosella |
0.5.5 |
|
|
GPL3 |
X | | | | Metagenomic binning pipeline and algorithm using UMAP and HDBSCAN |
| rotate |
1.0 |
|
|
MIT |
X | X | | | Simple program to rotate a circular sequence to start at a given... |
| rpbp |
3.0.4 |
doc |
dev |
MIT |
X | X | | | Ribosome profiling with Bayesian predictions (Rp-Bp) |
| rpf-count-cds |
0.0.1 |
|
|
MIT |
| | | X | A python script for counting RPF reads map to CDS region. |
| rpfa |
1.0.1 |
|
|
Apache-2.0 |
| | | X | Cli interface to run OptGene/OptKnock with an heterologous pathway |
| rpfbagr |
2.2.2 |
|
|
MIT |
| | | X | Cli interface to predict gene knockout targets with an heterologous pathway |
| rpkmforgenes |
1.0.1 |
|
|
Creative |
X | X | | X | Calculates gene expression from a read mapping file |
| rpsbproc |
0.5.0 |
|
|
Public |
X | X | | | RpsbProc, the post-RPSBLAST Processing Utility. |
| rpy2 |
2.7.8 |
|
|
GNU |
X | X | | | Python interface to the R language (embedded R) |
| rrikindp |
0.0.2 |
doc |
dev |
GPL-3.0-only |
X | X | | | Evaluation of thermodynamic and kinetic features of RNA-RNA interactions. |
| rrmscorer |
1.0.10 |
doc |
dev |
MIT |
| | | X | RRMScorer (RRM-RNA score predictor) predicts how likely a single RRM is... |
| rsa |
3.1.4 |
|
|
Apache |
X | X | | | Pure-Python RSA implementation |
| rsat-core |
2020.02.29 |
|
|
AGPL-3 |
X | X | | | Detection of regulatory signals in non-coding sequences. |
| rscape |
1.4.0 |
|
|
GPLv3 |
X | X | | | R-scape (RNA Structural Covariation Above Phylogenetic Expectation)... |
| rseg |
0.4.9 |
|
|
GPLv3 |
X | | | | The RSEG software package is used to analyze ChIP-Seq data, especially... |
| rsem |
1.3.3 |
|
|
GPL3 |
X | X | | | RSEM is a software package for estimating gene and isoform expression... |
| rseqc |
5.0.4 |
doc |
dev |
GPL-2.0-or-later |
X | X | | X | QC package for RNA-seq data. |
| rsidx |
0.3 |
|
dev |
BSD |
| | | X | Library for indexing VCF files for random access searches by rsID |
| rsrq |
1.1.0 |
|
|
GNU |
X | X | | | A minimal Redis-backed queue system. |
| rsv-typer |
0.4.0 |
|
|
MIT |
| | | X | Genotyping RSV samples from nanopore sequencing data |
| rtg-tools |
3.12.1 |
|
|
BSD |
X | X | | X | RealTimeGenomics Tools -- Utilities for accurate VCF comparison and manipulation |
| rtk |
0.93.2 |
|
|
GPLv2 |
X | X | | | rtk - rarefaction toolkit for OTU tables |
| rtk2 |
2.11.2 |
|
dev |
GPL-2.0-or-later |
X | X | | | rtk2 - a CLI rarefaction toolkit for OTU tables |
| ruby |
2.2.3 |
|
|
BSD |
X | X | | | Ruby is a dynamic, reflective, object-oriented, general-purpose... |
| ruby-dna-tools |
1.0 |
|
|
GPL-2.0 |
X | X | | X | Various libraries containing useful functions for working with DNA... |
| rucs |
1.0.2 |
doc |
|
Apache-2.0 |
| | | X | RUCS is a bioinformatics tool developed to ease the task of designing... |
| ruffus |
2.8.4 |
|
|
MIT |
X | X | | X | Light-weight Python Computational Pipeline Management |
| rukki |
0.3.0 |
doc |
dev |
Public |
X | X | | | Extracting paths from assembly graphs. |
| run-dbcan |
2.0.11 |
|
|
GPL-3.0-only |
| | | X | Standalone version of dbCAN annotation tool for automated CAZyme annotation |
| runjob |
2.10.9 |
doc |
dev |
MIT |
| | | X | Manage jobs or pipeline of bioinfomation. |
| rust-bio-tools |
0.42.2 |
|
dev |
MIT |
X | X | | | A growing collection of fast and secure command line utilities for... |
| rust-gtars |
0.2.4 |
doc |
dev |
BSD-2-Clause |
X | X | | | Performance-critical tools to manipulate, analyze, and process genomic... |
| rust-mdbg |
1.0.1 |
|
|
MIT |
X | X | | | An ultra-fast minimizer-space de Bruijn graph (mdBG) implementation,... |
| rust-ncbitaxonomy |
1.0.7 |
doc |
|
MIT |
X | X | | | A Rust crate for working with a local copy of the NCBI Taxonomy... |
| rust-overlaps |
0.1.1 |
|
|
MIT |
X | | | | A fast and secure command line utilility for enumerating all... |
| rustybam |
0.1.33 |
|
|
MIT |
X | X | | | Mitchell Vollger's bioinformatics rust utilities. |
| rustynuc |
0.3.1 |
|
|
MIT |
X | X | | | Quick analysis of pileups for likely 8-oxoG locations |
| rustyread |
0.4.1 |
|
|
MIT |
X | X | | | Rustyread, a long-read simulator |
| rvtests |
2.0.7 |
|
|
GPL |
X | X | | | Rare variant test software for next generation sequencing data |
| rxdock |
2013.1.1_148c5bd1 |
|
dev |
LGPL-3.0 |
X | X | | | RxDock is a fork of rDock (GitLab), a fast, versatile and open-source... |
| ryuto |
1.6.3 |
|
|
BSD |
X | X | | | Network-Flow based Transcriptome Reconstruction |
| s3gof3r |
0.5.0 |
|
|
MIT |
X | X | | | Fast, concurrent, streaming access to Amazon S3, including gof3r, a CLI |
| s4pred |
1.2.0 |
|
dev |
GPL-3.0-or-later |
| | | X | Accurate prediction of a protein's secondary structure from its... |
| sabre |
1.000 |
|
|
MIT |
X | X | | | A barcode demultiplexing and trimming tool for FastQ files |
| saccharis |
2.0.4 |
|
dev |
GPL-3.0-or-later |
| | | X | SACCHARIS Bioinformatics Pipeline |
| safesim |
0.1.6.8d44580 |
|
|
Apache-2.0 |
X | X | | | SafeSeqS variant simulator |
| saffrontree |
0.1.2 |
|
|
GNU |
X | X | | | SaffronTree: Reference free rapid phylogenetic tree construction from... |
| sage-proteomics |
0.14.7 |
doc |
dev |
MIT |
X | X | | | Proteomics searching so fast it feels like magic. |
| sailfish |
0.10.1 |
|
|
GPLv3 |
X | | | | Rapid Mapping-based Isoform Quantification from RNA-Seq Reads |
| sainsc |
0.3.1 |
doc |
dev |
MIT |
X | | | | Segmentation-free Analysis of In Situ Capture data. |
| saintbioutils |
0.0.25 |
|
|
MIT |
| | | X | A package of utility and miscellaneous functions for using in... |
| sak |
0.4.6 |
|
|
https://github. |
X | X | | | This tool allows one to cut sequences and parts of sequences out of... |
| salmid |
0.1.23 |
|
|
MIT |
| | | X | Rapid tool to check taxonomic ID of single isolate samples. Currently... |
| salmon |
1.10.3 |
doc |
dev |
GPL-3.0-or-later |
X | X | | | Highly-accurate & wicked fast transcript-level quantification from... |
| salsa2 |
2.3 |
|
|
MIT |
X | X | | | Salsa is a tool to scaffold long read assemblies with Hi-C. |
| salty |
1.0.6 |
|
|
GPL3 |
| | | X | SaLTy assigns a lineage to Staphylococcus aureus WGS data and is... |
| sam |
3.5 |
|
|
academic |
X | X | | | SAM - Sequence Alignment and Modeling System |
| sam-algorithm |
1.0.2 |
|
|
MIT |
| | | X | The Self-Assembling-Manifold algorithm |
| sam2lca |
1.1.4 |
|
|
GPL-3.0 |
| | | X | Lowest Common Ancestor on SAM/BAM/CRAM alignment files |
| sam2pairwise |
1.0.0 |
doc |
dev |
MIT |
X | X | | | sam2pairwise takes a SAM file and uses the CIGAR and MD tag to... |
| samap |
1.0.15 |
|
|
MIT |
| | | X | The SAMap algorithm |
| sambamba |
1.0.1 |
doc |
dev |
GPL-2.0-only |
X | X | | | Tools for working with SAM/BAM data. |
| samblaster |
0.1.26 |
|
|
MIT |
X | X | | | Mark duplicates in and extract discordant and split reads from SAM files. |
| samclip |
0.4.0 |
|
|
GPL-3.0 |
X | X | | X | Filter SAM file for soft and hard clipped alignments |
| samcut |
0.1.1 |
|
|
MIT |
X | X | | | samcut is `cut` for sam. Select (cut) columns from the output of... |
| samestr |
1.2024.8 |
doc |
dev |
AGPL-3.0-or-later |
| | | X | SameStr identifies shared strains between pairs of metagenomic samples... |
| samhaplotag |
0.0.4 |
|
|
MIT |
X | X | | | Processes haplotag barcodes in SAM format. |
| sampei |
0.0.9 |
|
|
MIT |
| | | X | SAMPEI, a searching method leveraging high quality query spectra within... |
| sample-sheet |
0.13.0 |
doc |
|
MIT |
| | | X | An Illumina Sample Sheet parsing library |
| samplot |
1.3.0 |
|
|
MIT |
| | | X | Plot structural variant signals from BAMs and CRAMs. |
| samrefiner |
1.4.1 |
|
dev |
GPLv3 |
| | | X | A program for gathering variant information from a SAM formated files |
| samshee |
0.2.9 |
|
|
MIT |
| | | X | A schema-agnostic parser and writer for illumina sample sheets v2. |
| samsift |
0.2.5 |
|
|
MIT |
X | X | | X | Advanced filtering and tagging of SAM/BAM alignments using Python expressions. |
| samsifter |
1.0.0 |
|
|
GNU |
X | X | | | Workflow editor for metagenomic analysis |
| samstats |
0.2.2 |
|
|
MIT |
| | | X | SAM file alignment statistics at the read level |
| samstrip |
0.2.1 |
|
|
MIT |
X | X | | | Strip SAM files of data not needed for alignment computations. |
| samsum |
0.1.4 |
|
|
GNU |
X | X | | | A light-weight python package for summarizing sequence coverage from... |
| samtools |
1.21 |
|
|
MIT |
X | X | | | Tools for dealing with SAM, BAM and CRAM files |
| samwell |
0.0.4 |
|
|
MIT |
X | X | | | Useful utilities for biological data formats and analyses |
| sanitizeme |
1.1 |
|
|
Apache |
| | | X | GUI and CLI tool for removing host DNA from NGS data. |
| sankoff |
0.2 |
|
|
GPL |
X | X | | | Fast implementation of sankoff algorithm on phylogeny |
| sanntis |
0.9.4.1 |
|
dev |
Apache-2.0 |
| | | X | SMBGC Annotation using Neural Networks Trained on Interpro Signatures. |
| sansa |
0.2.3 |
|
|
BSD-3-Clause |
X | X | | | Structural variant annotation |
| sap |
1.1.3 |
|
|
GPL-3.0-only |
X | X | | | Pairwise structure alignment via double dynamic programming |
| sarscov2formatter |
1.0 |
doc |
dev |
AFL-3.0 |
| | | X | Formatter for Galaxy SARS-CoV2 Selection Analysis Workflow |
| sarscov2summary |
0.5 |
doc |
dev |
Academic |
| | | X | Formatter for Galaxy SARS-CoV2 Selection Analysis Workflow |
| sashimi-py |
0.1.5 |
doc |
|
BSD-3-Clause |
| | | X | This is an pure Python version of sashimi plot |
| saspector |
0.0.5 |
|
|
MIT |
| | | X | A tool for analysis of missing regions in (bacterial) draft genomes. |
| sat-bsa |
1.12 |
|
|
GPL-3.0-or-later |
| | | X | Sat-BSA is a package used for applying local de novo assembly and... |
| sativa |
0.9.3 |
|
|
GPL-3 |
X | X | | | SATIVA Semi-Automatic Taxonomy Improvement and Validation Algorithm |
| satrap |
0.2 |
|
|
file |
X | X | | | A SOLiD assembly translation program. |
| satsuma2 |
20161123 |
|
|
GPL3 |
X | | | | FFT cross-correlation based synteny aligner, (re)designed to make full... |
| savage |
0.4.2 |
|
|
GPL |
X | | | | SAVAGE (Strain Aware VirAl GEnome assembly) reconstructs individual... |
| savana |
1.3.3 |
|
|
Apache-2.0 |
| | | X | SAVANA: a somatic structural variant caller for long-read data |
| savvy |
2.1.0 |
|
dev |
MPL-2.0 |
X | X | | | Interface to various variant calling formats. |
| sawfish |
0.12.10 |
|
|
Pacific |
X | | | | Structural variant discovery and genotyping from mapped PacBio HiFi data |
| sbg-cwl-runner |
2018.11 |
|
|
Apache-2.0 |
| | | X | A CWL Runner for SBG platform |
| sbol-utilities |
1.0a17 |
|
|
MIT |
| | | X | Collection of scripts and functions for manipulating SBOL 3 data that... |
| sbpipe |
4.21.0 |
|
|
MIT |
X | X | | X | SBpipe is a collection of pipelines for systems modelling of biological... |
| sbt |
0.13.12 |
|
|
BSD |
X | X | | | None |
| sc-musketeers |
0.4.1 |
|
|
GPL-3.0 |
| | | X | A tri-partite modular autoencoder for addressing imbalanced cell type... |
| sc3-scripts |
0.0.6 |
|
dev |
GPL-3 |
| | | X | A set of wrappers for individual components of the SC3 package.... |
| scaden |
1.1.2 |
|
|
MIT |
| | | X | Cell type deconvolution using single cell data |
| scaffold_builder |
2.3 |
|
dev |
GPL-3.0 |
X | X | | X | Scaffold_builder: Combining de novo and reference-guided assembly with... |
| scagaire |
0.0.4 |
|
|
GPLv3 |
| | | X | Scagaire allows you to take in gene predictions from a metagenomic... |
| scala |
2.11.8 |
|
|
BSD |
X | X | | | Scala combines object-oriented and functional programming in one... |
| scallop |
0.10.5 |
|
|
BSD |
X | X | | | Scallop is a reference-based transcriptome assembler for RNA-seq |
| scallop-lr |
0.9.2 |
|
|
BSD |
X | X | | | Scallop-LR is a reference-based transcriptome assembler for long-reads... |
| scallop-umi |
1.1.0 |
|
|
BSD-3-Clause |
X | X | | | A reference-based transcript assembler for linked-reads RNA-seq data. |
| scallop2 |
1.1.2 |
|
|
BSD-3-Clause |
X | X | | | A reference-based transcript assembler optimized for... |
| scalop |
2021.01.27 |
|
|
BSD-3-Clause |
| | | X | SCALOP - Sequence-based antibody Canonical LOoP structure annotation |
| scalpel |
0.5.4 |
|
|
MIT |
X | | | | Sensitive detection of INDELs (INsertions and DELetions) |
| scanindel |
1.3 |
|
|
GNU |
X | | | X | ScanIndel is a python program to detect indels (insertions and... |
| scanorama |
1.7.4 |
|
|
MIT |
| | | X | Panoramic stitching of heterogeneous single-cell transcriptomic data |
| scanpy |
1.7.2 |
|
dev |
BSD-3 |
X | X | | X | Single-Cell Analysis in Python. Scales to >1M cells. |
| scanpy-scripts |
1.9.301 |
|
dev |
Apache-2.0 |
| | | X | Scripts for using scanpy from the command line |
| scapp |
0.1.4 |
|
|
MIT |
| | | X | Plasmid assembly in metagenomes |
| scar |
0.7.0 |
|
|
MIT |
| | | X | scAR (single-cell Ambient Remover) is a deep learning model for ambient... |
| scarap |
1.0.0 |
|
dev |
GPL-3.0-or-later |
| | | X | A toolkit for prokaryotic comparative genomics |
| scarches |
0.6.1 |
|
|
BSD-3-Clause |
| | | X | Transfer learning with Architecture Surgery on Single-cell data |
| scater-scripts |
0.0.5 |
|
dev |
GPL-3 |
| | | X | A set of wrappers for individual components of the Scater package.... |
| sccaf |
0.0.10 |
doc |
dev |
MIT |
| | | X | Single-Cell Clustering Assessment Framework |
| sccaller |
2.0.0 |
|
|
GPL-3 |
X | X | | X | Dong X et al. Accurate identification of single-nucleotide variants in... |
| sccmec |
1.2.0 |
|
|
MIT |
| | | X | A tool for typing SCCmec cassettes in assemblies |
| scelestial |
1.2 |
|
|
GPL |
X | X | | | Scelestial, Single Cell Lineage Tree Inference based on a Steiner Tree... |
| scelvis |
0.8.9 |
|
|
MIT |
| | | X | SCelVis - web-based visualization of single-cell data |
| scepia |
0.5.1 |
|
|
MIT |
| | | X | Single Cell Epigenome-based Inference of Activity |
| scexecute |
1.3.3 |
|
|
MIT |
| | | X | SCExecute generates cell-barcode specific BAM files from aligned,... |
| scg |
0.3.1 |
|
|
GPL-3 |
X | X | | X | The single cell genotyper (SCG): "Roth A, McPherson A, Laks E,... |
| scglue |
0.3.2 |
doc |
dev |
MIT |
| | | X | Graph-linked unified embedding for unpaired single-cell multi-omics... |
| schavott |
0.5.0 |
|
|
MIT |
X | X | | X | Assembly and scaffolding of bacterial genomes in real time using... |
| schema |
0.7.0 |
|
|
MIT |
X | X | | X | Simple data validation library |
| schema-salad |
2.7.20180809223002 |
|
|
Apache-2.0 |
X | X | | X | Schema Annotations for Linked Avro Data (SALAD) |
| schicexplorer |
7 |
|
|
GPL3 |
| | | X | Set of programs to process, analyze and visualize single-cell Hi-C data. |
| schpl |
1.0.5 |
|
|
MIT |
| | | X | Hierarchical progressive learning pipeline for single-cell... |
| scib |
1.1.7 |
doc |
dev |
MIT |
X | X | | | Evaluating single-cell data integration methods |
| scikit-allel |
0.20.3 |
|
|
MIT |
X | | | | None |
| scikit-bio |
0.4.2 |
|
|
BSD |
X | X | | | Data structures, algorithms and educational resources for bioinformatics. |
| scikits-datasmooth |
0.7.1 |
|
|
BSD |
X | X | | X | Scikits data smoothing package |
| sciphi |
0.1.7 |
|
|
GNU |
X | X | | | Single-cell mutation identification via phylogenetic inference |
| sciphin |
1.0.1 |
|
|
GNU |
X | | | | Single-Cell mutation Identification via finite-sites Phylogenetic Inference |
| scirpy |
0.22.0 |
|
dev |
BSD-3-Clause |
| | | X | A Scanpy extension for analyzing single-cell T-cell and B-cell receptor... |
| scitrack |
2024.10.8 |
|
dev |
BSD-3-Clause |
| | | X | SciTrack provides basic logging capabilities to track scientific computations. |
| scmap-cli |
0.1.0 |
|
dev |
Apache |
| | | X | CLI scripts for the scmap package |
| scmidas |
0.1.7 |
doc |
dev |
MIT |
| | | X | A torch-based integration method for single-cell multi-omic data. |
| scnic |
0.6.6 |
|
dev |
BSD-3-Clause |
| | | X | SCNIC: Sparse Cooccurence Network Investigation for Compositional data |
| scoary |
1.6.16 |
|
|
GPL-3.0 |
X | X | | X | Microbial pan-GWAS using the output from Roary |
| scoop |
0.7.1.1 |
|
|
GNU |
X | X | | X | Scalable COncurrent Operations in Python |
| scoring-matrices |
0.3.0 |
doc |
dev |
MIT |
X | X | | | Dependency free, Cython-compatible scoring matrices to use with... |
| scorpio |
0.3.19 |
|
|
GPL-3.0-only |
| | | X | Serious constellations of reoccurring phylogenetically-independent origin |
| scpred-cli |
0.1.0 |
|
|
Apache-2.0 |
| | | X | A set of command-line wrappers for the core functions in the scPred package. |
| scprep |
1.2.3 |
|
|
GNU |
| | | X | Tools for loading and preprocessing biological matrices in Python. |
| scramble |
1.0.2 |
|
|
CC |
X | X | | | Soft Clipped Read Alignment Mapper |
| scran-cli |
0.0.1 |
|
dev |
Apache |
| | | X | A set of wrappers for individual components of the scran R package.... |
| scrappie |
1.4.2 |
|
|
Mozilla |
X | | | | Scrappie is a technology demonstrator for the Oxford Nanopore Research... |
| screadcounts |
1.4.0 |
|
|
MIT |
| | | X | SCReadCounts is a computational tool for a cell-level assessment of the... |
| screamingbackpack |
0.2.333 |
|
|
GPLv3 |
X | X | | X | ScreamingBackpack |
| screed |
1.0.4 |
|
|
BSD |
X | X | | X | Screed is a biological sequence parsing and storage/retrieval library... |
| scrm |
1.7.4 |
|
|
GPLv3+ |
X | X | | | A coalescent simulator for genome-scale sequences |
| scrnasim-toolz |
0.1.1 |
|
|
MIT |
| | | X | Tools used by scRNAsim workflow. |
| scrubby |
0.2.1 |
|
dev |
MIT |
X | X | | | Read depletion/extraction and database cleaning using k-mer and... |
| scrublet |
0.2.3 |
|
|
MIT |
X | X | | X | Doublet prediction in single-cell RNA-sequencing data |
| scspectra |
0.2.1 |
|
dev |
MIT |
| | | X | Supervised discovery of interpretable gene programs from single-cell data. |
| scsplit |
1.0.8.2 |
|
|
MIT |
| | | X | Genotype-free demultiplexing of pooled single-cell RNA-Seq |
| scssim |
1.0 |
|
|
BSD |
X | X | | | A bioinformatics tool for simulating single-cell genome sequencing data |
| sctagger |
1.1.1 |
|
|
MIT |
| | | X | Fast and accurate matching of cellular barcodes across short- and... |
| scte |
1.0.0 |
|
|
MIT |
| | | X | scTE builds genome indices for the fast alignment of reads to genes and TEs. |
| sctools |
1.0.0 |
|
|
AGPL-3.0 |
X | | | | SCTools is a suite of tools performing utility operations over... |
| sctriangulate |
0.13.0 |
|
|
MIT |
| | | X | A Python package to mix-and-match conflicting clustering results in... |
| scvelo |
0.2.5 |
|
|
BSD |
| | | X | single-cell RNA velocity generalized to transient cell states |
| scvi |
0.6.8 |
doc |
dev |
MIT |
| | | X | Single-cell Variational Inference |
| scvi-tools |
0.14.5 |
doc |
dev |
BSD-3-Clause |
| | | X | Deep probabilistic analysis of single-cell omics data. |
| scvis |
0.1.0 |
|
|
Creative |
| | | X | scvis is a python package for dimension reduction of high-dimensional... |
| scvis_galaxy |
0.1.1 |
|
|
Creative |
| | | X | scvis is a python package for dimension reduction of high-dimensional... |
| scxa-plots |
0.0.1 |
|
dev |
Apache-2.0 |
| | | X | A set of wrappers to produce some bespoke plots used by the team behind... |
| sdeper |
1.6.3 |
doc |
dev |
MIT |
| | | X | Spatial Deconvolution method with Platform Effect Removal |
| sdm |
3.08 |
|
|
GPL-3.0-or-later |
X | X | | | sdm - simple demultiplex tool for FASTQ demultiplexing and dereplication |
| sdrf-pipelines |
0.0.31 |
doc |
dev |
Apache-2.0 |
| | | X | Translate, convert SDRF to configuration pipelines |
| sdust |
0.1 |
|
dev |
Unknown |
X | X | | | Symmetric DUST for finding low-complexity regions in DNA sequences. |
| seacells |
0.3.3 |
|
dev |
GPL-2.0-or-later |
| | | X | SEACells algorithm for Inference of transcriptional and epigenomic... |
| seacr |
1.3 |
|
|
https://github. |
| | | X | SEACR is intended to call peaks and enriched regions from sparse... |
| search_ncbi |
0.1.2 |
|
|
MIT |
| | | X | A package for searching and processing NCBI data |
| searchgui |
4.3.11 |
doc |
dev |
Apache-2.0 |
X | X | | X | User-friendly graphical tool for using proteomics identification search engines. |
| secapr |
2.2.8 |
|
|
MIT |
X | X | | X | Process sequence-capture FASTQ files into alignments for phylogenetic... |
| secedo |
1.0.7 |
|
|
MIT |
X | X | | | SNV-based clustering for single-cell sequencing data |
| secimtools |
22.3.23 |
|
|
MIT |
X | X | | X | Metabolomics tools from the SECIM project |
| seedme |
1.2.4 |
|
|
GPL |
X | X | | X | Python REST like client for SeedMe.org |
| seer |
1.1.4 |
|
|
GPL-2 |
X | | | | sequence element (kmer) enrichment analysis |
| seg-suite |
98 |
|
|
GPL-3.0-or-later |
X | X | | | The seg suite provides tools for manipulating segments, alignments, and... |
| segalign-full |
0.1.2.7 |
doc |
dev |
MIT |
| | | X | SegAlign: A Scalable GPU-Based Whole Genome Aligner |
| segalign-galaxy |
0.1.2.7 |
doc |
dev |
MIT |
| | | X | SegAlign: A Scalable GPU-Based Whole Genome Aligner |
| segemehl |
0.3.4 |
|
|
GPL3 |
X | X | | | Short read mapping with gaps |
| segmentation-fold |
1.7.0 |
|
|
GNU |
X | X | | | RNA-Folding with predefined segments including K-turns and loop-E-motifs |
| segmetrics |
1.5 |
doc |
dev |
MIT |
| | | X | A Python package implementing image segmentation and object detection... |
| segtools |
1.3.0 |
|
|
GPL2 |
X | X | | X | a python package for analyzing genomic segmentations |
| segul |
0.22.1 |
|
|
MIT |
X | X | | | An ultrafast and memory efficient tool for phylogenomics |
| segway |
3.0.4 |
|
|
GPL2 |
X | X | | X | a tool for easy pattern discovery and identification in functional... |
| segzoo |
1.0.13 |
|
|
GPL-2.0-or-later |
| | | X | System for turnkey analysis of semi-automated genome annotations |
| seidr |
0.14.2 |
|
|
GPL-2.0-or-later |
X | | | | Community gene network inference and exploration toolkit |
| seismic-rna |
0.24.0 |
doc |
dev |
GPL-3.0-only |
X | X | | X | SEISMIC-RNA software by the Rouskin Lab. |
| selam |
0.9 |
|
|
GPL3 |
X | X | | | Simulation of Epistasis Local adaptation, with Ancestry and Mate choice |
| selectfasta |
3.1 |
|
|
GPL-3.0 |
X | | | | FASTA or FASTQ select from a list of header names |
| selectsequencesfrommsa |
1.0.5 |
|
|
GPL-3 |
X | | | | Tool to select representative sequences from a multiple sequence alignment |
| selene-sdk |
0.6.0 |
|
|
BSD |
X | X | | | Framework for developing sequence-level deep learning networks. |
| selenzy_wrapper |
0.3.0 |
|
|
MIT |
| | | X | Python wrapper of selenzy tool |
| selscan |
1.2.0a |
|
|
GPL-3.0 |
X | X | | | a program to calculate EHH-based scans for positive selection in genomes |
| sem |
1.2.3 |
|
|
MIT |
| | | X | A nucleosome calling package for nucleosome subtype detection |
| semeta |
1.0 |
|
|
GPL-3 |
X | X | | | SeMeta is a new software for taxonomic assignment of metagenomic reads.... |
| semibin |
2.1.0 |
doc |
|
MIT |
| | | X | Metagenomic binning with semi-supervised siamese neural networks |
| semidbm |
0.5.1 |
|
|
BSD |
X | X | | X | Cross platform (fast) DBM interface in python |
| sensv |
1.0.4 |
|
|
AGPLv3 |
X | | | | SENSV |
| sentieon |
202308.03 |
|
|
Commercial |
X | X | | | Accelerated performance bioinformatics tools for mapping and variant calling |
| sepp |
4.5.5 |
|
|
GPLv3 |
X | X | | | SATe-enabled phylogenetic placement |
| sepp-refgg138 |
4.5.1 |
|
|
GPLv3 |
| | | X | SATe-enabled phylogenetic placement |
| sepp-refsilva128 |
4.5.1 |
|
|
GPLv3 |
| | | X | SATe-enabled phylogenetic placement |
| seq-gen |
1.3.4 |
|
dev |
BSD-3-Clause |
X | X | | | Seq-Gen is a program that will simulate the evolution of nucleotide or... |
| seq-hasher |
0.2.0 |
|
|
MIT |
X | X | | | Compute hash digests for DNA sequences in a FASTA file, with support... |
| seq-seq-pan |
1.1.0 |
|
|
FreeBSD |
X | | | X | seq-seq-pan |
| seq-to-first-iso |
1.1.0 |
doc |
|
BSD |
| | | X | Compute first two isotopologues intensity from peptide sequence |
| seq2c |
2019.05.30 |
|
|
MIT |
X | X | | X | Cohort based copy number calling in gene regions |
| seq2hla |
2.3 |
|
|
MIT |
X | X | | X | Precision HLA typing and expression from next-generation RNA sequencing data |
| seq2onehot |
0.0.1 |
|
|
MIT |
| | | X | Encode biological sequences to a one-hot numpy array |
| seq2science |
1.2.2 |
doc |
dev |
MIT |
| | | X | Automated preprocessing of Next-Generation-Sequencing data. |
| seq2squiggle |
0.3.0 |
|
|
MIT |
| | | X | End-to-end simulation of nanopore sequencing signals with feed-forward... |
| seqan |
2.4.0 |
|
|
BSD-3-Clause |
X | X | | X | SeqAn is an open source C++ library of efficient algorithms and data... |
| seqan3 |
3.3.0 |
doc |
dev |
BSD-3-Clause |
| | | X | SeqAn3 is the new version of the popular SeqAn template library for the... |
| seqan_tcoffee |
1.13.8 |
doc |
dev |
GPL |
X | X | | | SeqAn::T-Coffee - Multiple Sequence Alignment |
| seqbuster |
3.5 |
|
|
MIT |
X | | | X | miRNA and isomiR annotation |
| seqchromloader |
0.7.8 |
doc |
dev |
MIT |
| | | X | Sequence and chromatin dataloader for deep learning |
| seqcluster |
1.2.9 |
|
|
MIT |
X | X | | X | small RNA analysis from NGS data |
| seqcomplexity |
0.1.2 |
|
|
MIT |
X | X | | | Calculates Per-Read and Total Sequence Complexity from FastQ file. |
| seqerakit |
0.5.3 |
|
|
Apache-2.0 |
| | | X | Automate creation of Seqera Platform resources |
| seqfold |
0.7.17 |
|
|
MIT |
| | | X | Predict the minimum free energy and structure of nucleic acids. |
| seqfu |
1.22.3 |
|
|
GPL-3.0-only |
X | X | | X | DNA sequence utilities |
| seqhax |
0.8.6 |
|
|
MPL2 |
X | | | | A collection of next-gen sequence data utilities |
| seqiolib |
0.2.4 |
doc |
dev |
MIT |
| | | X | Library to read, write sequence, variants, regions to use them for... |
| seqkit |
2.10.0 |
|
|
MIT |
X | X | | | a cross-platform and ultrafast toolkit for FASTA/Q file manipulation |
| seqlib |
1.2.0 |
doc |
dev |
Apache-2.0 |
X | X | | | C++ interface to HTSlib, BWA-MEM and Fermi. |
| seqlike |
1.1.6 |
|
|
Apache-2.0 |
| | | X | Flexible biological sequence objects in Python |
| seqlogo |
5.29.9 |
|
dev |
BSD-3-Clause |
X | X | | X | Python port of the R Bioconductor `seqlogo` package |
| seqmagick |
0.8.6 |
|
|
GNU |
X | X | | X | Tools for converting and modifying sequence files from the command-line |
| seqmap |
1.0.13 |
|
|
Custom |
X | X | | | SeqMap is a tool for mapping large amount of oligonucleotide to the genome. |
| seqnado |
0.6.6 |
|
|
GPL-3.0-or-later |
| | | X | Pipelines for genomics analysis |
| seqprep |
1.3.2 |
|
|
MIT |
X | | | | Tool for stripping adaptors and/or merging paired reads with overlap... |
| seqscreen |
4.4 |
|
|
GPL3 |
| | | X | SeqScreen was created to sensitively assign taxonomic classifications,... |
| seqsero2 |
1.3.1 |
|
dev |
GPL-2.0-or-later |
| | | X | Salmonella serotype prediction from genome sequencing data |
| seqsizzle |
0.1.5 |
|
|
AGPL-3.0-or-later |
X | X | | | A pager for viewing FASTQ files with fuzzy adaptor matching and coloring. |
| seqspec |
0.3.1 |
|
|
MIT |
| | | X | File format that describes data generated from genomics experiments. ... |
| seqstats |
1.0.0 |
|
|
MIT |
X | X | | | Quick summary statistics on fasta/fastq(.gz) files |
| seqstr |
0.1.0 |
|
|
MIT |
| | | X | Lightweight tool to compile simple string input into long genomic sequences |
| seqtk |
1.4 |
|
|
MIT |
X | X | | | Seqtk is a fast and lightweight tool for processing sequences in the... |
| sequali |
0.12.0 |
doc |
dev |
AGPL-3.0-or-later |
X | X | | | Fast sequencing quality metrics |
| sequana |
0.16.4 |
doc |
dev |
BSD-3-Clause |
X | X | | X | A set of standalone application and snakemake pipelines dedicated to... |
| sequana_pipetools |
0.9.4 |
|
|
BSD |
| | | X | A set of tools to help building or using Sequana pipelines |
| sequencetools |
1.6.0.0 |
|
|
MIT |
X | X | | | A tool (pileupCaller) for processing ancient DNA sequencing data |
| sequenoscope |
0.0.5 |
|
dev |
Apache-2.0 |
| | | X | sequenoscope is a versatile bioinformatic pipeline for the analysis of... |
| sequenza-utils |
3.0.0 |
|
|
GNU |
X | X | | | Analysis of cancer sequencing samples, utilities for the R package sequenza |
| sequip |
0.10 |
|
|
Public |
| | | X | Perl module for biological sequence analysis and supporting utilities.. |
| sequnwinder |
0.1.4 |
|
|
MIT |
| | | X | SeqUnwinder is a framework for characterizing class-discriminative... |
| seqverify |
1.3.0 |
|
|
GPL-3.0 |
| | | X | Seqverify analyzes whole genome sequencing data for gene-editing verification. |
| seqwish |
0.7.11 |
|
|
MIT |
X | | | | Alignment to variation graph inducer |
| seqyclean |
1.10.09 |
|
|
MIT |
X | X | | | Main purpose of this software is to pre-process NGS data in order to... |
| sercol |
1.0.0 |
|
|
Apache-2.0 |
| | | X | Rich collection class with grouping and filtering helpers |
| seroba |
1.0.2 |
|
|
GPL3.0 |
X | X | | X | SeroBA is a k-mer based Pipeline to identify the Serotype from Illumina... |
| serotypefinder |
2.0.2 |
|
|
Apache-2.0 |
| | | X | SerotypeFinder identifies the serotype in total or partial sequenced... |
| seshat |
0.10.0 |
doc |
|
MIT |
| | | X | Tools for programmatically annotating VCFs with the Seshat TP53 database. |
| sesimcmc |
4.36 |
|
|
MIT |
X | X | | | Motif finding with modified MCMC |
| setuptools_cython |
0.2.1 |
|
|
http://www.gnu. |
X | X | | X | Cython setuptools integration |
| seurat-scripts |
4.4.0 |
|
dev |
Apache-2.0 |
| | | X | A set of wrappers for individual components of the Seurat package. |
| sevenbridges-python |
2.11.2 |
|
dev |
Apache-2.0 |
X | X | | X | SBG API python client bindings |
| severus |
1.4 |
|
|
BSD-3-Clause |
| | | X | A tool for somatic structural variant calling using long reads |
| sexdeterrmine |
1.1.2 |
|
|
GPL-3.0-only |
| | | X | A python script carry out calculate the relative coverage of X and Y... |
| sff2fastq |
0.9.2 |
|
|
GPL-3 |
X | X | | | Extract 454 Genome Sequencer reads from a SFF file and convert them... |
| sfld |
1.1 |
|
dev |
Apache |
X | X | | | SFLD pre/post-processing |
| sfold |
2.2 |
|
|
OTHER |
X | | | | Software for Statistical Folding of Nucleic Acids |
| sfs |
0.1.0 |
|
|
MIT |
X | X | | | CLI tool for site frequency spectra. |
| sfs_code |
20150910 |
|
|
file |
X | X | | | This article introduces a new forward population genetic simulation... |
| sga |
0.10.15 |
|
|
GPLv3 |
X | X | | | SGA - String Graph Assembler. SGA is a de novo assembler for DNA... |
| sga_ice |
1.01 |
|
|
MIT |
| | | X | Iterative error correction of long 250 or 300 bp Illumina reads... |
| sgcocaller |
0.3.9 |
doc |
dev |
MIT |
X | X | | | Personalized haplotype construction and crossover calling in... |
| sgdemux |
1.2.0 |
|
|
For |
X | X | | | Tool for demultiplexing sequencing data generated on Singular... |
| shannon |
0.0.2 |
|
dev |
GPLv3 |
| | | X | A program for assembling transcripts from RNA-Seq data. |
| shannon_cpp |
0.5.0 |
|
|
GPL |
X | | | | shannon_cpp is command line tool for denovo rna assembly |
| shape_it |
1.0.1 |
|
|
LGPL |
X | | | | Shape alignment against a database of molecules |
| shapeit4 |
4.2.2 |
|
|
MIT |
X | | | | fast and accurate method for estimation of haplotypes (phasing) |
| shapeit5 |
5.1.1 |
doc |
dev |
MIT |
X | X | | | Fast and accurate method for estimation of haplotypes (phasing). |
| shapemapper |
1.2 |
|
|
GPL |
X | | | | ShapeMapper converts raw sequencing files into mutational profiles,... |
| shapeshifter |
1.1.1 |
|
|
MIT |
| | | X | A tool for managing large datasets |
| shapeshifter-cli |
1.0.0 |
|
|
MIT |
| | | X | A command-line tool for transforming large data sets |
| sharedmem |
0.3.6 |
|
|
GPL-3.0 |
X | X | | X | Dispatch your trivially parallizable jobs with sharedmem. |
| sharg |
1.1.1 |
doc |
dev |
BSD-3-Clause |
X | | | | A modern argument parser for C++ tools. |
| shark |
1.2.0 |
|
|
GPL-3.0-or-later |
X | X | | | Mapping-free filtering of useless RNA-Seq reads |
| shasta |
0.14.0 |
doc |
dev |
MIT |
X | X | | | De novo assembly from Oxford Nanopore reads. |
| shellescape |
3.4.1 |
|
|
MIT |
X | X | | X | Shell escape a string to safely use it as a token in a shell command... |
| sherpas |
1.0.2 |
|
|
MIT |
X | X | | | Screening Historical Events of Recombination in a Phylogeny via... |
| shigapass |
1.5.0 |
|
|
GPL3 |
| | | X | ShigaPass: An in silico tool to predict Shigella serotypes |
| shigatyper |
2.0.5 |
|
|
Public |
| | | X | Typing tool for Shigella spp. from WGS Illumina sequencing |
| shigeifinder |
1.3.5 |
|
|
GPL3 |
| | | X | Cluster informed Shigella and EIEC serotyping tool from Illumina reads... |
| shiptv |
0.4.1 |
|
|
Apache |
| | | X | Generate a standalone HTML file with an interactive phylogenetic tree... |
| shiver |
1.7.3 |
|
|
GPL-3.0 |
X | X | | X | SHIVER - Sequences from HIV Easily Reconstructed |
| shmlast |
1.6 |
|
|
BSD-3-Clause |
X | X | | X | conditional reciprocal best hits with LAST |
| shorah |
1.99.2 |
|
|
GPLv3 |
X | X | | | The Short Reads Assembly into Haplotypes (ShoRAH) program for inferring... |
| short-read-connector |
1.2.0 |
|
|
AGPL-3.0 |
X | | | | Short read connector enables the comparisons of two read sets |
| shortreadconnector |
1.1.3 |
|
|
GNU |
X | X | | | Short read connector enables the comparisons of two read sets |
| shortseq |
0.0.1 |
|
|
MIT |
X | X | | | \ ShortSeqs are compact and efficient Python objects that hold short... |
| shortstack |
4.1.1 |
|
|
MIT |
X | X | | X | ShortStack: Comprehensive annotation and quantification of small RNA genes |
| shorttracks |
1.2 |
|
dev |
MIT |
| | | X | ShortTracks : Useful length- and strand-based coverage files (bigwig)... |
| shovill |
1.1.0 |
|
|
GPL2 |
X | X | | X | Microbial assembly pipeline for Illumina paired-end reads |
| shovill-se |
1.1.0se |
|
|
GPL2 |
| | | X | An fork of Shovill (microbial assembly pipeline for Illumina paired-end... |
| showit |
1.1.4 |
|
|
MIT |
| | | X | simple and sensible display of images in python |
| shustring |
2.6 |
|
|
GPL-2 |
X | X | | | Program for Computing SHortest Unique SubSTRINGs |
| siann |
1.3 |
|
|
GPL3 |
| | | X | SIANN was created to allow creation of local small sets of... |
| sibelia |
3.0.7 |
|
|
GPLv2 |
X | X | | | Genome comparison via de Bruijn graph. |
| sibeliaz |
1.2.6 |
doc |
dev |
Custom |
X | X | | | A fast whole-genome aligner based on de Bruijn graphs. |
| sicer |
1.1 |
|
|
MIT |
X | X | | X | A clustering approach for identification of enriched domains from... |
| sicer2 |
1.0.3 |
|
dev |
MIT |
X | X | | | Redesigned and improved ChIP-seq broad peak calling tool SICER. |
| sickle |
0.7.0 |
|
|
BSD |
X | | | X | A lightweight OAI client library for Python |
| sickle-trim |
1.33 |
|
|
MIT |
X | X | | | Windowed Adaptive Trimming for fastq files using quality |
| sidr |
0.0.2a2 |
|
|
MIT |
| | | X | Sequence Idenification using Decision tRees; a tool to classify DNA... |
| sierrapy |
0.4.3 |
|
|
MIT |
| | | X | A Client of HIVdb Sierra GraphQL Webservice. |
| sift4g |
2.0.0 |
|
|
GPL-3.0 |
X | | | | SIFT 4G is a faster version of SIFT that enables us to scale up and... |
| sigmut |
1.0 |
|
dev |
BSD |
| | | X | Wrapper of SigProfiler (Copyright(c) 2019, Erik Bergstrom [Alexandrov Lab]) |
| sigprofilerassignment |
0.1.8 |
|
|
BSD-2-Clause |
| | | X | SigProfilerAssignment - Assignment of known mutational signatures to... |
| sigprofilermatrixgenerator |
1.2.31 |
|
dev |
BSD-2-Clause |
| | | X | SigProfiler matrix generator tool. |
| sigprofilerplotting |
1.4.1 |
doc |
dev |
BSD-2-Clause |
| | | X | SigProfiler plotting tool. |
| sim4db |
2008 |
|
|
GPL |
X | X | | | Sim4db and leaff: Utilities for fast batch spliced alignment and... |
| simba |
1.2 |
|
dev |
BSD-3 |
| | | X | SIMBA - SIngle-cell eMBedding Along with features |
| simba_pbg |
1.2 |
|
dev |
BSD-3 |
X | X | | | A customized PyTorch-BigGraph (PBG) package for `simba` |
| simbac |
0.1a |
|
|
GPL-3.0 |
X | X | | | SimBac simulates bacterial genomes with the clonal genealogy under a... |
| simka |
1.5.3 |
|
|
AGPL-3.0-or-later |
X | X | | | Simka and simkaMin are de novo comparative metagenomics tools. Simka... |
| simlord |
1.0.4 |
|
|
MIT |
X | X | | X | SimLoRD is a read simulator for long reads from third generation... |
| simple_sv_annotation |
2019.02.18 |
|
|
MIT |
X | X | | X | Simplify snpEff annotations for interesting cases |
| simpleaf |
0.19.4 |
|
|
BSD |
X | X | | | A rust framework to make using alevin-fry even simpler. |
| simplejson |
3.8.1 |
|
|
MIT |
X | X | | | Simple, fast, extensible JSON encoder/decoder for Python |
| simplesam |
0.1.4.1 |
doc |
dev |
MIT |
| | | X | Simple pure Python SAM parser and objects for working with SAM records |
| simscsntree |
0.0.9 |
|
|
MIT |
| | | X | Simulating single cell sequencing data |
| simug |
1.0.1 |
|
dev |
MIT |
| | | X | A simple, flexible, and powerful tool to simulate genome sequences with... |
| simwalk2 |
2.91 |
|
|
INDIVIDUAL |
X | | | | Stochastic Statistical Analysis of Qualitative Traits |
| sina |
1.7.2 |
doc |
|
GPLv3 |
X | X | | | Reference based multiple sequence alignment |
| sincei |
0.4 |
|
|
MIT |
| | | X | A user-friendly toolkit for QC, counting, clustering and plotting of... |
| singlecell-barcodes |
0.2 |
|
|
MIT |
X | X | | X | whitelisted singlecell barcodes and information regarding where... |
| singlecellnet-cli |
0.0.1 |
|
|
Apache-2.0 |
| | | X | A set of command-line wrappers for the core functions in the... |
| singlem |
0.18.3 |
doc |
dev |
GPL-3.0-or-later |
| | | X | SingleM is a tool for profiling shotgun metagenomes. It has a... |
| singularity |
2.4.2 |
|
|
BSD |
X | | | | Singularity - Enabling users to have full control of their environment |
| sinto |
0.10.1 |
doc |
dev |
MIT |
| | | X | sinto: tools for single-cell data processing |
| sipros |
4.01 |
|
|
MIT |
| | | X | Tools for stable isotopic mass spectrometry-based metaproteomics |
| sirius-csifingerid |
5.8.6 |
doc |
dev |
AGPL-3.0-only |
X | X | | | SIRIUS (CLI + GUI) LC-MS/MS data analyses framework. Includes: SIRIUS,... |
| sis |
0.1.2 |
|
|
GPLv2+ |
X | X | | X | A tool that uses mummer to scaffold small genomes. |
| sistr_cmd |
1.1.3 |
|
dev |
Apache-2.0 |
X | | | X | Salmonella In Silico Typing Resource (SISTR) commandline tool for... |
| sixgill |
0.2.4 |
|
dev |
Apache |
X | X | | X | six-frame genome-inferred libraries for LC-MS/MS |
| sizemeup |
1.3.0 |
|
|
MIT |
| | | X | A simple tool to determine the genome size of an organism |
| ska |
1.0 |
|
|
GPL-3 |
X | X | | | SKA (Split Kmer Analysis) |
| ska2 |
0.4.0 |
|
|
Apache-2.0 |
X | X | | | SKA (Split Kmer Analysis) version 2 |
| skani |
0.2.2 |
|
|
MIT |
X | X | | | skani is a fast and robust tool for calculating ANI between metagenome... |
| skc |
0.1.0 |
|
|
MIT |
X | X | | | Shared k-mer content between two genomes |
| skder |
1.2.9 |
|
dev |
BSD-3-Clause |
X | X | | | skDER & CiDDER: efficient & high-resolution dereplication... |
| skesa |
2.5.1 |
|
|
Public |
X | X | | | Strategic Kmer Extension for Scrupulous Assemblies & Sequence... |
| sketchy |
0.6.0 |
|
|
MIT |
X | X | | | Real-time lineage hashing and genotyping of bacterial pathogens |
| skewer |
0.2.2 |
|
|
MIT |
X | X | | | A fast and accurate adapter trimmer for paired-end reads. |
| skmer |
3.3.0 |
|
|
BSD-3-Clause |
X | X | | X | Assembly-free and alignment-free tool for estimating genomic distances... |
| skyline2isocor |
1.0.0 |
|
|
GPL-3.0-or-later |
| | | X | Convert skyline output to IsoCor input format |
| slamdunk |
0.4.3 |
doc |
dev |
GNU |
X | | | X | Slamdunk is a software tool for SLAMseq data analysis. |
| slamem |
0.8.5 |
|
|
GPL-3.0 |
X | X | | | slamem bioconda package from https://github.com/fjdf/slaMEM |
| slang |
2.3.0 |
|
|
GPL |
X | | | | S-Lang is a multi-platform programmer's library designed to allow a... |
| slclust |
02022010 |
|
|
Artistic |
X | X | | | A utility that performs single-linkage clustering with the option of... |
| slicedimage |
3.1.2 |
|
|
MIT |
| | | X | Python module to access sliced imaging data |
| slimfastq |
2.04 |
|
|
BSD-3-Clause |
X | X | | | slimfastq would efficiently compresses/decompresses fastq files |
| slimm |
0.3.4 |
|
|
https://github. |
X | X | | | SLIMM - Species Level Identification of Microbes from Metagenomes |
| slivar |
0.3.1 |
|
|
MIT |
X | | | | filter/annotate variants in VCF/BCF format with simple expressions |
| slncky |
1.0.4 |
|
|
MIT |
X | X | | X | slncky is a tool for lncRNA discovery from RNA-Seq data. slncky filters... |
| sloika |
2.0.1 |
|
|
Mozilla |
X | X | | | Sloika is Oxford Nanopore Technologies' software for training... |
| slow5curl |
0.2.1 |
|
|
MIT |
X | X | | | Tool for accessing remote BLOW5 files. |
| slow5tools |
1.3.0 |
|
|
MIT |
X | X | | | Toolkit for S/bLOW5 format |
| smaca |
1.2.3 |
|
|
GPL-3.0 |
X | | | | smaca is a python tool to detect putative SMA carriers and estimate the... |
| smafa |
0.8.0 |
|
dev |
GPL-3.0-or-later |
X | | | | smafa is a tool for querying and clustering pre-aligned small... |
| smallgenomeutilities |
0.5.0 |
|
|
GNU |
X | X | | X | A collection of scripts that are useful for dealing with viral RNA NGS data. |
| smalt |
0.7.6 |
|
|
GPLv3 |
X | X | | | SMALT aligns DNA sequencing reads with a reference genome. |
| smartdenovo |
1.0.0 |
|
|
GPLv3 |
X | X | | | Ultra-fast de novo assembler using long noisy reads |
| smartmap |
1.0.0 |
|
|
MIT |
X | X | | | SmartMap: Bayesian Analysis of Ambiguously Mapped Reads |
| smashbenchmarking |
1.0.1 |
|
|
BSD |
X | X | | | Check the accuracy of one VCF callset against another |
| smashpp |
23.09 |
|
|
GPL-3.0-or-later |
X | | | | A fast tool to find and visualize rearrangements in DNA sequences |
| smcounter2 |
0.1.2018.08.28 |
|
|
MIT |
X | X | | X | smCounter2: an accurate low-frequency variant caller for targeted... |
| smcpp |
1.15.4 |
|
dev |
BSD |
X | | | | SMC++ infers population history from whole-genome sequence data. |
| smeg |
1.1.5 |
|
|
MIT |
X | | | X | Strain-level Metagenomic Estimation of Growth rate (SMEG) measures... |
| smetana |
1.2.0 |
|
|
Apache-2.0 |
| | | X | Species METabolic interaction ANAlysis (SMETANA) is a python-based... |
| smhasher |
0.150.1 |
|
|
MIT |
X | X | | | Python extension for smhasher hash functions |
| smina |
2017.11.9 |
|
|
GNU |
X | X | | | A fork of AutoDock Vina that is customized to better support scoring... |
| smncopynumbercaller |
1.1.2 |
|
|
Apache |
| | | X | Call copy number of SMN1, SMN2, and SMN2Δ7–8 from a BAM file. |
| smof |
2.22.4 |
|
|
MIT |
| | | X | UNIX-style utilities for FASTA file exploration |
| smoothxg |
0.8.0 |
|
|
MIT |
X | | | | Local reconstruction of variation graphs using partial order alignment |
| smoove |
0.2.8 |
|
|
Apache-2.0 |
X | | | | structural variant calling and genotyping with existing tools, but, smoothly |
| smudgeplot |
0.4.0 |
|
dev |
Apache-2.0 |
X | X | | | Inference of ploidy and heterozygosity structure using whole genome... |
| smudgeplot_rn |
0.2.5_RN |
|
|
Apache-2.0 |
X | X | | | Inference of ploidy and heterozygosity structure using whole genome... |
| snakeatac_env |
0.1.1 |
doc |
|
GPL-3.0-or-later |
| | | X | snakemake based ATACseq pipeline |
| snakebids |
0.14.0 |
|
|
MIT |
| | | X | BIDS integration into snakemake workflows |
| snakedeploy |
0.10.4 |
|
dev |
MPL-2.0 |
| | | X | Helper for deploying published Snakemake pipelines. |
| snakefmt |
0.10.2 |
|
|
MIT |
| | | X | The uncompromising Snakemake code formatter |
| snakelines |
1.1.8 |
|
|
CC |
| | | X | Computational pipelines for processing of paired-end sequencing reads. |
| snakemake |
8.30.0 |
doc |
dev |
MIT |
X | X | | X | A popular workflow management system aiming at full in-silico reproducibility. |
| snakemake-executor-plugin-azure-batch |
0.1.3 |
|
|
MIT |
| | | X | A Snakemake executor plugin for submitting jobs to Microsoft Azure Batch. |
| snakemake-executor-plugin-cluster-generic |
1.0.9 |
|
|
MIT |
| | | X | Generic cluster executor for Snakemake |
| snakemake-executor-plugin-cluster-sync |
0.1.4 |
|
|
MIT |
| | | X | A Snakemake executor plugin for cluster jobs that are executed synchronously. |
| snakemake-executor-plugin-drmaa |
0.1.5 |
|
|
MIT |
| | | X | A snakemake executor plugin for submission of jobs via DRMAA. |
| snakemake-executor-plugin-googlebatch |
0.5.0 |
|
|
MIT |
| | | X | Snakemake executor plugin for Google Batch |
| snakemake-executor-plugin-kubernetes |
0.3.2 |
|
|
MIT |
| | | X | A snakemake executor plugin for submission of jobs to Kubernetes |
| snakemake-executor-plugin-lsf |
0.2.6 |
|
|
MIT |
| | | X | A Snakemake executor plugin for submitting jobs to a LSF cluster. |
| snakemake-executor-plugin-lsf-jobstep |
0.1.10 |
|
|
MIT |
| | | X | A Snakemake executor plugin for running bjobs jobs inside of LSF jobs... |
| snakemake-executor-plugin-slurm |
1.0.1 |
|
dev |
MIT |
| | | X | A Snakemake executor plugin for submitting jobs to a SLURM cluster. |
| snakemake-executor-plugin-slurm-jobstep |
0.3.0 |
|
|
MIT |
| | | X | A Snakemake executor plugin for running srun jobs inside of SLURM jobs... |
| snakemake-executor-plugin-tes |
0.1.3 |
|
|
MIT |
| | | X | A Snakemake executor plugin for submitting jobs to a GA4GH TES cluster. |
| snakemake-interface-common |
1.17.4 |
|
|
MIT |
| | | X | Common functions and classes for Snakemake and its plugins |
| snakemake-interface-executor-plugins |
9.3.3 |
|
|
MIT |
| | | X | This package provides a stable interface for interactions between... |
| snakemake-interface-report-plugins |
1.1.0 |
|
|
MIT |
| | | X | This package provides a stable interface for interactions between... |
| snakemake-interface-storage-plugins |
3.4.0 |
|
dev |
MIT |
| | | X | This package provides a stable interface for interactions between... |
| snakemake-minimal |
8.30.0 |
doc |
dev |
MIT |
X | X | | X | A popular workflow management system aiming at full in-silico reproducibility. |
| snakemake-storage-plugin-azure |
0.4.2 |
|
|
MIT |
| | | X | A Snakemake storage plugin to read and write from Azure Blob Storage |
| snakemake-storage-plugin-fs |
1.0.6 |
|
|
MIT |
| | | X | A Snakemake storage plugin that reads and writes from a locally mounted... |
| snakemake-storage-plugin-ftp |
0.1.2 |
|
|
MIT |
| | | X | A Snakemake plugin for handling input and output via FTP |
| snakemake-storage-plugin-gcs |
1.1.3 |
|
|
MIT |
| | | X | A Snakemake storage plugin for Google Cloud Storage |
| snakemake-storage-plugin-http |
0.2.3 |
|
|
MIT |
| | | X | Snakemake storage plugin for donwloading input files from HTTP(s). |
| snakemake-storage-plugin-irods |
0.2.0 |
|
|
MIT |
| | | X | A Snakemake plugin for handling input and output on iRODS |
| snakemake-storage-plugin-s3 |
0.3.1 |
doc |
|
MIT |
| | | X | A Snakemake storage plugin for S3 API storage (AWS S3, MinIO, etc.) |
| snakemake-storage-plugin-sftp |
0.1.2 |
|
|
MIT |
| | | X | A Snakemake storage plugin that handles files on an SFTP server. |
| snakemake-storage-plugin-sharepoint |
0.4.4 |
|
|
MIT |
| | | X | Snakemake storage plugin for reading and writing files on Microsoft SharePoint. |
| snakemake-storage-plugin-zenodo |
0.1.4 |
|
|
MIT |
| | | X | A Snakemake storage plugin for reading from and writing to zenodo.org |
| snakemake-wrapper-utils |
0.6.2 |
|
|
MIT |
| | | X | A collection of utility functions and classes for Snakemake wrappers. |
| snakeobjects |
3.1.4 |
|
dev |
MIT |
| | | X | Snakeobjects, an object-oriented workflow management system based on snakemake |
| snakeparse |
0.1.0 |
|
|
MIT |
X | X | | X | Making Snakemake workflows into full-fledged command line tools since 1999. |
| snakesv |
0.8 |
|
|
MIT |
| | | X | snakeSV: Flexible framework for large-scale SV discovery |
| snaketool-utils |
0.0.5 |
|
|
MIT |
| | | X | Utility functions for Snaketool CLI for bioinformatics tools |
| snap |
2013_11_29 |
|
|
MIT |
X | X | | | Semi-HMM-based Nucleic Acid Parser -- gene prediction tool |
| snap-aligner |
2.0.3 |
|
dev |
Apache |
X | | | | Scalable Nucleotide Alignment Program -- a fast and accurate read... |
| snapatac2 |
2.8.0 |
doc |
dev |
MIT |
X | X | | | SnapATAC2: Single-cell epigenomics analysis pipeline. |
| snapgene-reader |
0.1.21 |
doc |
dev |
MIT |
| | | X | Convert Snapgene *.dna files dict/json/biopython. |
| snaptools |
1.4.8 |
|
|
LICENSE |
| | | X | A module for working with snap files in Python |
| sneakernet-qc |
0.27.2 |
|
|
MIT |
| | | X | A QC pipeline for raw reads |
| sneep |
1.1 |
|
dev |
MIT |
X | X | | | Identify regulatory non-coding SNPs (rSNPs) |
| sniffles |
2.6.1 |
doc |
dev |
MIT |
X | X | | X | Sniffles is a structural variation caller using third generation... |
| snikt |
0.5.0 |
|
|
MIT |
| | | X | Identify and remove adapter/systemic contamination in metagenomic... |
| snipe |
0.1.6 |
|
|
AGPL-3.0-or-later |
| | | X | SRA-Scale sequence QC and analysis |
| snipit |
1.6 |
|
|
GPL-3.0-or-later |
| | | X | Visualize snps relative to a reference sequence |
| snippy |
4.6.0 |
|
|
GPL-2.0 |
X | X | | X | Rapid bacterial SNP calling and core genome alignments |
| snk |
0.31.1 |
|
dev |
MIT |
| | | X | A Snakemake CLI and Workflow Management System. |
| snk-cli |
0.7.2 |
|
dev |
MIT |
| | | X | Dynamically generate CLIs from Snakemake configuration files |
| snmf |
1.2 |
|
|
GNU |
X | X | | | Fast and efficient program for estimating individual admixture... |
| snns |
4.3 |
|
|
LGPL |
X | | | | Stuttgart Neural Network Simulator (SNNS) |
| snoscan |
1.0 |
|
|
GNU |
X | X | | | Search for C/D box methylation guide snoRNA genes in a genomic sequence |
| snostrip |
2.0.2 |
|
|
GPL3 |
X | | | | Automatic snoRNA annotation pipeline |
| snp-dists |
0.8.2 |
|
|
GPL3 |
X | X | | | Convert a FASTA alignment to SNP distance matrix |
| snp-mutator |
1.2.0 |
|
|
BSD |
| | | X | Generate mutated sequence files from a reference genome. |
| snp-pileup |
0.6.2 |
|
|
MIT |
X | | | | Compute SNP pileup at reference positions in one or more input bam... |
| snp-pipeline |
2.2.1 |
|
|
BSD |
X | X | | X | Script and functions for SNP matrix construction |
| snp-sites |
2.5.1 |
|
|
GPL-3.0 |
X | X | | | Finds SNP sites from a multi-FASTA alignment file. |
| snp2cell |
0.3.0 |
|
|
BSD-3-Clause |
| | | X | A package for finding enriched regulatory networks from GWAS and single... |
| snpeff |
5.2 |
|
|
LGPLv3 |
X | X | | X | Genetic variant annotation and effect prediction toolbox |
| snpgenie |
1.0 |
|
|
GPL-3.0 |
| | | X | Program for estimating πN/πS, dN/dS, and other diversity measures from... |
| snpick |
1.0.0 |
doc |
dev |
GPL-3.0-or-later |
X | X | | | A fast and memory-efficient tool for SNP extraction from genomic alignments. |
| snpiphy |
0.5 |
|
|
GPLv3 |
X | | | X | An automated snp phylogeny pipeline |
| snpomatic |
1.0 |
|
|
GPL3 |
X | X | | | SNP-o-matic is a fast, stringent short-read mapping software. |
| snpsift |
5.2 |
|
|
LGPLv3 |
X | X | | X | Toolbox that allows you to filter and manipulate annotated files |
| snpsplit |
0.6.0 |
|
|
GPL-3.0-or-later |
X | X | | X | SNPsplit is an allele-specific alignment sorter which is designed to... |
| snver |
0.5.3 |
|
|
GNU |
| | | X | SNVer is a statistical tool for calling common and rare variants in... |
| snvphyl-tools |
1.8.2 |
|
|
apache_2.0 |
X | | | | The SNVPhyl (Single Nucleotide Variant PHYLogenomics) pipeline is a... |
| soapaligner |
2.21 |
|
|
GPL |
X | X | | | SOAPaligner/soap2 is an updated version of SOAP software for short... |
| soapcoverage |
2.7.7 |
|
|
GPL |
X | X | | | SOAPcoverarge can calculate sequencing coverage or physical coverage as... |
| soapdenovo-trans |
1.04 |
|
|
GPLv3 |
X | X | | | SOAPdenovo-Trans is a de novo transcriptome assembler basing on the... |
| soapdenovo2 |
2.40 |
|
|
GPL |
X | X | | | SOAPdenovo is a novel short-read assembly method that can build a de... |
| soapdenovo2-errorcorrection |
2.0 |
|
|
GNU |
X | X | | | Error correction for soapdenovo2. |
| soapdenovo2-gapcloser |
1.12 |
|
|
GNU |
X | X | | | a tool named GapCloser for SOAPdenovo. |
| soapdenovo2-prepare |
2.0 |
|
|
GPL-3.0 |
X | X | | | SoapDenovo2 data prepare module using assembled contig to do scaffold assembly. |
| soapec |
2.03 |
|
|
GNU |
X | | | | a correction tool for SOAPdenovo |
| soapsplice |
1.10 |
|
|
freely |
X | | | | We have developed a tool SOAPsplice for genome-wide ab initio detection... |
| socksipy-branch |
1.01 |
|
|
BSD |
X | X | | X | A Python SOCKS module |
| socru |
2.2.4 |
|
|
GPLv3 |
X | X | | X | Order and orientation of complete bacterial genomes |
| soda-gallery |
1.2.0 |
doc |
|
MIT |
| | | X | Python-based UCSC genome browser gallery generator |
| sodar-cli |
0.1.0 |
|
|
MIT |
| | | X | Command line interface to SODAR via REST API |
| softsv |
1.4.2 |
doc |
|
GPL-3.0-only |
X | | | | SoftSV is a tool for the detection of small and large deletions,... |
| solexaqa |
3.1.7.1 |
|
|
GPLv3 |
X | | | | Quality statistics and visual representations for second-generation... |
| solote |
1.09 |
|
|
GPL |
| | | X | A conversion utility is conveniently packaged with SoloTE, in order to... |
| solvebio |
2.30.0 |
doc |
|
MIT |
X | X | | X | The SolveBio Python client |
| somalier |
0.2.19 |
doc |
dev |
MIT |
X | | | | fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs. |
| somatic-sniper |
1.0.5.0 |
|
|
MIT |
X | X | | | A tool to call somatic single nucleotide variants. |
| somaticseq |
3.10.0 |
|
dev |
BSD-2-Clause |
X | | | X | An ensemble approach to accurately detect somatic mutations. |
| sompy |
0.1.1 |
|
|
MIT |
X | X | | X | Numpy based SOM Library. |
| sonicparanoid |
2.0.8 |
doc |
dev |
GPL-3.0-only |
X | X | | | SonicParanoid: fast, accurate, and comprehensive orthology inference... |
| sonlib |
2.0.dev88 |
|
|
MIT |
X | X | | X | Small general purpose library for C and Python with focus on bioinformatics. |
| sonneityping |
20210201 |
|
|
None |
| | | X | Sonneityping parses the output of mykrobe predict for Shigella sonnei |
| sopa |
1.1.5 |
|
dev |
BSD-3-Clause |
| | | X | Spatial-omics pipeline and analysis. |
| sorted_nearest |
0.0.39 |
|
dev |
BSD-3-Clause |
X | X | | | Find nearest interval. |
| sortmerna |
4.3.7 |
doc |
dev |
LGPL-3.0-only |
X | X | | | SortMeRNA is a biological sequence analysis tool for filtering, mapping... |
| souporcell |
2.5 |
|
|
MIT |
X | | | | Clustering scRNAseq by genotypes. |
| sourcepredict |
0.5.1 |
|
dev |
GPL-3.0-or-later |
| | | X | Classification and prediction of the origin of metagenomic samples. |
| sourcetracker |
2.0.1 |
doc |
dev |
modified |
| | | X | Python implementation of the SourceTracker R package. |
| sourmash |
4.8.14 |
doc |
dev |
BSD-3-Clause |
X | X | | X | Compute and compare MinHash signatures for DNA data sets. |
| spacepharer |
5.c2e680a |
|
|
GPL-3 |
X | X | | | SpacePHARER: Sensitive identification of phages from CRISPR spacers in... |
| spades |
4.1.0 |
doc |
dev |
GPL-2.0-only |
X | X | | | SPAdes (St. Petersburg genome assembler) is intended for both standard... |
| spagrn |
1.1.0 |
|
|
GPL-3.0-or-later |
| | | X | A comprehensive tool to infer TF-centered, spatial gene regulatory... |
| spaln |
3.0.6 |
doc |
dev |
GPL-2.0-or-later |
X | X | | | Map and align a set of cDNA/EST or protein sequences onto a genome |
| spanki |
0.5.1 |
|
|
GPLv3 |
X | X | | | Spanki is a set of tools to facilitate analysis of alternative splicing... |
| spapros |
0.1.5 |
|
|
MIT |
| | | X | Probe set selection for targeted spatial transcriptomics. |
| sparc |
20160205 |
|
|
MIT |
X | X | | | A sparsity-based consensus algorithm for long erroneous sequencing reads. |
| sparcc |
0.1.0 |
|
|
MIT |
| | | X | SparCC is a python module for computing correlations in compositional... |
| sparse-neighbors-search |
0.7 |
|
|
MIT |
X | X | | | Approximate k-nearest neighbors search on sparse datasets |
| sparseassembler |
20160205 |
|
|
GPL-3.0 |
X | X | | | A sparse k-mer graph based, memory-efficient genome assembler |
| sparsehash |
2.0.2 |
|
|
|
X | | | | None |
| spatialleiden |
0.2.0 |
doc |
|
MIT |
| | | X | Implementation of multiplex Leiden for analysis of spatial omics data. |
| spatyper |
0.3.3 |
|
|
LGPL-3 |
| | | X | Computational method for finding spa types. |
| spclust |
28.5.19 |
|
|
gpl-3.0-or-later |
X | X | | | Spectral clustering for biological sequences |
| spec2vec |
0.8.0 |
doc |
dev |
Apache-2.0 |
| | | X | Word2Vec based similarity measure of mass spectrometry data. |
| spectacle |
1.4 |
|
|
GPL-3.0 |
X | | | X | This software implements a spectral learning algorithm for hidden... |
| spectra-cluster-cli |
1.1.2 |
|
|
Apache-2.0 |
X | X | | X | This is a stand-alone implementation of the new updated PRIDE Cluster... |
| spectral_hk |
0.1 |
|
|
PUBLIC |
X | X | | | NCGC Spectral HashKey |
| spectrassembler |
0.0.1a1 |
|
|
MIT |
X | | | X | Tool (experimental) to compute layout from overlaps with spectral algorithm |
| spectrum_utils |
0.4.2 |
doc |
dev |
Apache |
| | | X | Mass spectrometry utility functions |
| sphae |
1.4.6 |
doc |
dev |
MIT |
| | | X | Phage toolkit |
| sphinx-argparse |
0.1.15 |
|
|
MIT |
X | X | | | Sphinx extension that automatically document argparse commands and options |
| sphinxcontrib-programoutput |
0.8 |
|
|
BSD |
X | X | | | Sphinx extension to include program output |
| spine |
0.3.2 |
|
|
GPL-3.0 |
X | X | | X | Identification of conserved nucleotide core genome of bacteria and... |
| spingo |
1.3 |
|
|
https://github. |
X | | | | Species level IdentificatioN of metaGenOmic amplicons |
| splash |
2.11.0 |
|
|
GPL-3.0-or-later |
X | X | | | Unsupervised and reference-free unifying framework to discover... |
| spliceai |
1.3.1 |
|
|
GPLv3 |
| | | X | A deep learning-based tool to identify splice variants. |
| spliceai-wrapper |
0.1.0 |
|
|
MIT |
| | | X | A caching wrapper for Illumina SpliceAI. |
| spliced_bam2gff |
1.3 |
doc |
dev |
MPL-2 |
X | X | | | A tool to convert spliced BAM alignments into GFF2 format |
| splicemap |
3.3.5.2 |
|
|
file |
X | X | | | Detects splice junctions from RNA-seq data. This method does not depend... |
| splitcode |
0.31.2 |
doc |
dev |
BSD-2-Clause |
X | X | | | Flexible parsing, interpretation, and editing of technical sequences |
| splitmem |
1.0 |
|
|
Apache |
X | X | | | Graphical pan-genome analysis with suffix skips |
| splitp |
0.2.0 |
|
|
BSD-3-Clause |
X | X | | | splitp is a streaming read pre-preprocessor. |
| splitubam |
0.1.1 |
|
dev |
MIT |
X | X | | | Split one ubam into multiple, per line, fast |
| spoa |
4.1.4 |
doc |
dev |
MIT |
X | X | | | SIMD partial order alignment tool/library. |
| spotyping |
2.1 |
|
|
GPL-3 |
X | X | | X | SpoTyping: fast and accurate in silico Mycobacterium spoligotyping from... |
| spotyping3 |
3.0 |
|
|
GPL-3 |
| | | X | SpoTyping3: fast and accurate in silico Mycobacterium spoligotyping... |
| spp-dcj |
2.0.0 |
|
dev |
MIT |
| | | X | A tool for solving the small parsimony problem for natural genomes |
| sprai |
0.9.9.23 |
|
|
MIT |
X | | | | Sprai (single-pass read accuracy improver) is a tool to correct... |
| spreadgltools |
1.1.0 |
doc |
|
MIT |
| | | X | Visualising pathogen dispersal in a high-performance browser application |
| spring |
1.1.1 |
|
dev |
Free |
X | | | | Spring is a compression tool for Fastq files. |
| springsuite |
0.2 |
|
|
GPL-2.0-only |
| | | X | The Spring Suite contains tools to predict and model protein-protein... |
| sprinkles |
0.4.6 |
|
|
MIT |
X | X | | | Plugins! Easy! |
| sprinter |
1.0.0 |
doc |
dev |
ACADEMIC |
| | | X | Single-cell Proliferation Rate Inference in Non-homogeneous Tumours... |
| spydrpick |
1.2.0 |
|
|
GNU |
X | X | | | Mutual information based detection of pairs of genomic loci co-evolving... |
| sqlalchemy-datatables |
2.0.1 |
|
|
MIT |
X | X | | X | SQLAlchemy integration of jQuery DataTables |
| sqlalchemy-utils |
0.31.6 |
|
|
BSD |
X | | | | Various utility functions for SQLAlchemy. |
| sqlitebrowser |
3.8.0 |
|
|
GPLv3 |
X | | | | None |
| sqt |
0.8.0 |
|
|
MIT |
X | X | | | Command-line tools for the analysis of high-throughput sequencing data |
| squeakr |
0.7 |
|
dev |
BSD-3-Clause |
X | X | | | An Exact and Approximate k-mer Counting System |
| squeegee |
0.2.0 |
|
|
MIT |
| | | X | squeegee, de novo computational contamination detection tool for... |
| squid |
1.5 |
|
|
BSD |
X | X | | | Detector for fusion-gene and non-fusion-gene transcriptomic structural... |
| squigualiser |
0.6.3 |
|
|
MIT |
| | | X | Visualise ONT raw signals |
| squigulator |
0.4.0 |
|
|
MIT |
X | X | | | A tool for simulating nanopore raw signal data |
| squire |
0.9.9.92 |
|
|
GNU |
| | | X | Quantitative, locus-specific view of transposable element expression. |
| squirrel |
1.0.13 |
|
|
GPL-3.0-only |
| | | X | Some QUIck Reconstruction to Resolve Evolutionary Links |
| squizz |
0.99d |
|
|
GPL-2.0-only |
X | X | | | Squizz is a sequence/alignment format checker, but it has some... |
| sra-human-scrubber |
2.2.1 |
|
|
Public |
| | | X | An SRA tool identifies and removes any significant human read, and... |
| sra-tools |
3.2.0 |
doc |
dev |
Public |
X | X | | | The SRA Toolkit and SDK from NCBI. |
| sracat |
0.2 |
|
dev |
BSD-3-Clause |
X | X | | | a command-line tool for extracting unordered read data from SRA files |
| srahunter |
0.0.7 |
|
dev |
MIT |
| | | X | srahunter is a tool for processing SRA accession numbers. |
| srax |
1.5 |
doc |
dev |
GPL-3.0-only |
| | | X | Systematic Resistome Analysis |
| srnamapper |
1.0.11 |
|
|
GPL-3.0-or-later |
X | X | | | Mapping small RNA data to a genome. |
| srnaminer |
1.1.2 |
|
dev |
CC |
| | | X | sRNAminer: a Multifunctional Toolkit for Next Generation Sequencing... |
| srnapipe |
1.2 |
|
|
Academic |
X | X | | X | Pipeline for bioinformatic in-depth exploration of small RNA-seq data |
| srprism |
2.4.24 |
|
|
Public |
X | X | | | SRPRISM - Short Read Alignment Tool |
| srst2 |
0.2.0 |
|
|
BSD |
X | X | | X | Short Read Sequence Typing for Bacterial Pathogens |
| ssake |
4.0 |
|
|
GPL-2.0 |
X | X | | X | SSAKE is a genomics application for de novo assembly of millions of... |
| sscocaller |
0.2.2 |
doc |
dev |
MIT |
X | X | | | Haplotyping single-cell DNA sequenced gamete cells. |
| ssdrippipeline |
0.0.5 |
doc |
dev |
GPL3 |
| | | X | Useful tools for the analysis of ssDRIP-seq data |
| sshmm |
1.0.7 |
|
|
GPL-3.0 |
X | | | | ssHMM is an RNA motif finder that recovers sequence-structure motifs... |
| sspace_basic |
2.1.1 |
doc |
dev |
GPL-2.0-only |
| | | X | Scaffolding Pre-Assemblies After Contig Extension (SSPACE) |
| ssu-align |
0.1.1 |
|
|
BSD |
X | X | | | SSU-ALIGN: structural alignment of SSU rRNA sequences |
| ssuissero |
1.0.1 |
|
|
MIT |
| | | X | Rapid Streptococcus suis serotyping pipeline for Nanopore Data |
| stacks |
2.68 |
|
|
GPL-3 |
X | X | | | Stacks is a software pipeline for building loci from short-read sequences. |
| stacks_summary |
1.1 |
|
|
GNU |
X | X | | | Stacks reports generator |
| staden_io_lib |
1.15.0 |
doc |
dev |
BSD-3-Clause |
X | X | | | Staden io_lib is a library of file reading and writing code e.g. for... |
| stag |
0.8.3 |
|
dev |
GPL-3.0 |
| | | X | A hierarchical taxonomic classifier for metagenomic sequences |
| stamp |
2.1.3 |
|
|
GPL-3.0 |
X | X | | X | A graphical software package for analyzing taxonomic and functional profiles. |
| staphb_toolkit |
2.0.1 |
doc |
dev |
GPLv3 |
| | | X | A ToolKit of commonly used Public Health Bioinformatics Tools |
| staphopia-sccmec |
1.0.0 |
|
|
MIT |
| | | X | Predicts Staphylococcus aureus SCCmec type based on primers. |
| star |
2.7.11b |
doc |
dev |
GPL-3.0-or-later |
X | X | | | An RNA-seq read aligner. |
| star-fusion |
1.14.0 |
doc |
dev |
BSD-3-Clause |
X | X | | X | STAR-Fusion fusion variant caller. All dependencies required to run... |
| staramr |
0.11.0 |
doc |
dev |
Apache |
X | X | | X | Scan genome contigs against the ResFinder and PointFinder databases |
| starcatpy |
1.0.8 |
|
dev |
MIT |
| | | X | Implements *CellAnnotator (aka *CAT/starCAT), annotating scRNA-Seq with... |
| starcode |
1.4 |
|
|
GPLv3 |
X | X | | | Starcode: sequence clustering based on all-pairs search |
| stare-abc |
1.0.4 |
|
|
MIT |
X | X | | | Calculate Gene-TF affinities via enhancer-gene interactions |
| starfish |
0.3.1 |
doc |
dev |
MIT |
| | | X | Standardized analysis pipeline for image-based transcriptomics. |
| stark |
0.1.1 |
|
|
MIT |
X | X | | | A tool for bluntifying a bidirected de bruijn graph by removing overlaps. |
| starseqr |
0.6.7 |
|
|
../../LICENSE |
X | X | | | RNA Fusion Detection and Quantification |
| start-asap |
1.3.0 |
|
|
MIT |
| | | X | Prepare project directory and project sheet for ASA3P |
| steamboat |
1.0.0 |
|
|
MIT |
| | | X | A collection of tools/scripts for microbial bioinformatics |
| stecfinder |
1.1.2 |
|
|
GPL3 |
| | | X | Cluster informed Shigatoxin producing E. coli (STEC) serotyping tool... |
| stellar |
1.4.9 |
|
|
LGPLv3+ |
X | X | | X | STELLAR is a tool for finding pairwise local alignments between long... |
| stereogene |
2.20 |
|
|
Artistic-2.0 |
X | X | | | StereoGene: Rapid Estimation of Genomewide Correlation of Continuous or... |
| stoatydive |
1.1.1 |
|
|
GPLv3 |
| | | X | StoatyDive is a tool to evaluate and classify predicted peak profiles... |
| straglr |
1.5.3 |
|
dev |
GPL-3.0-or-later |
| | | X | Short-tandem repeat genotyping using long reads |
| straindesign |
3.2.3 |
|
|
MIT |
| | | X | Library to perform metabolic engineering tasks |
| strainest |
1.2.4 |
|
|
GPL-3.0 |
X | X | | | Abundance estimation of strains |
| strainflye |
0.2.0 |
|
|
BSD-3-Clause |
| | | X | Pipeline for analyzing rare mutations in metagenomes assembled using... |
| strainge |
1.3.9 |
|
dev |
BSD-3-Clause |
X | X | | | Strain Genome Explorer: a tool suite for tracking and characterizing... |
| strainr2 |
2.1.0 |
|
|
MIT |
X | X | | | StrainR2 accurately deconvolutes strain-level abundances in synthetic... |
| strainscan |
1.0.14 |
|
|
MIT |
| | | X | One efficient and accurate strain-level microbiome composition analysis... |
| strainseeker |
1.5.1 |
|
dev |
BSD |
X | | | | A bacterial identification program for fast identification of bacterial... |
| strainy |
1.2 |
|
|
GPL-3.0-or-later |
| | | X | Assembly-based metagenomic strain phasing using long reads. |
| straitrazor |
3.0.1 |
|
|
MIT |
X | X | | | The STR Allele Identification Tool |
| strandphaser |
1.0.2 |
|
|
MIT |
| | | X | Phase Strand-seq data |
| strangepg |
0.8.18.1 |
|
|
MIT |
X | X | | | Strange pangenome-scale interactive graph visualizer |
| stranger |
0.9.4 |
doc |
dev |
MIT |
| | | X | Annotate VCF files with STR variants with pathogenicity implications. |
| strawc |
0.0.2.1 |
|
|
MIT |
X | X | | | Straw bound with pybind11 |
| strcount |
0.1.1 |
|
|
MIT |
| | | X | A package to count the number of repeats in a Short Tandem Repeat... |
| strdust |
0.11.0 |
doc |
dev |
MIT |
X | X | | | Tandem repeat genotyper for long reads. |
| stream |
1.1 |
|
|
AGPL-3 |
X | X | | X | STREAM-Single-cell Trajectories Reconstruction, Exploration And Mapping |
| stream_atac |
0.3.5 |
|
|
AGPL-3 |
X | X | | X | STREAM-Single-cell Trajectories Reconstruction, Exploration And Mapping... |
| strelka |
2.9.10 |
|
|
GPL-3.0 |
X | | | X | Strelka calls somatic and germline small variants from mapped sequencing reads |
| stride |
1.0 |
|
|
GPL3 |
X | | | | The StriDe Assembler integrates string and de Bruijn graph by... |
| strike |
1.2 |
|
|
file |
X | X | | | A program to evaluate protein multiple sequence alignments using a... |
| stringdecomposer |
1.1.2 |
|
|
GPLv2 |
X | | | | A tool for decomposing of strings into a set of given monomers |
| stringmeup |
0.1.4 |
|
|
MIT |
| | | X | A post-processing tool to reclassify Kraken 2 output based on the... |
| stringmlst |
0.6.3 |
|
|
CC |
X | X | | X | Fast k-mer based tool for multi locus sequence typing (MLST) directly... |
| stringtie |
3.0.0 |
doc |
dev |
MIT |
X | X | | | StringTie employs efficient algorithms for transcript structure... |
| strip_it |
1.0.2 |
|
|
LGPL |
X | | | | Strip-it is a program that extracts predefined scaffolds from organic... |
| stripepy-hic |
0.0.2 |
doc |
dev |
MIT |
| | | X | StripePy recognizes architectural stripes in 3C and Hi-C contact maps... |
| strling |
0.5.2 |
|
|
MIT |
X | | | | STRling (pronounced like “sterling”) is a method to detect large STR... |
| strobealign |
0.15.0 |
|
|
MIT |
X | X | | | Align short reads using dynamic seed size with strobemers |
| strobemap |
0.0.2 |
|
|
GPL-3.0 |
X | X | | | Efficient string matching using strobemers |
| structure |
2.3.4 |
|
|
MIT |
X | X | | | The program structure is a free software package for using multi-locus... |
| structureharvester |
0.6.94 |
|
|
MIT |
X | X | | X | structureHarvester.py is a Python script capable of extracting all the... |
| strucvis |
0.9 |
|
|
GPL-3.0 |
| | | X | strucVis : Display small RNA depth of coverage on a predicted RNA... |
| strudel |
1.15.08.25 |
|
|
BSD-2-Clause |
X | X | | X | Strudel is a graphical tool for visualizing genetic and physical maps... |
| sts-smctc |
1.0 |
|
|
GPL-3.0 |
X | | | | A C++ template class library for the efficient and convenient... |
| stxtyper |
1.0.25 |
|
dev |
Public |
X | X | | | Accurately type both known and unknown Shiga toxin operons from... |
| submission-excel2xml |
3.3 |
|
|
Apache |
| | | X | Generate DRA metadata XML files from Excel spreadsheet |
| submission-tool-validator |
1.0.7 |
|
|
Apache-2.0 |
| | | X | This tool helps user to validate submissions in the client side before... |
| subread |
2.0.8 |
doc |
dev |
GPL-3.0-only |
X | X | | | High-performance read alignment, quantification, and mutation discovery. |
| subset-bam |
1.1.0 |
doc |
dev |
MIT |
X | X | | | A tool to subset a 10x Genomics BAM file based on a tag, most commonly... |
| suchtree |
1.2 |
doc |
dev |
BSD |
X | X | | | A python library for doing fast, thread-safe computations on phylogenetic trees |
| suds-jurko |
0.6 |
|
|
GNU |
X | X | | | Lightweight SOAP client (Jurko's fork) |
| suma_package |
1.0.00 |
|
|
CeCILL |
X | | | | Fast and exact comparison of sequences |
| sumaclust |
1.0.31 |
|
|
CeCILL |
X | X | | | Sumaclust clusters sequences in a way that is fast and exact at the... |
| super-focus |
1.6 |
|
dev |
GPL-3.0 |
X | X | | X | SUPER-FOCUS: A tool for agile functional analysis of shotgun metagenomic data |
| super_distance |
1.1.0 |
|
|
GPLv3 |
X | | | | Supertree method with distances |
| superdsm |
0.4.0 |
doc |
dev |
MIT |
| | | X | SuperDSM is a globally optimal segmentation method based on... |
| superintervals |
0.2.10 |
|
dev |
MIT |
X | X | | | Rapid interval intersections |
| superstr |
1.0.1 |
|
|
GPL-2.0 |
X | X | | | A lightweight, alignment-free utility for detecting repeat-containing... |
| suppa |
2.3 |
|
|
MIT |
X | X | | X | A tool to study splicing across multiple conditions at high speed and accuracy. |
| sure |
2.0.1 |
|
|
GNU |
X | X | | X | utility belt for automated testing in python for python |
| surpyvor |
0.15.0 |
|
|
MIT |
| | | X | Evaluating, merging and plotting SV vcf files |
| survindel2 |
1.1.3 |
|
|
GPL-3.0-only |
X | X | | | A CNV caller for Illumina paired-end WGS data. |
| survivor |
1.0.7 |
|
|
MIT |
X | X | | | Toolset for SV simulation, comparison and filtering |
| sv2 |
1.4.3.4 |
|
|
MIT |
X | X | | | Support Vector Structural Variation Genotyper |
| svaba |
1.2.0 |
|
|
GPLv3 |
X | X | | | Structural variation and indel detection by local assembly |
| svanalyzer |
0.36 |
|
|
CC0 |
| | | X | SVanalyzer: tools for the analysis of structural variation in genomes |
| svclone |
1.1.3 |
|
dev |
BSD-3-Clause |
| | | X | Computational method for inferring cancer cell fraction of tumour SVs from WGS |
| svdb |
2.8.2 |
|
|
MIT |
X | X | | | structural variant database software |
| svdss |
2.0.0 |
doc |
dev |
MIT |
X | | | | Structural Variant Discovery from Sample-specific Strings. |
| svgutils |
0.1.0 |
|
|
MIT |
X | | | | Python SVG editor that allows to automatically create publication ready... |
| svgwrite |
1.1.6 |
|
|
MIT |
X | X | | | A Python library to create SVG drawings. |
| svhip |
1.0.9 |
|
|
MIT |
| | | X | Retrainable machine learning pipeline for the detection of secondary... |
| svict |
1.0.1 |
|
|
Apache-2.0 |
X | X | | | SViCT is a computational tool for detecting structural variations from... |
| svim |
2.0.0 |
doc |
dev |
GPL-3.0 |
| | | X | SVIM is a structural variant caller for long reads. |
| svim-asm |
1.0.3 |
|
|
GPL-3.0 |
| | | X | SVIM-asm is a fork of the SV caller SVIM for genome-genome alignments. |
| svision-pro |
2.4 |
doc |
dev |
GPL-3.0-or-later |
| | | X | Neural-network-based long-read SV caller. |
| svist4get |
1.3.1.1 |
|
|
WTFPL |
| | | X | A simple visualization tool for genomic tracks from sequencing experiments |
| svjedi |
1.1.6 |
|
|
AGPL-3.0-or-later |
| | | X | SVJedi is a structural variation (SV) genotyper for long read data. |
| svjedi-graph |
1.2.1 |
|
|
AGPL-3.0-or-later |
| | | X | SVJedi-graph is a structural variation (SV) genotyper for long read... |
| svmlight |
6.02 |
|
|
Modified |
X | X | | | SVMLight Library by Thorsten Joachim |
| svseq2 |
2 |
doc |
|
CC-PDDC |
X | X | | | An improved approach for accurate and efficient calling of structural... |
| svsolver |
2022.07.20 |
|
dev |
BSD |
X | | | | The svSolver includes three executable programs: Presolver(svpre),... |
| svtk |
0.0.20190615 |
|
|
MIT |
X | X | | | Utilities for consolidating, filtering, resolving, and annotating... |
| svtools |
0.5.1 |
|
|
MIT |
X | X | | X | Tools for processing and analyzing structural variants |
| svtopo |
0.1.3 |
|
|
Pacific |
X | | | | Complex structural variant visualization for HiFi sequencing data:... |
| svtopovz |
0.2.1 |
|
dev |
Pacific |
| | | X | Complex structural variant visualization for HiFi sequencing data:... |
| svtyper |
0.7.1 |
|
|
MIT |
X | X | | X | Bayesian genotyper for structural variants |
| svviz |
1.6.2 |
|
|
MIT |
X | X | | X | A read visualizer for structural variants |
| svync |
0.1.2 |
|
|
MIT |
X | X | | | A tool to standardize VCF files from structural variant callers |
| swalign |
0.3.7 |
|
|
BSD |
X | X | | X | Smith-Waterman local aligner |
| swarm |
3.1.5 |
|
|
Affero |
X | X | | | A robust and fast clustering method for amplicon-based studies. |
| sweepfinder2 |
1.0 |
|
|
Unknown |
X | X | | | The BWA read mapper. |
| swga |
0.4.4 |
|
|
GPL-3.0 |
X | X | | | Select primer sets for selective whole genome amplification (SWGA) |
| swiftlink |
1.0 |
|
|
GPLv3 |
X | X | | | A multipoint parametric linkage analysis tool for large consanguineous... |
| swipe |
2.1.1 |
|
dev |
AGPL-3.0 |
X | X | | | Tool for performing rapid local alignment searches in amino acid or... |
| sword |
1.0.4 |
|
|
GPL3 |
X | X | | | SWORD - a highly efficient protein database search |
| sylph |
0.8.0 |
doc |
dev |
MIT |
X | X | | | sylph quickly enables querying of genomes against even low-coverage... |
| sylph-tax |
1.2.0 |
doc |
dev |
MIT |
| | | X | Integrating taxonomic information into the sylph metagenome profiler. |
| symbiontscreener |
1.0.0 |
|
|
GPL-3.0-only |
X | X | | | Symbiont-Screener is a reference-free approach to identifying... |
| synapseclient |
4.5.0 |
doc |
dev |
Apache-2.0 |
X | X | | X | Python client for Synapse |
| syngap |
1.2.5 |
|
dev |
CC-BY-NC-SA-4.0 |
| | | X | SynGAP: Synteny-based Gene structure Annotation Polisher |
| syny |
1.2 |
|
|
MIT |
| | | X | Genome collinearity inferences |
| syri |
1.7.0 |
|
|
MIT |
X | X | | | Synteny and rearrangement identifier between whole-genome assemblies |
| t-coffee |
13.46.1.b8b01e06 |
|
|
GPL-2.0-only |
X | X | | | A collection of tools for Multiple Alignments of DNA, RNA, Protein Sequence |
| t1dgrs2 |
0.1.2 |
|
|
GPLv3 |
| | | X | Generate a Type 1 Diabetes Genetic Risk Score (T1D GRS) that accounts... |
| t1k |
1.0.7 |
|
|
MIT |
X | X | | | T1K is a versatile methods to genotype highly polymorphic genes (e.g.... |
| t_coffee |
11.0.8 |
|
|
GNU |
X | | | | A collection of tools for Computing, Evaluating and Manipulating... |
| tabix |
1.11 |
|
|
MIT |
X | X | | X | C library and command line tools for high-throughput sequencing data formats. |
| tabixpp |
1.1.2 |
|
dev |
MIT |
X | X | | | A C++ wrapper around the tabix project, a generic indexer for... |
| table2asn |
1.28.1179 |
doc |
|
Public |
X | X | | | table2asn is a command-line program that creates sequence records for... |
| tablet |
1.17.08.17 |
|
|
BSD-2-Clause |
X | X | | | Tablet is a lightweight, high-performance graphical viewer for next... |
| tabview |
1.4.3 |
|
|
MIT |
X | X | | X | A curses command-line CSV and list (tabular data) viewer |
| taco |
0.7.3 |
|
|
MIT |
X | X | | | A tool for multi-sample transcriptome assembly from RNA-Seq |
| tadarida-c |
1.2 |
|
|
GNU |
X | | | | Tadarida-C (Toolbox for Animal Detection on Acoustic Recordings -... |
| tadarida-d |
1.03 |
|
|
LGPL-3.0 |
X | | | | Tadarida-D (Toolbox for Animal Detection on Acoustic Recordings -... |
| tadbit |
1.0.1 |
|
|
GPL-3.0 |
X | X | | | TADbit is a complete Python library to deal with all steps to analyze,... |
| tadlib |
0.4.5.post1 |
|
dev |
GPLv3 |
| | | X | A Library to Explore Chromatin Interaction Patterns for Topologically... |
| tadrep |
0.9.2 |
doc |
dev |
GPL-3.0-or-later |
| | | X | TaDRep: Targeted Detection and Reconstruction of Plasmids |
| tadtool |
0.84 |
|
|
MIT |
X | X | | X | TADtool is an interactive tool for the identification of meaningful... |
| taeper |
0.1.0 |
|
|
MIT |
X | X | | X | Simulate repeating a nanopore experiment. |
| tag |
0.5.1 |
|
dev |
BSD |
| | | X | Genome annotation data analysis and management implemented in pure Python. |
| tagbam |
0.1.0 |
|
|
MIT |
X | | | | A tool for tagging BAM files. |
| tagger |
1.1 |
|
|
BSD |
X | | | | tagger allows you to tag a corpus of documents with search terms that... |
| tagore |
1.1.2 |
|
|
GPLv3 |
| | | X | A simple way to visualize features on human chromosome ideograms |
| tajimas_d |
2.0.2 |
doc |
dev |
GPL-3.0-or-later |
| | | X | Computes Tajimas D, the Pi- or Watterson-Estimator for multiple sequences. |
| takeabreak |
1.1.2 |
|
|
GNU |
X | X | | | tool that can detect inversion breakpoints directly from raw NGS reads,... |
| talloc |
2.1.9 |
|
|
LGPL-3.0 |
X | | | | talloc is a hierarchical, reference counted memory pool system with destructors. |
| talon |
6.0.1 |
|
|
MIT |
| | | X | TALON is a Python package for identifying and quantifying known and... |
| tandem-genotypes |
1.9.2 |
|
|
GPL-3.0-or-later |
| | | X | Find tandem repeat length changes, from "long" DNA reads... |
| tango |
0.5.7 |
|
|
MIT |
| | | X | Assign taxonomy to metagenomic contigs |
| tantan |
51 |
doc |
dev |
GPL-3.0-or-later |
X | X | | | tantan masks simple regions (low complexity & short-period tandem... |
| tapestry |
1.0.1 |
|
dev |
MIT |
| | | X | Validate and edit small eukaryotic genome assemblies |
| taranis |
2.0.1 |
|
|
GPLv3 |
| | | X | Pipeline for wg/cgMLST allele calling |
| taranys |
3.0.1 |
|
|
GPL-3.0-or-later |
| | | X | cg/wgMLST allele calling software, schema evaluation and allele... |
| tardis |
1.0.19 |
|
dev |
GPL-2.0 |
X | X | | | Pre-processor for bioinformatics cluster job submission |
| targetdb |
1.3.1 |
|
|
GNU |
| | | X | Package with an application to generate report on potential drug targets |
| targetfinder |
1.7 |
|
|
MIT |
X | X | | X | Plant small RNA target prediction tool |
| targetscan |
7.0 |
|
|
MIT |
| | | X | Search for predicted microRNA targets in mammals |
| targqc |
1.8.1 |
|
|
GNU |
X | X | | X | Target capture coverage QC |
| taseq |
1.1.1 |
|
|
MIT |
| | | X | Downstream analysis for targetted amplicon sequencing. |
| tasmanian-mismatch |
1.0.7 |
|
|
GNU |
| | | X | Tasmanian tool to analyze mismatches at read and position in high... |
| tassel |
5.2.89 |
|
|
LGPL |
X | | | X | TASSEL is a software package to evaluate traits associations,... |
| tatajuba |
1.0.4 |
|
|
GPLv3 |
X | | | | Identification and classification of homopolymeric tracts from reads |
| taxadb |
0.12.1 |
|
|
MIT |
| | | X | locally query the ncbi taxonomy |
| taxator-tk |
1.3.3e |
|
|
GPLv3 |
X | | | X | Taxator-tk sequence taxonomic annotaion |
| taxmapper |
1.0.2 |
|
|
MIT |
X | | | X | Analysis pipeline for metagenomic, microeukaryotic sequencing data. |
| taxmyphage |
0.3.4 |
|
|
MIT |
| | | X | Script to assign taxonomy to a bacteriophage at the genus and species level |
| taxonkit |
0.19.0 |
|
|
MIT |
X | X | | | A Cross-platform and Efficient NCBI Taxonomy Toolkit |
| taxonomy |
0.10.0 |
|
|
MIT |
X | X | | | Python and Rust library for loading, saving, and manipulating taxonomic trees |
| taxonomy_ranks |
0.0.10 |
|
|
GPL-3.0-or-later |
| | | X | To get taxonomy ranks information for taxid, species name, or higher... |
| taxopy |
0.14.0 |
|
|
GNU |
| | | X | A Python package for obtaining complete lineages and the lowest common... |
| taxor |
0.2.0 |
|
|
BSD-3-Clause |
X | | | | Fast and space-efficient taxonomic classification of long reads |
| taxpasta |
0.7.0 |
|
|
Apache-2.0 |
| | | X | TAXonomic Profile Aggregation and STAndardisation |
| taxsbp |
1.1.1 |
|
|
MIT |
| | | X | TaxSBP: taxonomic structured bin packing |
| taxtastic |
0.11.0 |
|
|
GPL-3.0 |
X | X | | X | Tools for taxonomic naming and annotation |
| tb-ml |
0.1.1 |
|
|
GPL3 |
| | | X | A simple tool for creating machine learning antimicrobial resistance... |
| tb-profiler |
6.6.3 |
|
|
GPL-3.0-or-later |
| | | X | Profiling tool for Mycobacterium tuberculosis to detect drug resistance... |
| tb_variant_filter |
0.4.0 |
|
|
GPL-3.0 |
| | | X | VCF variant filter optimised for filter M. tuberculosis H37Rv variants |
| tbl2asn |
25.7 |
|
|
Public |
X | X | | | tbl2asn is a program that automates the creation of sequence records... |
| tbl2asn-forever |
25.7.2f |
|
|
Public |
X | X | | | tbl2asn is a program that automates the creation of sequence records... |
| tbox-scan |
1.0.2 |
|
|
MIT |
| | | X | tbox-scan is for detecting and classifying T-boxes in DNA sequences. |
| tbpore |
0.7.1 |
|
|
MIT |
| | | X | Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data |
| tbtamr |
1.0.3 |
|
dev |
GPL-3.0-or-later |
| | | X | A tool implementing TB-Profiler for reporting of genomic DST for M.... |
| tbvcfreport |
1.0.1 |
doc |
|
GNU |
| | | X | Parses SnpEff annotated M.tb VCF(s) and generates an interactive... |
| tcdemux |
0.1.1 |
|
|
GPL-3 |
| | | X | Demultiplex files and prepare reads for the target capture analysis pipeline. |
| tcfinder |
1.0.0 |
|
|
GPL-3.0-only |
X | X | | | A lightweight tool to find clusters of samples within a phylogeny. |
| tciaclient |
0.0.3 |
doc |
dev |
Apache-2.0 |
| | | X | TCIA (The Cancer Imaging Archive) Download Client for Python |
| tclap |
1.2.1 |
|
|
MIT |
X | X | | | TCLAP is a small, flexible library that provides a simple interface for... |
| tdrmapper |
1.1 |
|
|
academic |
X | | | X | tRNA detection and quantification |
| te-aid |
1.0.0 |
|
dev |
MIT |
| | | X | Annotation helper tool for the manual curation of transposable element... |
| tecount |
1.0.1 |
|
|
MIT |
| | | X | A package to count read alignments on transposable elements... |
| tedna |
1.2.2 |
|
|
GNU |
X | X | | | Tedna is a lightweight de novo transposable element assembler |
| tefinder |
2.32 |
|
dev |
CeCILL |
X | X | | | Programs for transposable element search and annotation in large... |
| telescope |
1.0.3 |
|
|
MIT |
X | X | | | Single locus resolution of Transposable ELEment expression. |
| teloclip |
0.1.0 |
doc |
dev |
MIT |
X | X | | X | A tool for the recovery of unassembled telomeres from soft-clipped read... |
| telometer |
1.1 |
|
dev |
MIT |
| | | X | A simple regular expression based method for measuring individual,... |
| teloscope |
0.0.8 |
|
|
MIT |
X | X | | | A telomere annotation tools for genome assemblies |
| telosearchlr |
1.0.1 |
|
|
Academic |
| | | X | TeloSearchLR (telomere search using long sequencing reads) is a Python... |
| telr |
1.1 |
|
|
BSD-2-Clause |
| | | X | A a fast non-reference transposable element (TE) detector from long... |
| telseq |
0.0.2 |
|
|
GPL-3 |
X | X | | | A software for calculating telomere length |
| tendo |
0.3.0 |
doc |
dev |
BSD |
| | | X | Tendo is a python module that adds basic functionality that is not... |
| tepeaks |
0.1 |
|
|
GPL3 |
X | | | | Package for including repetitive regions in peak calling from ChIP-seq datasets. |
| tepid |
0.10 |
|
|
GPL-3.0-only |
X | | | X | TEPID uses paired-end illumina sequencing reads to identify novel TE variants. |
| terminus |
0.1.0 |
|
|
BSD |
X | X | | | Terminus enables the discovery of data-driven, robust transcript groups... |
| terrace |
1.1.2 |
|
|
BSD-3-Clause |
X | X | | | TERRACE is an assembler for circular RNAs. |
| tesorter |
1.4.7 |
doc |
dev |
GPL-3.0-or-later |
| | | X | Lineage-level classification of transposable elements using conserved... |
| tesseract |
3.04.01 |
|
|
Apache |
X | | | | OCR engine |
| test |
0.4 |
|
|
MIT |
| | | | Test recipe, copied from the seqtk recipe |
| test-glibc |
0.1 |
|
|
|
X | | | | None |
| testfixtures |
4.8.0 |
|
|
MIT |
X | | | | A collection of helpers and mock objects for unit tests and doc tests. |
| tetoolkit |
2.0.3 |
|
|
GNU |
X | X | | X | Tools for estimating differential enrichment of Transposable Elements... |
| tetranscripts |
2.2.3 |
|
|
GPL-3.0-only |
| | | X | A package for including transposable elements in differential... |
| tetrimmer |
1.4.0 |
|
|
GPL-3.0-only |
| | | X | TETrimmer is designed to replace and assist TE manual curation. |
| tetyper |
1.1 |
|
|
GPL-3.0 |
| | | X | Typing of a specific transposable element (TE) of interest from... |
| textinput |
0.2 |
|
|
GNU |
X | X | | X | streamlined version of stdlib fileinput |
| tf-comb |
1.1 |
doc |
dev |
MIT |
X | X | | | Transcription Factor Co-Occurrence using Market Basket analysis |
| tgsgapcloser |
1.2.1 |
doc |
dev |
GPL-3.0-only |
X | X | | | A gap-closing software tool that uses error-prone long reads generated... |
| tgt |
1.4.3 |
|
|
GPL-3.0+ |
X | X | | | TextGridTools -- Read, write, and manipulate Praat TextGrid files |
| thapbi-pict |
1.0.20 |
doc |
dev |
MIT |
| | | X | THAPBI Phytophthora ITS1 Classifier Tool (PICT). |
| theiacov-gc |
2.3.2 |
|
|
AGPL-3.0 |
| | | X | Command-line version of the TheiaCov genomic characterization workflow... |
| thermorawfileparser |
1.4.5 |
doc |
dev |
Apache |
X | X | | X | Wrapper around the .net (C#) ThermoFisher ThermoRawFileReader library... |
| thesias |
3.1.1 |
|
|
GPL-3+ |
X | | | | Testing Haplotype Effects In Association Studies |
| theta2 |
0.7 |
|
|
Modified |
X | | | X | Estimate tumor purity and clonal/subclonal copy number aberrations... |
| tiberius |
1.1.1 |
|
dev |
MIT |
| | | X | Tiberius is a programme for quantifying and analysing genetic sequence data. |
| tiddit |
3.9.2 |
doc |
dev |
GPL-3.0-only |
X | X | | | TIDDIT - structural variant calling. |
| tidehunter |
1.5.5 |
|
dev |
MIT |
X | X | | | TideHunter: efficient and sensitive tandem repeat detection from noisy... |
| tides-ml |
1.3.5 |
|
dev |
MIT |
| | | X | Tool for ORF-calling and ORF-classification using ML approaches. |
| tidk |
0.2.65 |
|
|
MIT |
X | X | | | Identify and find telomeres, or telomeric repeats in a genome. |
| tidyp |
1.04 |
|
|
BSD-like |
X | X | | | Program for cleaning up and validating HTML |
| tigmint |
1.2.10 |
doc |
dev |
GPL-3.0 |
X | X | | X | Correct misassemblies using linked or long reads |
| tin-score-calculation |
0.6.3 |
|
|
GNU |
| | | X | Given a set of BAM files and a gene annotation BED file, calculates the... |
| tinker |
8.11.3 |
|
dev |
Custom |
X | X | | | The Tinker molecular modeling software is a complete and general... |
| tinscan |
0.2.1 |
doc |
dev |
MIT |
X | X | | X | Find alignment signatures characteristic of transposon insertion sites. |
| tiny-count |
1.5.0 |
|
|
GPLv3 |
X | X | | | \ A precision counting tool for hierarchical classification and... |
| tinyalign |
0.2.2 |
|
|
MIT |
X | X | | | A small Python module providing edit distance and Hamming distance computation. |
| tinyfasta |
0.1.0 |
|
|
MIT |
| | | X | Tiny Python package, with no external dependencies, for parsing FASTA... |
| tinysink |
1.0 |
|
|
MIT |
X | X | | X | Synchronise Nanopore reads with a server. |
| tipp |
1.3.0 |
|
|
GPL-3.0-or-later |
X | | | | TIPPo: A User-Friendly Tool for De Novo Assembly of Organellar Genomes... |
| tiptoft |
1.0.2 |
doc |
dev |
GPL3 |
X | X | | | Predict plasmids from uncorrected long read data. |
| tir-learner |
3.0.6 |
doc |
dev |
GPL-3.0-or-later |
| | | X | An ensemble pipeline for terminal inverted repeat (TIR) transposable... |
| tirmite |
1.1.6 |
|
|
MIT |
X | X | | X | Map TIR-pHMM models to genomic sequences for annotation of MITES and... |
| tissuumaps |
3.2.1.12 |
|
|
MIT |
| | | X | TissUUmaps is a lightweight viewer that uses basic web tools to... |
| titan-gc |
1.5.3 |
|
|
AGPL-3.0 |
| | | X | Command-line version of the Titan genomic characterization workflow for... |
| titanomics |
0.1 |
|
|
BSD |
| | | X | A comprehensive multi-omics data analysis pipeline. |
| tksm |
0.6.1 |
|
|
MIT |
X | | | | Very modular, very cool long-read transcriptomic simulator |
| tmalign |
20220227 |
doc |
dev |
BSD-like |
X | X | | | TM-align sequence-order independent protein structure alignment. |
| tmb |
1.3.0 |
|
|
CeCILL |
| | | X | This tool was designed to calculate a Tumor Mutational Burden (TMB)... |
| tmhg |
1.0.3 |
|
dev |
MIT |
| | | X | tMHG-Finder is a tree-guided tool to partition whole genomes into... |
| tn93 |
1.0.14 |
|
|
MIT |
X | X | | | This is a simple program meant to compute pairwise distances between... |
| tntblast |
2.66 |
doc |
dev |
BSD |
X | X | | | Searching DNA/RNA sequence databases with PCR and/or probe queries |
| tobias |
0.17.1 |
doc |
dev |
MIT |
X | X | | | Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal |
| toil |
7.0.0 |
doc |
dev |
Apache-2.0 |
X | X | | X | A scalable, efficient, cross-platform and easy-to-use workflow engine... |
| tolkein |
0.5.0 |
doc |
dev |
MIT |
| | | X | Tree of Life Kit of Evolutionary Informatics Novelties |
| tooldistillator |
0.9.1 |
doc |
dev |
GPLv3 |
| | | X | Tool to extract and aggregate information from different tool outputs... |
| toolshed |
0.4.6 |
|
|
MIT |
X | X | | X | flexible and easy file manipulation |
| topas |
1.0.1 |
|
|
CC-BY |
| | | X | This toolkit allows the efficient manipulation of sequence data in... |
| tophat |
2.1.1 |
|
|
Boost |
X | X | | | A spliced read mapper for RNA-Seq |
| tophat-recondition |
1.4 |
|
|
BSD_2_clause |
X | X | | X | Post-processor for TopHat unmapped reads |
| toposort |
1.4 |
|
|
Apache |
X | X | | | None |
| toulligqc |
2.7.1 |
doc |
dev |
GPL-3.0-or-later |
X | X | | X | A post sequencing QC tool for Oxford Nanopore sequencers. |
| tower-cli |
0.11.1 |
|
|
MPL-2.0 |
X | X | | X | The Tower CLI an interface to Nextflow Tower via the CLI |
| tpmcalculator |
0.0.5 |
|
|
Public |
X | X | | | TPMCalculator quantifies mRNA abundance directly from the alignments by... |
| tpp |
5.0.0 |
|
|
GPL |
X | | | | The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools... |
| tqdist |
1.0.0 |
|
|
GPL |
X | | | | computes the triplet distance between rooted trees in O(n log n) time... |
| tqdm |
4.7.2 |
|
|
Mozilla |
X | X | | | A Fast, Extensible Progress Meter |
| tr-trimmer |
0.4.0 |
|
|
MIT |
X | X | | | Identify and trim terminal repeats from sequences in FASTA files |
| tracegroomer |
0.1.4 |
|
|
MIT |
| | | X | Format and normalise tracer metabolomics given file(s), to produce the... |
| tracer |
1.7.2 |
|
|
LGPLv2.1 |
X | X | | X | Tracer is a program for analysing the trace files generated by Bayesian... |
| trackhub |
1.0 |
|
|
MIT |
X | X | | X | Create and manage UCSC track hubs from Python |
| tracknado |
0.2.4 |
|
|
GPL-3.0-or-later |
| | | X | CLI library to generate UCSC trackhubs from sequencing data |
| trackplot |
0.5.2 |
doc |
|
BSD-3-Clause |
| | | X | The trackplot is a tool for visualizing various next-generation... |
| tracs |
1.0.1 |
doc |
|
MIT |
X | X | | | Tracs - Fast pairwise transmission inference from single genome and/or... |
| tracy |
0.7.8 |
|
|
BSD-3-Clause |
X | X | | | Basecalling, alignment, assembly and deconvolution of Sanger... |
| traitar |
3.0.1 |
doc |
|
GNU |
| | | X | traitar - The microbial trait analyzer |
| trand |
22.10.13 |
|
|
MIT |
| | | X | transcript event and distance |
| transabyss |
2.0.1 |
|
|
GPL-3.0 |
X | X | | X | de novo assembly of RNA-Seq data using ABySS |
| transanno |
0.4.5 |
|
|
GPL-3.0-only |
X | X | | | accurate VCF/GFF3/GTF LiftOver tool for new genome assemblies |
| transannot |
4.0.0 |
doc |
dev |
GPL-3.0-or-later |
X | X | | | TransAnnot: a fast transcriptome annotation pipeline. |
| transcomb |
1.0 |
|
|
|
X | X | | | A sparse k-mer graph based, memory-efficient genome assembler |
| transcov |
1.1.3 |
doc |
|
GNU |
| | | X | A software for mapping coverage around transcription start sites |
| transcriptm |
0.2 |
|
|
GPL-3.0 |
| | | X | Metagenomics analyses. |
| transdecoder |
5.7.1 |
|
dev |
Broad |
X | X | | X | TransDecoder identifies candidate coding regions within transcript... |
| transgenescan |
1.3.0 |
|
|
GPL-3.0-only |
X | X | | | Software tool for finding genes in assembled transcripts from... |
| transindel |
2.0 |
|
|
GNU |
| | | X | transIndel is used to detect indels (insertions and deletions) from... |
| transit |
3.2.3 |
|
dev |
GPL-3 |
X | X | | X | TRANSIT |
| translate-gard |
1.0.4 |
|
|
MIT |
X | | | | Converts HyPhy 2.3.2 GARD output to JSON |
| translatorx |
1.1 |
|
|
unknown |
X | X | | X | Multiple alignment of nucleotide sequences guided by amino acid information |
| translig |
1.3 |
|
|
GPL3 |
X | | | | A de novo transcriptome assembler that uses line graph iteration |
| transposcope |
2.0.1 |
|
|
MIT |
| | | X | A package for visualizing read coverage in areas flanking mobile... |
| transposonpsi |
1.0.0 |
|
|
artistic-2.0 |
| | | X | TransposonPSI is an analysis tool to identify protein or nucleic acid... |
| transrate |
1.0.3 |
|
|
MIT |
X | | | | Reference free quality assessment of de-novo transcriptome assemblies |
| transrate-tools |
1.0.0 |
|
|
MIT |
X | X | | | Command-line tools used by transrate for processing bam files. |
| transtermhp |
2.09 |
|
|
GPL |
X | X | | | TransTermHP finds rho-independent transcription terminators in bacterial genomes |
| trawler |
2.0 |
|
|
GPLv2 |
X | X | | X | Trawler is a motif discovery tool used to identify enriched motifs in a... |
| tree-qmc |
3.0.4 |
|
|
MIT |
X | X | | | TREE-QMC is a quartet-based method for estimating species trees from gene trees. |
| treebest |
1.9.2.post1 |
|
|
GPLv2 |
X | X | | | TreeBeST: Tree Building guided by Species Tree, used in the Ensembl... |
| treecluster |
1.0.4 |
|
|
GPL-3.0-only |
| | | X | Identify clusters in phylogenetic trees based on a distance threshold... |
| treekin |
0.5.1 |
|
|
GPL |
X | X | | | Compute folding dynamics on coarse grained version of an energy... |
| treemaker |
1.4 |
|
|
BSD-3-Clause |
X | X | | X | A python tool for generating a Newick formatted tree from alist of... |
| treemix |
1.13 |
|
|
GPLv3 |
X | X | | | TreeMix is a method for inferring the patterns of population splits and... |
| treeqmc |
3.0.1 |
|
dev |
MIT |
X | X | | | TREE-QMC is a quartet-based method for estimating species trees from gene trees. |
| treerecs |
1.2 |
|
|
AGPL |
X | X | | | correct, rearrange and (re-)root gene trees with regard to a given species tree |
| treesap |
1.0.10 |
|
dev |
GPL-3.0-or-later |
| | | X | TreeSAP: Tree SAmpling under Phylogenetic models |
| treesapp |
0.11.4 |
|
|
GPL-3.0-only |
X | X | | | TreeSAPP is a functional and taxonomic annotation tool for microbial... |
| treeshrink |
1.3.9 |
|
|
GPL-3 |
| | | X | an algorithm for detecting (and removing) abnormally long branches in... |
| treesimulator |
0.2.4 |
doc |
dev |
GPL-3.0-or-later |
| | | X | Simulation of rooted phylogenetic trees under a given Multitype... |
| treeswift |
1.1.45 |
|
dev |
GPL-3.0-or-later |
| | | X | TreeSwift: Fast tree module for Python 2 and 3 |
| treetime |
0.11.4 |
doc |
dev |
MIT |
X | X | | X | Maximum-Likelihood dating and ancestral inference for phylogenetic trees |
| trf |
4.09.1 |
doc |
dev |
AGPL-3.0-or-later |
X | X | | | Tandem Repeats Finder is a program to locate and display tandem repeats... |
| trgt |
1.5.1 |
|
|
Pacific |
X | | | X | Tandem repeat genotyping and visualization from PacBio HiFi data |
| tribal |
0.1.1 |
doc |
|
BSD-3-Clause |
X | X | | | TRIBAL is a package to infer B cell lineage trees from single-cell RNA... |
| triform2 |
0.0.5 |
|
|
GNU |
X | X | | | Improved sensitivity, specificity and control of false discovery rates... |
| trim-galore |
0.6.10 |
|
dev |
GPL |
X | X | | X | Trim Galore! is a wrapper script to automate quality and adapter... |
| trim_isoseq_polya |
0.0.3 |
|
|
BSD-3-Clause-Clear |
X | X | | | Trims polyA tails from IsoSeq FASTA files |
| trimadap |
r11 |
|
|
MIT |
X | X | | | Fast but inaccurate adapter trimmer for Illumina reads. |
| trimal |
1.5.0 |
doc |
dev |
GPL-3.0-or-later |
X | X | | | A tool for the automated removal of spurious sequences or poorly... |
| trimap |
1.0.15 |
|
|
Apache-2.0 |
| | | X | TriMap: Large-scale Dimensionality Reduction Using Triplets |
| trimmomatic |
0.39 |
|
|
GPLv3 |
X | X | | X | A flexible read trimming tool for Illumina NGS data |
| trimnami |
0.1.4 |
|
|
MIT |
| | | X | Read-trimming pipelines for multiple samples |
| trimns_vgp |
1.0 |
|
|
BSD-3 |
| | | X | TrimNs is used to trim and remove fake cut sites from bionano hybrid... |
| trinculo |
0.96 |
|
|
MIT |
X | | | | A toolkit for carrying out genetic association for multi-category... |
| trinity |
2.15.2 |
doc |
dev |
BSD-3-Clause |
X | X | | | Trinity assembles transcript sequences from Illumina RNA-Seq data. |
| trinotate |
4.0.2 |
|
|
BSD-3-Clause |
X | X | | X | Trinotate is a comprehensive annotation suite designed for automatic... |
| triqler |
0.6.2 |
|
|
Apache |
| | | X | A combined identification and quantification error model of label-free... |
| tritimap |
0.9.7 |
doc |
dev |
MIT |
| | | X | Triti-Map is a Snakemake-based pipeline for gene mapping in Triticeae. |
| trnanalysis |
0.1.10 |
|
|
MIT |
X | X | | X | tRNA analysis pipeline |
| trnascan-se |
2.0.12 |
doc |
dev |
GPL-3.0-or-later |
X | X | | | tRNA detection in large-scale genomic sequences |
| troika-tb |
0.0.5 |
|
|
GPL-3.0 |
| | | X | A pipeline implementing TB-Profiler for batch detection and reporting... |
| trtools |
6.1.0 |
doc |
dev |
MIT |
| | | X | Toolkit for genome-wide analysis of tandem repeats |
| trumicount |
0.9.14 |
|
dev |
AGPL-3.0 |
X | X | | X | For NGS experiments using unique molecular identifiers (UMIs),... |
| trust4 |
1.1.5 |
|
|
MIT |
X | X | | | TCR and BCR assembly from bulk or single-cell RNA-seq data |
| truvari |
5.2.0 |
doc |
dev |
MIT |
X | X | | X | Structural variant comparison tool for VCFs |
| trycycler |
0.5.5 |
|
|
GPLv3 |
| | | X | Trycycler is a tool for generating consensus long-read assemblies for... |
| tsebra |
1.1.2.5 |
|
|
Artistic-2.0 |
| | | X | TSEBRA is a combiner tool that selects transcripts from gene... |
| tspex |
0.6.3 |
|
|
GNU |
| | | X | A Python package for calculating tissue-specificity metrics for gene expression. |
| tssar |
1.0.1 |
|
|
GNU |
X | | | | TSSAR is a Web Service for predicting bacterial Transcription Start... |
| tssv |
1.1.2 |
doc |
dev |
MIT |
X | X | | | Targeted characterisation of short structural variation. |
| tsv-utils |
2.2.0 |
doc |
dev |
BSL-1.0 |
X | X | | | eBay's TSV Utilities |
| tttrlib |
0.25.1 |
doc |
dev |
BSD-3-Clause |
X | X | | | A file format agnostic library for time-resolved imaging and spectroscopic data. |
| turbocor |
0.1.1 |
|
|
MIT |
X | X | | | A command line tool to compute very large correlation matrices. |
| twobitreader |
3.1.7 |
|
|
Artistic |
X | X | | X | A fast python package for reading .2bit files (used by the UCSC genome browser) |
| twopaco |
1.1.0 |
|
dev |
Custom |
X | X | | | A fast constructor of the compressed de Bruijn graph from many genomes. |
| tximport-scripts |
0.0.1 |
|
dev |
GPL-3 |
| | | X | A set of wrappers for individual components of the tximport package.... |
| typing |
3.5.2.2 |
|
|
Python |
X | X | | | Type Hints for Python |
| tyto |
1.4 |
|
|
Apache-2.0 |
| | | X | Tyto (Take Your Terms from Ontologies) provides a handy interface for... |
| ucsc-addcols |
469 |
doc |
dev |
Varies; |
X | X | | | Sum columns in a text file. |
| ucsc-ameme |
469 |
doc |
dev |
Varies; |
X | X | | | find common patterns in DNA |
| ucsc-autodtd |
469 |
doc |
dev |
Varies; |
X | X | | | Give this a XML document to look at and it will come up with a DTD |
| ucsc-autosql |
469 |
doc |
dev |
Varies; |
X | X | | | create SQL and C code for permanently storing |
| ucsc-autoxml |
469 |
doc |
dev |
Varies; |
X | X | | | Generate structures code and parser for XML file from DTD-like spec |
| ucsc-ave |
357 |
|
|
varies; |
| X | | | Compute average and basic stats |
| ucsc-avecols |
469 |
doc |
dev |
Varies; |
X | X | | | average together columns |
| ucsc-axtchain |
469 |
doc |
dev |
Varies; |
X | X | | | Chain together axt alignments. |
| ucsc-axtsort |
469 |
doc |
dev |
Varies; |
X | X | | | Sort axt files |
| ucsc-axtswap |
469 |
doc |
dev |
Varies; |
X | X | | | Swap source and query in an axt file |
| ucsc-axttomaf |
469 |
doc |
dev |
Varies; |
X | X | | | Convert from axt to maf format |
| ucsc-axttopsl |
469 |
doc |
dev |
Varies; |
X | X | | | Convert axt to psl format |
| ucsc-bamtopsl |
469 |
doc |
dev |
Varies; |
X | X | | | Convert a bam file to a psl and optionally also a fasta file that... |
| ucsc-bedclip |
469 |
doc |
dev |
Varies; |
X | X | | | Remove lines from bed file that refer to off-chromosome locations. |
| ucsc-bedcommonregions |
469 |
doc |
dev |
Varies; |
X | X | | | Create a bed file (just bed3) that contains the regions common to all inputs. |
| ucsc-bedcoverage |
469 |
doc |
dev |
Varies; |
X | X | | | Analyse coverage by bed files - chromosome by |
| ucsc-bedextendranges |
469 |
doc |
dev |
Varies; |
X | X | | | extend length of entries in bed 6+ data to be at least the given length, |
| ucsc-bedgeneparts |
469 |
doc |
dev |
Varies; |
X | X | | | Given a bed, spit out promoter, first exon, or all introns. |
| ucsc-bedgraphpack |
469 |
doc |
dev |
Varies; |
X | X | | | Pack together adjacent records representing same value. |
| ucsc-bedgraphtobigwig |
472 |
doc |
dev |
Varies; |
X | X | | | Convert a bedGraph file to bigWig format. |
| ucsc-bedintersect |
469 |
doc |
dev |
Varies; |
X | X | | | Intersect two bed files |
| ucsc-beditemoverlapcount |
469 |
doc |
dev |
Varies; |
X | X | | | count number of times a base is overlapped by the |
| ucsc-bedjointaboffset |
377 |
|
|
varies; |
X | X | | | given a bed file and tab file where each have a column with matching... |
| ucsc-bedpileups |
469 |
doc |
dev |
Varies; |
X | X | | | Find (exact) overlaps if any in bed input |
| ucsc-bedremoveoverlap |
469 |
doc |
dev |
Varies; |
X | X | | | Remove overlapping records from a (sorted) bed file. Gets rid of |
| ucsc-bedrestricttopositions |
469 |
doc |
dev |
Varies; |
X | X | | | Filter bed file, restricting to only ones that match chrom/start/ends... |
| ucsc-bedsort |
469 |
doc |
dev |
Varies; |
X | X | | | Sort a .bed file by chrom,chromStart |
| ucsc-bedtobigbed |
473 |
doc |
dev |
Varies; |
X | X | | | Convert bed file to bigBed. (BigBed version: 4) |
| ucsc-bedtogenepred |
469 |
doc |
dev |
Varies; |
X | X | | | convert bed format files to genePred format |
| ucsc-bedtopsl |
469 |
doc |
dev |
Varies; |
X | X | | | convert bed format files to psl format |
| ucsc-bedweedoverlapping |
469 |
doc |
dev |
Varies; |
X | X | | | Filter out beds that overlap a 'weed.bed' file. |
| ucsc-bigbedinfo |
469 |
doc |
dev |
Varies; |
X | X | | | Show information about a bigBed file. |
| ucsc-bigbednameditems |
469 |
doc |
dev |
Varies; |
X | X | | | Extract item of given name from bigBed |
| ucsc-bigbedsummary |
469 |
doc |
dev |
Varies; |
X | X | | | Extract summary information from a bigBed file. |
| ucsc-bigbedtobed |
469 |
doc |
dev |
Varies; |
X | X | | | Convert from bigBed to ascii bed format. |
| ucsc-bigmaftomaf |
469 |
doc |
dev |
Varies; |
X | X | | | convert bigMaf to maf file |
| ucsc-bigpsltopsl |
469 |
doc |
dev |
Varies; |
X | X | | | convert bigPsl file to psl |
| ucsc-bigwigaverageoverbed |
469 |
doc |
dev |
Varies; |
X | X | | | Compute average score of big wig over each bed, which may have introns. |
| ucsc-bigwigcat |
469 |
doc |
dev |
Varies; |
X | X | | | merge non-overlapping bigWig files |
| ucsc-bigwigcluster |
469 |
doc |
dev |
Varies; |
X | X | | | Cluster bigWigs using a hacTree |
| ucsc-bigwigcorrelate |
469 |
doc |
dev |
Varies; |
X | X | | | Correlate bigWig files, optionally only on target regions. |
| ucsc-bigwiginfo |
469 |
doc |
dev |
Varies; |
X | X | | | Print out information about bigWig file. |
| ucsc-bigwigmerge |
469 |
doc |
dev |
Varies; |
X | X | | | Merge together multiple bigWigs into a single output bedGraph. |
| ucsc-bigwigsummary |
469 |
doc |
dev |
Varies; |
X | X | | | Extract summary information from a bigWig file. |
| ucsc-bigwigtobedgraph |
469 |
doc |
dev |
Varies; |
X | X | | | Convert from bigWig to bedGraph format. |
| ucsc-bigwigtowig |
469 |
doc |
dev |
Varies; |
X | X | | | Convert bigWig to wig. This will keep more of the same structure of the |
| ucsc-blasttopsl |
469 |
doc |
dev |
Varies; |
X | X | | | Convert blast alignments to PSLs. |
| ucsc-blat |
472 |
doc |
dev |
Varies; |
X | X | | | Standalone BLAT v. 39x1 fast sequence search command line tool. |
| ucsc-calc |
357 |
|
|
varies; |
| X | | | Little command line calculator |
| ucsc-catdir |
469 |
doc |
dev |
Varies; |
X | X | | | concatenate files in directory to stdout. |
| ucsc-catuncomment |
469 |
doc |
dev |
Varies; |
X | X | | | Concatenate input removing lines that start with '#' |
| ucsc-cell-browser |
1.2.12 |
doc |
dev |
GPL-3.0-or-later |
| | | X | A browser for single-cell data, main site at http://cells.ucsc.edu.... |
| ucsc-chainantirepeat |
469 |
doc |
dev |
Varies; |
X | X | | | Get rid of chains that are primarily the results of repeats and degenerate DNA |
| ucsc-chainbridge |
377 |
|
|
varies; |
X | X | | | Attempt to extend alignments through double-sided gaps of similar size |
| ucsc-chaincleaner |
455 |
|
|
varies; |
X | | | | Remove chain-breaking alignments from chains that break nested chains. |
| ucsc-chainfilter |
469 |
doc |
dev |
Varies; |
X | X | | | Filter chain files. Output goes to standard out. |
| ucsc-chainmergesort |
469 |
doc |
dev |
Varies; |
X | X | | | Combine sorted files into larger sorted file |
| ucsc-chainnet |
469 |
doc |
dev |
Varies; |
X | X | | | Make alignment nets out of chains |
| ucsc-chainprenet |
469 |
doc |
dev |
Varies; |
X | X | | | Remove chains that don't have a chance of being netted |
| ucsc-chainscore |
455 |
|
|
varies; |
X | | | | Remove chain-breaking alignments from chains that break nested chains. |
| ucsc-chainsort |
469 |
doc |
dev |
Varies; |
X | X | | | Sort chains. By default sorts by score. |
| ucsc-chainsplit |
469 |
doc |
dev |
Varies; |
X | X | | | Split chains up by target or query sequence |
| ucsc-chainstitchid |
469 |
doc |
dev |
Varies; |
X | X | | | Join chain fragments with the same chain ID into a single |
| ucsc-chainswap |
469 |
doc |
dev |
Varies; |
X | X | | | Swap target and query in chain |
| ucsc-chaintoaxt |
469 |
doc |
dev |
Varies; |
X | X | | | Convert from chain to axt file |
| ucsc-chaintopsl |
469 |
doc |
dev |
Varies; |
X | X | | | Convert chain file to psl format |
| ucsc-chaintopslbasic |
469 |
doc |
dev |
Varies; |
X | X | | | Basic conversion chain file to psl format |
| ucsc-checkagpandfa |
469 |
doc |
dev |
Varies; |
X | X | | | takes a .agp file and .fa file and ensures that they are in synch |
| ucsc-checkcoveragegaps |
469 |
doc |
dev |
Varies; |
X | X | | | Check for biggest gap in coverage for a list of tracks. |
| ucsc-checkhgfindspec |
377 |
|
|
varies; |
X | X | | | test and describe search specs in hgFindSpec tables. |
| ucsc-checktablecoords |
469 |
doc |
dev |
Varies; |
X | X | | | check invariants on genomic coords in table(s). |
| ucsc-chopfalines |
469 |
doc |
dev |
Varies; |
X | X | | | Read in FA file with long lines and rewrite it with shorter lines |
| ucsc-chromgraphfrombin |
469 |
doc |
dev |
Varies; |
X | X | | | Convert chromGraph binary to ascii format. |
| ucsc-chromgraphtobin |
469 |
doc |
dev |
Varies; |
X | X | | | Make binary version of chromGraph. |
| ucsc-clustergenes |
377 |
|
|
varies; |
X | X | | | Cluster genes from genePred tracks |
| ucsc-coltransform |
469 |
doc |
dev |
Varies; |
X | X | | | Add and/or multiply column by constant. |
| ucsc-countchars |
469 |
doc |
dev |
Varies; |
X | X | | | Count the number of occurrences of a particular char |
| ucsc-crtreeindexbed |
469 |
doc |
dev |
Varies; |
X | X | | | Create an index for a bed file. |
| ucsc-crtreesearchbed |
469 |
doc |
dev |
Varies; |
X | X | | | Search a crTree indexed bed file and print all items that overlap query. |
| ucsc-dbsnoop |
469 |
doc |
dev |
Varies; |
X | X | | | Produce an overview of a database. |
| ucsc-dbtrash |
469 |
doc |
dev |
Varies; |
X | X | | | drop tables from a database older than specified N hours |
| ucsc-endsinlf |
377 |
|
|
varies; |
X | X | | | Check that last letter in files is end of line |
| ucsc-estorient |
469 |
doc |
dev |
Varies; |
X | X | | | Read ESTs from a database and determine orientation based on... |
| ucsc-expmatrixtobarchartbed |
469 |
doc |
dev |
varies; |
X | X | | | Generate a barChart bed6+5 file from a matrix, meta data, and coordinates. |
| ucsc-faalign |
469 |
doc |
dev |
Varies; |
X | X | | | Align two fasta files |
| ucsc-facmp |
469 |
doc |
dev |
Varies; |
X | X | | | Compare two .fa files |
| ucsc-facount |
469 |
doc |
dev |
Varies; |
X | X | | | count base statistics and CpGs in FA files. |
| ucsc-fafilter |
469 |
doc |
dev |
Varies; |
X | X | | | Filter fa records, selecting ones that match the specified conditions |
| ucsc-fafiltern |
469 |
doc |
dev |
Varies; |
X | X | | | Get rid of sequences with too many N's |
| ucsc-fafrag |
469 |
doc |
dev |
Varies; |
X | X | | | Extract a piece of DNA from a .fa file. |
| ucsc-fanoise |
469 |
doc |
dev |
Varies; |
X | X | | | Add noise to .fa file |
| ucsc-faonerecord |
469 |
doc |
dev |
Varies; |
X | X | | | Extract a single record from a .FA file |
| ucsc-fapolyasizes |
469 |
doc |
dev |
Varies; |
X | X | | | get poly A sizes |
| ucsc-farandomize |
469 |
doc |
dev |
Varies; |
X | X | | | Program to create random fasta records |
| ucsc-farc |
469 |
doc |
dev |
Varies; |
X | X | | | Reverse complement a FA file |
| ucsc-fasize |
469 |
doc |
dev |
Varies; |
X | X | | | print total base count in fa files. |
| ucsc-fasomerecords |
469 |
doc |
dev |
Varies; |
X | X | | | Extract multiple fa records |
| ucsc-fasplit |
469 |
doc |
dev |
Varies; |
X | X | | | Split an fa file into several files. |
| ucsc-fastqstatsandsubsample |
469 |
doc |
dev |
Varies; |
X | X | | | Go through a fastq file doing sanity checks and collecting stats |
| ucsc-fastqtofa |
469 |
doc |
dev |
Varies; |
X | X | | | Convert from fastq to fasta format. |
| ucsc-fatofastq |
469 |
doc |
dev |
Varies; |
X | X | | | Convert fa to fastq format, just faking quality values. |
| ucsc-fatotab |
469 |
doc |
dev |
Varies; |
X | X | | | convert fa file to tab separated file |
| ucsc-fatotwobit |
472 |
doc |
dev |
Varies; |
X | X | | | Convert DNA from fasta to 2bit format. |
| ucsc-fatovcf |
473 |
doc |
dev |
Varies; |
X | X | | | Extract VCF from a multi-sequence FASTA alignment. |
| ucsc-fatrans |
469 |
doc |
dev |
Varies; |
X | X | | | Translate DNA .fa file to peptide |
| ucsc-featurebits |
469 |
doc |
dev |
Varies; |
X | X | | | Correlate tables via bitmap projections. |
| ucsc-fetchchromsizes |
469 |
doc |
dev |
Varies; |
X | X | | | used to fetch chrom.sizes information from UCSC for the given <db> |
| ucsc-findmotif |
469 |
doc |
dev |
Varies; |
X | X | | | find specified motif in sequence |
| ucsc-gaptolift |
469 |
doc |
dev |
Varies; |
X | X | | | create lift file from gap table(s) |
| ucsc-genepredcheck |
469 |
doc |
dev |
Varies; |
X | X | | | validate genePred files or tables |
| ucsc-genepredfilter |
469 |
doc |
dev |
Varies; |
X | X | | | filter a genePred file |
| ucsc-genepredhisto |
469 |
doc |
dev |
Varies; |
X | X | | | get data for generating histograms from a genePred file. |
| ucsc-genepredsinglecover |
469 |
doc |
dev |
Varies; |
X | X | | | create single-coverage genePred files |
| ucsc-genepredtobed |
469 |
doc |
dev |
Varies; |
X | X | | | Convert from genePred to bed format. Does not yet handle genePredExt |
| ucsc-genepredtobiggenepred |
469 |
doc |
dev |
Varies; |
X | X | | | converts genePred or genePredExt to bigGenePred input (bed format with... |
| ucsc-genepredtofakepsl |
469 |
doc |
dev |
Varies; |
X | X | | | Create a psl of fake-mRNA aligned to gene-preds from a file or table. |
| ucsc-genepredtogtf |
469 |
doc |
dev |
Varies; |
X | X | | | Convert genePred table or file to gtf. |
| ucsc-genepredtomafframes |
469 |
doc |
dev |
Varies; |
X | X | | | create mafFrames tables from a genePreds |
| ucsc-genepredtoprot |
469 |
doc |
dev |
Varies; |
X | X | | | create protein sequences by translating gene annotations |
| ucsc-gensub2 |
469 |
doc |
dev |
Varies; |
X | X | | | version 12.18 |
| ucsc-getrna |
469 |
doc |
dev |
Varies; |
X | X | | | Get mrna for GenBank or RefSeq sequences found in a database |
| ucsc-getrnapred |
469 |
doc |
dev |
Varies; |
X | X | | | Get virtual RNA for gene predictions |
| ucsc-gff3togenepred |
469 |
doc |
dev |
Varies; |
X | X | | | convert a GFF3 file to a genePred file |
| ucsc-gff3topsl |
469 |
doc |
dev |
Varies; |
X | X | | | convert a GFF3 CIGAR file to a PSL file |
| ucsc-gmtime |
469 |
doc |
dev |
Varies; |
X | X | | | convert unix timestamp to date string |
| ucsc-gtftogenepred |
469 |
doc |
dev |
Varies; |
X | X | | | convert a GTF file to a genePred |
| ucsc-headrest |
469 |
doc |
dev |
Varies; |
X | X | | | Return all *but* the first N lines of a file. |
| ucsc-hgbbidblink |
469 |
doc |
dev |
Varies; |
X | X | | | Add table that just contains a pointer to a bbiFile to database. This program |
| ucsc-hgfakeagp |
469 |
doc |
dev |
Varies; |
X | X | | | Create fake AGP file by looking at N's |
| ucsc-hgfindspec |
469 |
doc |
dev |
Varies; |
X | X | | | Create hgFindSpec table from trackDb.ra files. |
| ucsc-hggcpercent |
469 |
doc |
dev |
Varies; |
X | X | | | Calculate GC Percentage in 20kb windows |
| ucsc-hggoldgapgl |
377 |
|
|
varies; |
X | X | | | Put chromosome .agp and .gl files into browser database. |
| ucsc-hgloadbed |
469 |
doc |
dev |
Varies; |
X | X | | | Load a generic bed file into database |
| ucsc-hgloadchain |
469 |
doc |
dev |
Varies; |
X | X | | | Load a generic Chain file into database |
| ucsc-hgloadmaf |
469 |
doc |
dev |
Varies; |
X | X | | | Load a maf file index into the database |
| ucsc-hgloadnet |
469 |
doc |
dev |
Varies; |
X | X | | | Load a generic net file into database |
| ucsc-hgloadout |
469 |
doc |
dev |
Varies; |
X | X | | | load RepeatMasker .out files into database |
| ucsc-hgloadoutjoined |
469 |
doc |
dev |
Varies; |
X | X | | | load new style (2014) RepeatMasker .out files into database |
| ucsc-hgloadsqltab |
469 |
doc |
dev |
Varies; |
X | X | | | Load table into database from SQL and text files. |
| ucsc-hgloadwiggle |
469 |
doc |
dev |
Varies; |
X | X | | | Load a wiggle track definition into database |
| ucsc-hgspeciesrna |
469 |
doc |
dev |
Varies; |
X | X | | | Create fasta file with RNA from one species |
| ucsc-hgsqldump |
469 |
doc |
dev |
Varies; |
X | X | | | Execute mysqldump using passwords from .hg.conf |
| ucsc-hgtrackdb |
377 |
|
|
varies; |
X | X | | | Create trackDb table from text files. |
| ucsc-hgvstovcf |
377 |
|
|
varies; |
X | X | | | Convert HGVS terms to VCF tab-separated output |
| ucsc-htmlcheck |
469 |
doc |
dev |
Varies; |
X | X | | | Do a little reading and verification of html file |
| ucsc-hubcheck |
377 |
|
|
varies; |
X | X | | | Check a track data hub for integrity. |
| ucsc-hubpubliccheck |
469 |
doc |
dev |
Varies; |
X | X | | | checks that the labels in hubPublic match what is in the hub labels |
| ucsc-ixixx |
469 |
doc |
dev |
Varies; |
X | X | | | Create indices for simple line-oriented file of format |
| ucsc-lavtoaxt |
469 |
doc |
dev |
Varies; |
X | X | | | Convert blastz lav file to an axt file (which includes sequence) |
| ucsc-lavtopsl |
469 |
doc |
dev |
Varies; |
X | X | | | Convert blastz lav to psl format |
| ucsc-ldhggene |
469 |
doc |
dev |
Varies; |
X | X | | | load database with gene predictions from a gff file. |
| ucsc-liftover |
469 |
doc |
dev |
Varies; |
X | X | | | Move annotations from one assembly to another |
| ucsc-liftup |
469 |
doc |
dev |
Varies; |
X | X | | | change coordinates of .psl, .agp, .gap, .gl, .out, .align, .gff, .gtf |
| ucsc-linestora |
469 |
doc |
dev |
Varies; |
X | X | | | generate .ra format from lines with pipe-separated fields |
| ucsc-localtime |
469 |
doc |
dev |
Varies; |
X | X | | | convert unix timestamp to date string |
| ucsc-mafaddirows |
469 |
doc |
dev |
Varies; |
X | X | | | add 'i' rows to a maf |
| ucsc-mafaddqrows |
469 |
doc |
dev |
Varies; |
X | X | | | Add quality data to a maf |
| ucsc-mafcoverage |
469 |
doc |
dev |
Varies; |
X | X | | | Analyse coverage by maf files - chromosome by |
| ucsc-maffetch |
469 |
doc |
dev |
Varies; |
X | X | | | get overlapping records from an MAF using an index table |
| ucsc-maffilter |
469 |
doc |
dev |
Varies; |
X | X | | | Filter out maf files. Output goes to standard out |
| ucsc-maffrag |
469 |
doc |
dev |
Varies; |
X | X | | | Extract maf sequences for a region from database |
| ucsc-maffrags |
469 |
doc |
dev |
Varies; |
X | X | | | Collect MAFs from regions specified in a 6 column bed file |
| ucsc-mafgene |
469 |
doc |
dev |
Varies; |
X | X | | | output protein alignments using maf and genePred |
| ucsc-mafmefirst |
469 |
doc |
dev |
Varies; |
X | X | | | Move component to top if it is one of the named ones. |
| ucsc-maforder |
469 |
doc |
dev |
Varies; |
X | X | | | order components within a maf file |
| ucsc-mafranges |
469 |
doc |
dev |
Varies; |
X | X | | | Extract ranges of target (or query) coverage from maf and |
| ucsc-mafsinregion |
469 |
doc |
dev |
Varies; |
X | X | | | Extract MAFS in a genomic region |
| ucsc-mafspecieslist |
469 |
doc |
dev |
Varies; |
X | X | | | Scan maf and output all species used in it. |
| ucsc-mafspeciessubset |
469 |
doc |
dev |
Varies; |
X | X | | | Extract a maf that just has a subset of species. |
| ucsc-mafsplit |
469 |
doc |
dev |
Varies; |
X | X | | | Split multiple alignment files |
| ucsc-mafsplitpos |
469 |
doc |
dev |
Varies; |
X | X | | | Pick positions to split multiple alignment input files |
| ucsc-maftoaxt |
469 |
doc |
dev |
Varies; |
X | X | | | Convert from maf to axt format |
| ucsc-maftobigmaf |
469 |
doc |
dev |
Varies; |
X | X | | | Put ucsc standard maf file into bigMaf format |
| ucsc-maftopsl |
469 |
doc |
dev |
Varies; |
X | X | | | Convert maf to psl format |
| ucsc-maftosnpbed |
469 |
doc |
dev |
Varies; |
X | X | | | finds SNPs in MAF and builds a bed with their functional consequence |
| ucsc-maketablelist |
469 |
doc |
dev |
Varies; |
X | X | | | create/recreate tableList tables (cache of SHOW TABLES and DESCRIBE) |
| ucsc-maskoutfa |
469 |
doc |
dev |
Varies; |
X | X | | | Produce a masked .fa file given an unmasked .fa and |
| ucsc-mktime |
469 |
doc |
dev |
Varies; |
X | X | | | convert date string to unix timestamp |
| ucsc-mrnatogene |
469 |
doc |
dev |
Varies; |
X | X | | | convert PSL alignments of mRNAs to gene annotations |
| ucsc-netchainsubset |
469 |
doc |
dev |
Varies; |
X | X | | | Create chain file with subset of chains that appear in the net |
| ucsc-netclass |
469 |
doc |
dev |
Varies; |
X | X | | | Add classification info to net |
| ucsc-netfilter |
469 |
doc |
dev |
Varies; |
X | X | | | Filter out parts of net. What passes |
| ucsc-netsplit |
469 |
doc |
dev |
Varies; |
X | X | | | Split a genome net file into chromosome net files |
| ucsc-netsyntenic |
469 |
doc |
dev |
Varies; |
X | X | | | Add synteny info to net. |
| ucsc-nettoaxt |
469 |
doc |
dev |
Varies; |
X | X | | | Convert net (and chain) to axt. |
| ucsc-nettobed |
469 |
doc |
dev |
Varies; |
X | X | | | Convert target coverage of net to a bed file. |
| ucsc-newprog |
469 |
doc |
dev |
Varies; |
X | X | | | make a new C source skeleton. |
| ucsc-newpythonprog |
469 |
doc |
dev |
Varies; |
X | X | | | Make a skeleton for a new python program |
| ucsc-nibfrag |
469 |
doc |
dev |
Varies; |
X | X | | | Extract part of a nib file as .fa (all bases/gaps lower case by default) |
| ucsc-nibsize |
469 |
doc |
dev |
Varies; |
X | X | | | print size of nibs |
| ucsc-oligomatch |
469 |
doc |
dev |
Varies; |
X | X | | | find perfect matches in sequence. |
| ucsc-overlapselect |
469 |
doc |
dev |
Varies; |
X | X | | | Select records based on overlapping chromosome ranges. The ranges are... |
| ucsc-para |
469 |
doc |
dev |
Varies; |
X | X | | | version 12.18 |
| ucsc-parafetch |
469 |
doc |
dev |
Varies; |
X | X | | | try to fetch url with multiple connections |
| ucsc-parahub |
469 |
doc |
dev |
Varies; |
X | X | | | parasol hub server version 12.18 |
| ucsc-parahubstop |
469 |
doc |
dev |
Varies; |
X | X | | | version 12.18 |
| ucsc-paranode |
469 |
doc |
dev |
Varies; |
X | X | | | version 12.18 |
| ucsc-paranodestart |
469 |
doc |
dev |
Varies; |
X | X | | | version 12.18 |
| ucsc-paranodestatus |
469 |
doc |
dev |
Varies; |
X | X | | | version 12.18 |
| ucsc-paranodestop |
469 |
doc |
dev |
Varies; |
X | X | | | Shut down parasol node daemons on a list of machines |
| ucsc-parasol |
469 |
doc |
dev |
Varies; |
X | X | | | Parasol is the name given to the overall system for managing jobs on a... |
| ucsc-parasync |
469 |
doc |
dev |
Varies; |
X | X | | | uses paraFetch to recursively mirror url to given path |
| ucsc-paratestjob |
469 |
doc |
dev |
Varies; |
X | X | | | version 12.18 |
| ucsc-positionaltblcheck |
469 |
doc |
dev |
Varies; |
X | X | | | check that positional tables are sorted |
| ucsc-pslcat |
469 |
doc |
dev |
Varies; |
X | X | | | concatenate psl files |
| ucsc-pslcdnafilter |
472 |
doc |
dev |
Varies; |
X | X | | | Filter cDNA alignments in psl format. Filtering criteria are... |
| ucsc-pslcheck |
469 |
doc |
dev |
Varies; |
X | X | | | validate PSL files |
| ucsc-psldropoverlap |
469 |
doc |
dev |
Varies; |
X | X | | | deletes all overlapping self alignments. |
| ucsc-pslfilter |
469 |
doc |
dev |
Varies; |
X | X | | | filter out psl file |
| ucsc-pslhisto |
469 |
doc |
dev |
Varies; |
X | X | | | Collect counts on PSL alignments for making histograms. These then be... |
| ucsc-pslliftsubrangeblat |
469 |
doc |
dev |
Varies; |
X | X | | | lift PSLs from blat subrange alignments |
| ucsc-pslmap |
469 |
doc |
dev |
Varies; |
X | X | | | map PSLs alignments to new targets using alignments of |
| ucsc-pslmappostchain |
469 |
doc |
dev |
Varies; |
X | X | | | Post genomic pslMap (TransMap) chaining. This takes transcripts that... |
| ucsc-pslmrnacover |
469 |
doc |
dev |
Varies; |
X | X | | | Make histogram of coverage percentage of mRNA in psl. |
| ucsc-pslpairs |
469 |
doc |
dev |
Varies; |
X | X | | | join paired ends in psl alignments |
| ucsc-pslpartition |
469 |
doc |
dev |
Varies; |
X | X | | | split PSL files into non-overlapping sets |
| ucsc-pslpostarget |
469 |
doc |
dev |
Varies; |
X | X | | | flip psl strands so target is positive and implicit |
| ucsc-pslpretty |
469 |
doc |
dev |
Varies; |
X | X | | | Convert PSL to human-readable output |
| ucsc-pslrc |
469 |
doc |
dev |
Varies; |
X | X | | | reverse-complement psl |
| ucsc-pslrecalcmatch |
469 |
doc |
dev |
Varies; |
X | X | | | Recalculate match,mismatch,repMatch columns in psl file. |
| ucsc-pslreps |
469 |
doc |
dev |
Varies; |
X | X | | | Analyze repeats and generate genome-wide best alignments from a |
| ucsc-pslscore |
469 |
doc |
dev |
Varies; |
X | X | | | calculate web blat score from psl files |
| ucsc-pslselect |
469 |
doc |
dev |
Varies; |
X | X | | | select records from a PSL file. |
| ucsc-pslsomerecords |
469 |
doc |
dev |
Varies; |
X | X | | | Extract multiple psl records |
| ucsc-pslsort |
469 |
doc |
dev |
Varies; |
X | X | | | Merge and sort psCluster .psl output files |
| ucsc-pslsortacc |
455 |
|
|
varies; |
X | | | | Remove chain-breaking alignments from chains that break nested chains. |
| ucsc-pslstats |
469 |
doc |
dev |
Varies; |
X | X | | | collect statistics from a psl file. |
| ucsc-pslswap |
469 |
doc |
dev |
Varies; |
X | X | | | Swap target and query in psls |
| ucsc-psltobed |
469 |
doc |
dev |
Varies; |
X | X | | | transform a psl format file to a bed format file. |
| ucsc-psltobigpsl |
469 |
doc |
dev |
Varies; |
X | X | | | converts psl to bigPsl input (bed format with extra fields) |
| ucsc-psltochain |
469 |
doc |
dev |
Varies; |
X | X | | | Convert psl records to chain records |
| ucsc-psltopslx |
469 |
doc |
dev |
Varies; |
X | X | | | Convert from psl to pslx format, which includes sequences |
| ucsc-pslxtofa |
469 |
doc |
dev |
Varies; |
X | X | | | convert pslx (with sequence) to fasta file |
| ucsc-qacagplift |
469 |
doc |
dev |
Varies; |
X | X | | | Use AGP to combine per-scaffold qac into per-chrom qac. |
| ucsc-qactoqa |
469 |
doc |
dev |
Varies; |
X | X | | | convert from compressed to uncompressed |
| ucsc-qactowig |
469 |
doc |
dev |
Varies; |
X | X | | | convert from compressed quality score format to wiggle format. |
| ucsc-qatoqac |
469 |
doc |
dev |
Varies; |
X | X | | | convert from uncompressed to compressed |
| ucsc-randomlines |
469 |
doc |
dev |
Varies; |
X | X | | | Pick out random lines from file |
| ucsc-rasqlquery |
469 |
doc |
dev |
Varies; |
X | X | | | Do a SQL-like query on a RA file. |
| ucsc-ratolines |
469 |
doc |
dev |
Varies; |
X | X | | | Output .ra file stanzas as single lines, with pipe-separated fields. |
| ucsc-ratotab |
469 |
doc |
dev |
Varies; |
X | X | | | Convert ra file to table. |
| ucsc-rmfadups |
469 |
doc |
dev |
Varies; |
X | X | | | remove duplicate records in FA file |
| ucsc-rowstocols |
469 |
doc |
dev |
Varies; |
X | X | | | Convert rows to columns and vice versa in a text file. |
| ucsc-spacedtotab |
469 |
doc |
dev |
Varies; |
X | X | | | Convert fixed width space separated fields to tab separated |
| ucsc-splitfile |
469 |
doc |
dev |
Varies; |
X | X | | | Split up a file |
| ucsc-splitfilebycolumn |
469 |
doc |
dev |
Varies; |
X | X | | | Split text input into files named by column value |
| ucsc-sqltoxml |
469 |
doc |
dev |
Varies; |
X | X | | | dump out all or part of a relational database to XML, guided |
| ucsc-stringify |
472 |
doc |
dev |
Varies; |
X | X | | | Convert file to C strings. |
| ucsc-subchar |
469 |
doc |
dev |
Varies; |
X | X | | | Substitute one character for another throughout a file. |
| ucsc-subcolumn |
469 |
doc |
dev |
Varies; |
X | X | | | Substitute one column in a tab-separated file. |
| ucsc-taillines |
469 |
doc |
dev |
Varies; |
X | X | | | add tail to each line of file |
| ucsc-tdbquery |
469 |
doc |
dev |
Varies; |
X | X | | | Query the trackDb system using SQL syntax. |
| ucsc-texthistogram |
469 |
doc |
dev |
Varies; |
X | X | | | Make a histogram in ascii |
| ucsc-ticktodate |
469 |
doc |
dev |
Varies; |
X | X | | | Convert seconds since 1970 to time and date |
| ucsc-tolower |
469 |
doc |
dev |
Varies; |
X | X | | | Convert upper case to lower case in file. Leave other chars alone |
| ucsc-toupper |
469 |
doc |
dev |
Varies; |
X | X | | | Convert lower case to upper case in file. Leave other chars alone |
| ucsc-transmappsltogenepred |
469 |
doc |
dev |
Varies; |
X | X | | | convert PSL alignments of mRNAs to gene annotations. |
| ucsc-trfbig |
469 |
doc |
dev |
Varies; |
X | X | | | Mask tandem repeats on a big sequence file. |
| ucsc-twobitdup |
469 |
doc |
dev |
Varies; |
X | X | | | check to see if a twobit file has any identical sequences in it |
| ucsc-twobitinfo |
472 |
doc |
dev |
Varies; |
X | X | | | Get information about sequences in a .2bit file. |
| ucsc-twobitmask |
469 |
doc |
dev |
Varies; |
X | X | | | apply masking to a .2bit file, creating a new .2bit file |
| ucsc-twobittofa |
472 |
doc |
dev |
Varies; |
X | X | | | Convert all or part of .2bit file to fasta. |
| ucsc-validatefiles |
469 |
doc |
dev |
Varies; |
X | X | | | Validates the format of different genomic files. |
| ucsc-validatemanifest |
469 |
doc |
dev |
Varies; |
X | X | | | Validates the ENCODE3 manifest.txt file. |
| ucsc-websync |
469 |
doc |
dev |
varies; |
X | X | | | download from https server, using files.txt on their end to get the... |
| ucsc-wigcorrelate |
469 |
doc |
dev |
Varies; |
X | X | | | Produce a table that correlates all pairs of wigs. |
| ucsc-wigtobigwig |
472 |
doc |
dev |
Varies; |
X | X | | | Convert ascii format wig file (in fixedStep, variableStep). |
| ucsc-wordline |
469 |
doc |
dev |
Varies; |
X | X | | | chop up words by white space and output them with one |
| ucsc-xmlcat |
469 |
doc |
dev |
Varies; |
X | X | | | Concatenate xml files together, stuffing all records inside a single outer tag. |
| ucsc-xmltosql |
469 |
doc |
dev |
Varies; |
X | X | | | Convert XML dump into a fairly normalized relational database |
| udocker |
1.1.1 |
|
|
Apache-2.0 |
X | | | | Freely available tools for computational molecular biology. |
| ufcg |
1.0.6 |
doc |
dev |
GNU |
| | | X | UFCG pipeline provides methods for a genome-wide taxonomic profiling... |
| ultra_bioinformatics |
0.1 |
doc |
dev |
GNU |
| | | X | Splice aligner of long transcriptomic reads to genome. |
| ultraheatmap |
1.3.1 |
|
|
MIT |
| | | X | ultraheatmaps facilitates the production of deepTools heatmaps |
| ultraplex |
1.2.9 |
|
|
MIT |
X | X | | X | fastq demultiplexer |
| umap |
1.1.1 |
|
|
GNU |
| | | X | Umap and Bismap: tools for genome and methylome mappability |
| umi-transfer |
1.5.0 |
|
|
MIT |
X | X | | | A tool for transferring Unique Molecular Identifiers (UMIs) from a... |
| umi_tools |
1.1.6 |
doc |
dev |
MIT |
X | X | | | Tools for dealing with Unique Molecular Identifiers (UMIs) / Random... |
| umicollapse |
1.1.0 |
|
|
MIT |
| | | X | Accelerating the deduplication and collapsing process for reads with... |
| umis |
1.0.9 |
|
dev |
MIT |
X | X | | | Tools for processing UMI RNA-tag data |
| umitools |
0.3.4 |
|
|
GPL3 |
X | X | | X | A toolset for handling sequencing data with unique molecular identifiers (UMIs) |
| unassigner |
1.1.0 |
|
dev |
GPL-2.0-or-later |
| | | X | Type strain identification for 16S reads |
| unfazed |
1.0.2 |
|
|
MIT |
| | | X | Extended read-backed and allele-balance phasing for de novo variation... |
| unicore |
1.1.0 |
|
|
GNU-3.0-or-later |
X | X | | | Universal and efficient core gene phylogeny with Foldseek and ProstT5 |
| unicycler |
0.5.1 |
doc |
dev |
GPL-3.0-or-later |
X | X | | | Hybrid assembly pipeline for bacterial genomes. |
| unifeb |
0.1.1 |
|
|
MIT |
X | | | | unifeb is an non-linear dimension reduction/embedding algorithm for... |
| unifrac |
1.3 |
doc |
dev |
BSD-3-Clause |
X | X | | | Fast phylogenetic diversity calculations |
| unifrac-binaries |
1.4 |
doc |
dev |
BSD-3-Clause |
X | X | | | Fast phylogenetic diversity calculations |
| unikmer |
0.20.0 |
|
|
MIT |
X | X | | | A versatile toolkit for k-mers with taxonomic information |
| unikseq |
2.0.1 |
doc |
|
GPL-3.0 |
| | | X | Unique DNA sequence region identification using a k-mer approach |
| unimap |
0.1 |
doc |
dev |
MIT |
X | X | | | Unimap is a fork of minimap2 optimized for assembly-to-reference alignment. |
| uniprot |
1.3 |
|
|
BSD |
X | X | | X | Retrieve protein sequence identifiers and metadata from http://uniprot.org |
| unitas |
1.6.1 |
|
|
Creative |
X | X | | X | unitas is a convenient tool for efficient annotation of small... |
| unitem |
1.2.6 |
|
|
GPL-3.0-only |
| | | X | Ensemble binning strategies for combining the output of multiple... |
| unitig-caller |
1.3.1 |
|
dev |
Apache-2.0 |
X | X | | | Determines presence/absence of sequence elements in bacterial sequence data. |
| unitig-counter |
1.1.0 |
|
|
GNU |
X | | | | Uses a compressed de Bruijn graph (implemented in GATB) to count... |
| unmerge |
1.0 |
|
|
GPL-3.0 |
X | | | | Interlaced forward and reverse paired-end reads to individual forward... |
| upd |
0.1.1 |
|
|
MIT |
| | | X | Simple software to call UPD regions from germline exome/wgs trios. |
| updio |
1.1.0 |
|
|
gpl-2.0-or-later |
| | | X | UPDio is designed to identify uniparental disomy in probands of trio VCF data. |
| upimapi |
1.13.1 |
doc |
dev |
BSD-3-Clause |
| | | X | UniProt Id Mapping through API |
| uritemplate |
0.6 |
|
|
Apache |
X | X | | | Python implementation of RFC6570, URI Template, and can expand... |
| urllib3 |
1.12 |
|
|
MIT |
X | X | | | HTTP library with thread-safe connection pooling, file post, and more. |
| uropa |
4.0.3 |
doc |
|
MIT |
X | X | | X | UROPA (Universal RObust Peak Annotator) is a command line based tool,... |
| usalign |
2024.07.30 |
doc |
dev |
UNKNOWN |
X | X | | | Universal structure alignment of monomeric, complex proteins and nucleic acids |
| uscdc-datasets-sars-cov-2 |
0.7.2 |
|
|
Apache-2.0 |
| | | X | Benchmark datasets for WGS analysis of SARS-CoV-2 |
| usearch |
12.0_beta |
|
|
GPL-3.0-or-later |
X | X | | | USEARCH is a unique sequence analysis tool which offers search and... |
| usher |
0.6.3 |
doc |
|
MIT |
X | X | | | Ultrafast Sample Placement on Existing Trees (UShER) |
| ushuffle |
1.2.2 |
|
|
custom |
X | X | | | uShuffle---a useful tool for shuffling biological sequences while... |
| uvaia |
2.0.1 |
|
|
GPLv3 |
X | | | | Reference-based alignment and sequence database search |
| uvp |
2.7.0 |
|
|
MIT |
| | | X | A Unified Variant Pipeline to identify variants and assign lineage from... |
| vadr |
1.6.4 |
|
|
Public |
X | X | | X | Viral Annotation DefineR - classification and annotation of viral... |
| vafator |
2.2.0 |
doc |
|
MIT |
| | | X | VAFator annotates the variants in a VCF file with technical annotations... |
| valet |
1.0 |
|
|
MIT |
X | X | | X | Pipeline for detecting mis-assemblies in metagenomic assemblies |
| validate-fasta-database |
1.0 |
|
|
GPL-3.0 |
X | X | | X | Code for Galaxy tool for quality control on FASTA database |
| validators |
0.14.0 |
|
|
BSD |
X | X | | X | Python Data Validation for Humans. |
| validictory |
1.0.1 |
|
|
BSD |
X | X | | | general purpose python data validator |
| vamb |
4.1.3 |
|
|
MIT |
X | X | | | Variational autoencoder for metagenomic binning |
| vamos |
2.1.5 |
|
|
USC-RL |
X | X | | | VNTR annotation using efficient motif selection |
| vapor |
1.0.2 |
doc |
|
GPL-3.0-only |
| | | X | VAPOR is a tool for classification of Influenza samples from raw short... |
| var-agg |
0.1.1 |
|
|
MIT |
X | X | | | A simple helper for aggregating multi-sample VCF files into "site... |
| varcode |
1.2.1 |
|
|
Apache-2.0 |
| | | X | Variant annotation in Python |
| varda2-client |
0.9 |
|
|
MIT |
| | | X | A python CLI to Varda2 frequency database server. |
| vardict |
2019.06.04 |
|
|
MIT |
X | X | | X | A sensitive variant caller for both single and paired sample variant calling |
| vardict-java |
1.8.3 |
|
|
MIT |
X | X | | X | Java port of the VarDict variant discovery program |
| varfish-annotator-cli |
0.34 |
|
|
MIT |
| | | X | Annotate variants for import into VarFish Server. |
| varfish-cli |
0.7.0 |
|
|
MIT |
| | | X | Command line interface to VarFish via REST API |
| varfish-server-worker |
0.13.0 |
|
|
MIT |
X | | | | Rust-based tool for the heavy lifting in varfish-server. |
| vargeno |
1.0.3 |
|
|
MIT |
X | X | | | Fast SNP genotyping tool for whole genome sequence data and large SNP database. |
| variabel |
1.0.0 |
|
|
MIT |
| | | X | Variabel is a novel approach and method for intrahost variant detection... |
| variant-effect-predictor |
87 |
|
|
Apache |
X | | | | The VEP determines the effect of your variants (SNPs, insertions,... |
| variant_tools |
3.1.3 |
|
|
GNU |
X | X | | | Integrated annotation and analysis of next gen sequencing data |
| variantbam |
1.4.4a |
|
|
GPLv3 |
X | | | | Filtering and profiling of next-generational sequencing data using... |
| variantbreak |
1.0.4 |
|
|
GNU |
| | | X | Structural variant analyzer for data visualization on VariantMap |
| variantmap |
1.0.2 |
|
|
GNU |
| | | X | Interactive heatmap for multi-sample structural variant analysis |
| varifier |
0.4.0 |
|
|
MIT |
| | | X | varifier: variant call verification |
| varlociraptor |
8.7.1 |
doc |
dev |
GPL-3.0-or-later |
X | X | | | Flexible, uncertainty-aware variant calling with parameter free... |
| varscan |
2.4.6 |
|
|
The |
X | X | | X | variant detection in massively parallel sequencing data |
| vartrix |
1.1.22 |
|
dev |
MIT |
X | X | | | VarTrix is a software tool for extracting single cell variant... |
| varvamp |
1.2.2 |
|
dev |
GPL-3.0-or-later |
| | | X | Variable VirusAMPlicons (varVAMP) is a tool to design primers for... |
| vase |
0.5.1 |
|
|
MIT |
| | | X | Variant Annotation, Segregation and Exclusion for family or cohort... |
| vawk |
0.0.2 |
|
|
MIT |
X | | | X | An awk-like VCF parser |
| vcf-annotator |
0.7 |
|
|
MIT |
X | X | | X | Use the reference GenBank file to add biological annotations to the... |
| vcf-validator |
0.10.0 |
|
|
Apache-2.0 |
X | X | | | EBI EVA - Validation tool for VCF file format compliance |
| vcf2circos |
1.2.0 |
|
|
AGPL-3.0-or-later |
| | | X | A python package based on Plotly to help generate Circos plots from a... |
| vcf2cytosure |
0.9.1 |
|
|
MIT |
| | | X | Convert VCF with structural variations to CytoSure format |
| vcf2db |
2020.02.24 |
|
|
MIT |
X | X | | X | Create a gemini-compatible database from a VCF |
| vcf2genome |
0.91 |
|
|
GPLv3 |
X | X | | X | A tool to create a draft genome file out of a GATK VCF file and... |
| vcf2maf |
1.6.22 |
|
dev |
Apache-2.0 |
X | | | X | Convert a VCF into a MAF where each variant is annotated to only one of... |
| vcf2maf-umccr |
1.6.21.20230511 |
|
|
Apache-2.0 |
| | | X | Convert a VCF into a MAF where each variant is annotated to only one of... |
| vcf2parquet |
0.5.0 |
|
|
MIT |
X | X | | | Convert a vcf in parquet. |
| vcf2tsvpy |
0.6.1 |
|
|
MIT |
| | | X | Genomic VCF to tab-separated values (TSV) |
| vcf2variants |
1.3 |
|
|
MIT |
| | | X | Convert vcf files to varda variant files. |
| vcfanno |
0.3.5 |
|
|
MIT |
X | X | | | annotate a VCF with other VCFs/BEDs/tabixed files |
| vcfbub |
0.1.1 |
|
dev |
MIT |
X | X | | | Popping bubbles in vg deconstruct VCFs |
| vcfdist |
2.5.3 |
doc |
|
GPL-3.0-only |
X | X | | | vcfdist: benchmarking phased germline variant calls in VCF format |
| vcferr |
1.0.2 |
|
|
MIT |
| | | X | Probabilistic VCF genotype error simulation |
| vcfexpress |
0.3.4 |
|
|
MIT |
X | | | | expressions on VCFs |
| vcfkit |
0.2.9 |
|
|
MIT |
X | X | | X | VCF-kit is a command-line based collection of utilities for performing... |
| vcflatten |
0.5.2 |
|
|
BSD |
X | | | X | A command line tool for flattening VCF files down to simpler TSV files. |
| vcflib |
1.0.12 |
doc |
dev |
MIT |
X | X | | | Command-line tools for manipulating VCF files. |
| vcfphasesets |
0.3 |
|
|
MIT |
| | | X | Get variants as phase sets from a VCF file using pysam. |
| vcfpy |
0.13.8 |
|
|
MIT |
X | X | | X | Python 3 VCF library with good support for both reading and writing |
| vcfpy2 |
0.1.2 |
|
|
MIT |
| | | X | Python 3 VCF library, based on vcfpy. |
| vcfsamplecompare |
2.013 |
|
|
GNU |
X | X | | X | This script sorts and (optionally) filters the rows/variants of a VCF... |
| vcfsim |
1.0.16.alpha |
|
|
MIT |
| | | X | Script for generating simulated VCF's leveraging a coalescent... |
| vcftoolbox |
1.5.1 |
|
|
MIT |
X | X | | X | Tools for manipulating and parsing vcf files |
| vcftools |
0.1.16 |
|
|
LGPL |
X | X | | | A set of tools written in Perl and C++ for working with VCF files. |
| vclean |
0.2.1 |
|
dev |
GPL-3.0-only |
| | | X | vClean: Assessing the contamination of viral genomes |
| vclust |
1.2.9 |
|
|
GPL-3.0-or-later |
X | X | | | Fast and accurate tool for calculating ANI and clustering virus genomes... |
| vcontact2 |
0.11.3 |
doc |
|
GPL-3.0-only |
| | | X | Viral Contig Automatic Clustering and Taxonomy |
| vcontact3 |
3.0.0.b74 |
doc |
|
GPLv3 |
| | | X | Viral Contig Automatic Clustering and Taxonomy |
| vdjer |
0.12 |
|
|
https://github. |
X | | | | B Cell Receptor Repertoire Reconstruction from short read mRNA-Seq data |
| vechat |
1.1.1 |
|
|
GPL-3.0 |
X | | | | Correcting errors in noisy long reads using variation graphs |
| velocyto.py |
0.17.17 |
|
|
MIT |
X | X | | | A library for the analysis of RNA velocity. |
| velvet |
1.2.10 |
doc |
dev |
GPL-2.0-only |
X | X | | | Sequence Assembler for short reads |
| velvet-sc |
0.7.62 |
|
|
GPL-2.0 |
X | X | | | Efficient de novo assembly of single-cell bacterial genomes from... |
| vembrane |
1.0.7 |
|
|
MIT |
| | | X | Filter VCF/BCF files with Python expressions. |
| venndata |
0.1.0 |
|
|
MIT |
| | | X | Package for plotting Venn diagrams with more than 3 sets |
| verifybamid |
1.1.3 |
|
|
GPL3 |
X | X | | | verifyBamID verifies identity and purity of sequence data |
| verifybamid2 |
2.0.1 |
|
|
MIT |
X | X | | | A robust tool for DNA contamination estimation from sequence reads... |
| verifyidintensity |
0.0.1 |
|
|
GPL3 |
X | X | | | verifyIDintensity detects and estimates sample contamination using... |
| verkko |
2.2.1 |
doc |
dev |
CC0 |
X | X | | | A hybrid genome assembly pipeline developed for telomere-to-telomere... |
| verse |
0.1.5 |
|
|
GPL-3.0 |
X | X | | | VERSE: a versatile and efficient RNA-Seq read counting tool |
| versionix |
0.99.2 |
|
dev |
BSD-3-Clause |
| | | X | Get version of any tools. |
| verticall |
0.4.2 |
doc |
|
GPL-3.0-or-later |
| | | X | A tool for building recombination-free trees |
| veryfasttree |
4.0.4 |
doc |
dev |
GPL-3.0-only |
X | X | | | VeryFastTree -- speeding up the estimation of phylogenies for large... |
| vg |
1.63.1 |
|
|
MIT |
X | | | | Variation graph data structures, interchange formats, alignment,... |
| vgan |
3.0.0 |
|
|
GPLv3.0 |
X | | | | Suite of tools for pangenomics built using vg |
| vgorient |
0.1.1 |
doc |
dev |
MIT |
| | | X | Scripts for processing mitochondrial graphs. |
| vibrant |
1.2.1 |
|
|
GPL-3.0 |
| | | X | Virus Identification By iteRative ANnoTation |
| viennarna |
2.7.0 |
|
|
custom |
X | X | | | ViennaRNA package -- RNA secondary structure prediction and comparison |
| viewbs |
0.1.11 |
|
dev |
GPLv3 |
X | | | | ViewBS is a powerful toolkit for visualization of high-throughput... |
| viguno |
0.3.2 |
|
|
MIT |
X | | | | Lookup OMIM genes and HPO terms and compute similarities |
| viloca |
1.1.0 |
doc |
dev |
GNU |
| | | X | VILOCA is a tool to analyse short- and long-read sequencing viral... |
| viral_consensus |
0.0.6 |
|
dev |
GPL-3.0-or-later |
X | X | | | Fast viral consensus genome reconstruction |
| viralflye |
0.2 |
|
|
BSD-3-Clause |
| | | X | viralFlye is a pipeline to recover high-quality viral genomes from... |
| viralmsa |
1.1.44 |
|
|
GNU |
| | | X | Reference-guided multiple sequence alignment of viral genomes |
| viralverify |
1.1 |
|
|
GPLv3 |
| | | X | viral contig verification tool |
| viramp-hub |
0.1.0 |
doc |
|
MIT |
| | | X | VirAmp-Hub lets you manipulate/convert viral amplicon/primer scheme information. |
| virchip |
1.2.2 |
|
|
General |
| | | X | Virtual ChIP-seq predicts transcription factor binding in any cell type... |
| virdig |
1.0.0 |
|
dev |
MIT |
X | X | | | A de novo transcriptome assembler for coronavirus. |
| virema |
0.6 |
|
|
Custom |
X | X | | X | ViReMa (Viral Recombination Mapper) detects and reports recombination... |
| vireosnp |
0.5.8 |
doc |
|
Apache-2.0 |
| | | X | vireoSNP - donor deconvolution for multiplexed scRNA-seq data |
| virheat |
0.7.3 |
|
|
GPL-3.0-or-later |
| | | X | Visualize microbial evolution at the SNP level by creating a heatmap... |
| virmet |
1.1.1 |
|
dev |
MIT |
X | X | | X | A pipeline for viral metagenomics |
| viroconstrictor |
1.5.1 |
doc |
dev |
GNU |
| | | X | ViroConstrictor is a flexible pipeline for analysis of targeted viral... |
| viromeqc |
1.0.2 |
|
|
MIT |
| | | X | Provides an enrichment score for VLP viromes with respect to metagenomes |
| virsorter |
2.2.4 |
|
dev |
GPL-2.0 |
X | X | | X | VirSorter2 -- A multi-classifier, expert-guided approach to detect... |
| virstrain |
1.17 |
|
|
MIT |
| | | X | An RNA/DNA virus strain-level identification tool for short reads. |
| virulencefinder |
2.0.4 |
|
|
Apache-2.0 |
| | | X | VirulenceFinder identifies virulence genes in total or partial... |
| virulign |
1.1.1 |
|
|
GPL-2.0-only |
X | X | | | VIRULIGN is a tool for codon-correct pairwise alignments, with an... |
| virusrecom |
1.3.7 |
|
|
LGPL-2.1-or-later |
| | | X | An information-theory-based method for recombination detection of viral... |
| visceral-evaluatesegmentation |
2015.07.03 |
|
|
Apache |
X | | | | EvaluateSegmentation is a tool that compares two volumes (a test... |
| visitor |
0.1.2 |
|
|
MIT |
X | X | | | A tiny pythonic visitor implementation. |
| visor |
1.1.2.1 |
|
|
LGPL-3.0 |
| | | X | Haplotype-aware structural variants simulator for short, long and linked reads |
| vispr |
0.4.17 |
|
|
MIT |
X | X | | X | VISPR is a visualization framework and analysis workflow for... |
| vitap |
1.7.1 |
doc |
|
GPL-3.0-only |
| | | X | Viral Taxonomic Assignment Pipeline |
| vkmz |
1.4.6 |
|
|
MIT |
| | | X | metabolomics formula prediction and van Krevelen diagram generation |
| vmatch |
2.3.0 |
|
|
Unknown |
X | X | | | The Vmatch large scale sequence analysis software |
| vnl |
1.17.0 |
|
|
BSD |
X | | | | A multi-platform collection of C++ software libraries for Computer... |
| voluptuous |
0.8.8 |
|
|
BSD |
X | X | | | Python data validation library |
| voyager |
0.1.4 |
doc |
dev |
LGPL-3.0-only |
| | | X | Rapid and efficient mapping algorithm for long sequencing reads with... |
| vphaser2 |
2.0 |
|
|
single |
X | X | | | V-Phaser 2 is a tool to call variants in genetically heterogeneous... |
| vpolo |
0.3.0 |
|
|
GPL3 |
| | | X | Support package for Alevin tools |
| vpt |
1.3.0 |
|
|
Apache-2.0 |
| | | X | Command line tool for highly parallelized processing of Vizgen data |
| vpt-core |
1.2.0 |
|
|
Apache-2.0 |
| | | X | Core components for the Vizgen Post-processing Tool |
| vpt-segmentation-packing |
1.0.1 |
|
|
Apache-2.0 |
| | | X | Packs cell boundaries for the Vizgen vzg2 file format |
| vqsr_cnn |
0.0.194 |
|
|
MIT |
X | X | | X | Variant quality score recalibration with Convolutional Neural Networks |
| vrhyme |
1.1.0 |
|
dev |
GPL-3.0 |
| | | X | Binning Virus Genomes from Metagenomes. |
| vsclust |
0.91 |
|
|
GPL |
X | X | | X | Interactive tool for statistical testing, data browsing and interactive... |
| vsearch |
2.30.0 |
|
|
GPL-3.0-or-later |
X | X | | | A versatile open source tool for metagenomics (USEARCH alternative) |
| vsnp |
2.03 |
|
dev |
GPL3 |
| | | X | Rapidly call, validate, and compare SNPs from FASTQ files in a timely... |
| vsnp3 |
3.26 |
|
dev |
GPL3 |
| | | X | Rapidly call, validate, and compare SNPs from FASTQ files in a timely... |
| vt |
2015.11.10 |
|
|
MIT |
X | X | | | A tool set for short variant discovery in genetic sequence data |
| vtools |
1.1.0 |
|
|
MIT |
X | | | | Various tools operating over VCF files. Uses cyvcf2 and cython under... |
| vuegen |
0.2.2 |
doc |
dev |
MIT |
| | | X | VueGen automates the creation of reports from bioinformatics outputs,... |
| vulcan |
1.0.3 |
|
|
MIT |
| | | X | vulcan, map long reads and prosper🖖, a long read mapping pipeline that... |
| vvv2_display |
0.2.3.5 |
|
|
GPL-3.0-only |
| | | X | Creates png image file with all [vardict] variants proportions... |
| w4mclassfilter |
0.98.19 |
|
|
MIT |
X | X | | X | Filter Workflow4Metabolomics feature list, optionally imputing NA values. |
| w4mclstrpeakpics |
0.98.1 |
|
|
MIT |
X | X | | | Visualize W4M sample-cluster peaks - Produce a figure to assess the... |
| wade |
0.2.6 |
|
|
Apache |
| | | X | WADE provides a flexible and customizable method to extract specific... |
| wakhan |
0.1.1 |
|
|
MIT |
| | | X | A tool to analyze haplotype-specific chromosome-scale somatic copy... |
| wally |
0.6.1 |
|
|
BSD-3-Clause |
X | X | | | Visualization of aligned sequencing reads and genomic variants. |
| watchdog |
0.8.3 |
|
|
Apache |
X | X | | | Filesystem events monitoring |
| watchdog-wms |
2.0.8 |
|
|
GNU |
X | X | | X | Watchdog, a WMS for the automated and distributed analysis of... |
| wbuild |
1.8.2 |
|
|
UNKNOWN |
| | | X | Automatic build tool for R Reports |
| wdltool |
0.14 |
|
|
BSD |
X | X | | X | Command line utilities for interacting with WDL |
| web.py |
0.37 |
|
|
Public |
X | X | | | web.py makes web apps |
| weblogo |
3.7.9 |
|
|
MIT |
X | X | | X | WebLogo3 : Sequence Logos Redrawn |
| weeder |
2.0 |
|
|
GPL3 |
X | X | | | Motif (transcription factor binding sites) discovery in sequences from... |
| wes-service-client |
2.7 |
|
|
Apache |
| | | X | Implementation of the GA4GH Workflow Execution Service, a REST service... |
| wfa2-lib |
2.3.5 |
doc |
dev |
MIT |
X | X | | | Wavefront alignment algorithm library v2. |
| wfmash |
0.22.0 |
|
|
MIT |
X | | | | a pangenome-scale aligner |
| wg-blimp |
0.10.0 |
|
|
AGPL-3.0 |
| | | X | wg-blimp (Whole Genome BisuLfIte sequencing Methylation analysis Pipeline) |
| wgatools |
1.0.0 |
|
dev |
MIT |
X | X | | | A Rust library and tools for whole genome alignment files. |
| wgd |
2.0.38 |
doc |
dev |
GPL-3.0-or-later |
| | | X | wgd v2: a suite of tools to uncover and date ancient polyploidy and... |
| wgdi |
0.74 |
|
dev |
BSD-2-Clause |
| | | X | Whole Genome Duplication Identification. |
| wgfast |
1.0.4 |
|
|
GPL |
X | | | X | The whole genome focused array SNP typing (WG-FAST) pipeline |
| wgs-assembler |
8.3 |
|
|
MIT |
X | | | | Celera Assembler (wgs-assembler) is a de novo whole-genome shotgun... |
| wgs2ncbi |
1.1.2 |
|
|
BSD-3-Clause |
X | X | | X | Toolkit for preparing genomes for submission to NCBI |
| wgsim |
1.0 |
|
|
MIT |
X | X | | | Wgsim is a small tool for simulating sequence reads from a reference genome. |
| wham |
1.8.0.1.2017.05.03 |
|
|
MIT |
X | | | | Structural variant detection and association testing |
| whatsgnu |
1.5 |
|
dev |
GPLv3 |
| | | X | WhatsGNU A Tool For Identifying Proteomic Novelty |
| whatshap |
2.4 |
doc |
dev |
MIT |
X | X | | | Phase genomic variants using DNA sequencing reads (haplotype assembly). |
| wheezy.template |
0.1.178 |
|
|
MIT |
X | X | | X | A lightweight template library |
| whokaryote |
1.1.2 |
|
dev |
AGPL-3.0 |
| | | X | Classify metagenomic contigs as eukaryotic or prokaryotic |
| wiggletools |
1.2.11 |
|
|
Apache |
X | X | | | The WiggleTools package allows genomewide data files to be manipulated... |
| winnowmap |
2.03 |
doc |
dev |
LicenseRef-Publ |
X | X | | | Winnowmap is a long-read mapping algorithm optimized for mapping ONT... |
| wipertools |
1.1.5 |
|
|
GPL-2.0-or-later |
| | | X | A suite of programs that drop or fix pesky lines in FASTQ files and... |
| wise2 |
2.4.1 |
|
|
Public |
X | X | | | The Wise2.4 package is the "revival" release of Wise2 |
| wisecondorx |
1.2.9 |
|
|
Attribution-Non |
X | X | | X | WIthin-SamplE COpy Number aberration DetectOR, including sex chromosomes |
| wisestork |
0.1.2 |
|
|
GNU |
| | | X | Within-sample CNV calling |
| wkhtmltopdf |
0.12.3 |
|
|
LGPLv3 |
X | | | | None |
| wlogdate |
1.0.4 |
|
|
GNU |
| | | X | An implementation of the wLogDate algorithm for dating phylogenetic trees |
| woltka |
0.1.7 |
|
|
BSD-3-Clause |
| | | X | versatile meta-omic data classifier |
| womtool |
61 |
|
|
BSD-3-Clause |
X | X | | X | Command line utilities for interacting with WDL |
| workspace |
0.3.1 |
|
|
MIT |
X | X | | | Workspace Overmind |
| ws4py |
0.3.2 |
|
|
BSD |
X | X | | | WebSocket library for Python |
| wtdbg |
2.5 |
|
|
GPL-3.0+ |
X | | | | Wtdbg2: A fuzzy Bruijn graph approach to long noisy reads assembly |
| wtforms-alchemy |
0.16.9 |
|
|
BSD |
X | | | X | Generates WTForms forms from SQLAlchemy models. |
| wtforms-components |
0.10.0 |
|
|
BSD |
X | X | | X | Additional fields, validators and widgets for WTForms. |
| wub |
0.5.1 |
|
|
MPL-2.0 |
X | X | | X | Tools and software library developed by the ONT Applications group |
| xatlas |
0.3 |
|
|
BSD-3-Clause |
X | X | | | xAtlas is a fast and retrainable small variant caller that has been... |
| xbioc |
0.1.19 |
|
|
GPL |
| | | X | Extra Base Functions for Bioconductor |
| xcftools |
1.0.7 |
|
|
GPL |
X | | | | Provides xcf2pnm, xcf2png, and xcfinfo binaries |
| xclone |
0.3.8 |
doc |
dev |
Apache-2.0 |
| | | X | Inference of clonal Copy Number Alterations in single cells. |
| xdg |
1.0.5 |
|
|
ISC |
X | X | | | Variables defined by the XDG Base Directory Specification |
| xengsort |
2.0.8 |
|
dev |
MIT |
| | | X | A fast xenograft read sorter based on space-efficient k-mer hashing |
| xgboost |
0.6a2 |
|
|
UNKNOWN |
X | | | | XGBoost Python Package |
| xhmm |
0.0.0.2016_01_ |
|
|
GPL3 |
X | | | | XHMM (eXome-Hidden Markov Model). |
| xmatchview |
1.2.5 |
doc |
|
GNU |
| | | X | Genome sequence alignment visualization |
| xmlbuilder |
1.0 |
|
|
LGPL |
X | X | | | pythonic way to crate xml/(x)html files |
| xmltodict |
0.9.2 |
|
|
MIT |
X | X | | | Makes working with XML feel like you are working with JSON |
| xmltramp2 |
3.1.1 |
|
|
GNU |
X | X | | X | A modern refactoring of the venerable xmltramp application |
| xopen |
0.7.3 |
|
|
MIT |
X | X | | X | Open compressed files transparently in Python |
| xpclr |
1.1.2 |
|
|
MIT |
| | | X | Code to compute xp-clr values to detect selection as per Chen,... |
| xpore |
2.1 |
doc |
dev |
MIT |
| | | X | xpore is a python package for Nanopore data analysis of differential... |
| xpressplot |
0.2.5 |
|
|
GPL-3.0 |
| | | X | A toolkit for navigating and analyzing gene expression datasets. |
| xs-sim |
2 |
|
|
GPL-2.0 |
X | X | | | Simulates NGS reads |
| xsd |
4.0.0_dep |
|
|
GPL |
X | | | | CodeSynthesis XSD is an open-source, cross-platform W3C XML Schema to... |
| xsv |
0.10.3 |
|
|
MIT |
X | X | | | A fast CSV toolkit written in Rust. |
| xtail |
1.1.5 |
|
|
GPL-3 |
X | X | | X | Genome-wide assessment of differential translations with ribosome profiling data |
| xtandem |
15.12.15.2 |
|
|
Artistic |
X | X | | | X! Tandem open source is software that can match tandem mass spectra... |
| xtea |
0.1.9 |
|
|
Academic |
| | | X | TE insertion caller for both short and long reads |
| xtermcolor |
1.3 |
|
|
MIT |
X | X | | X | Python library for terminal color support (including 256-color support |
| xunit-wrapper |
0.12 |
|
|
GNU |
X | X | | X | Wrap python functions with a decorator to handle building XUnit reports |
| xxhash |
1.0.1 |
|
|
BSD |
X | X | | | Python binding for xxHash |
| xxmotif |
1.6 |
|
|
GPLv3 |
X | X | | | eXhaustive, weight matriX-based motif discovery in nucleotide sequences |
| xyalign |
1.1.5 |
|
|
GPL-3.0 |
X | X | | X | Command line tools and python library to infer ploidy, correct for sex... |
| yacht |
1.3.0 |
doc |
dev |
MIT |
X | | | X | YACHT is a mathematically rigorous hypothesis test for the presence or... |
| yacrd |
1.0.0 |
|
|
MIT |
X | X | | | Yet Another Chimeric Read Detector, with long-read mapper result as input. |
| yaggo |
1.5.10 |
|
|
GPL-3.0 |
X | X | | X | Yaggo is a tool to generate command line parsers for C++. Yaggo stands... |
| yaha |
0.1.83 |
|
|
GPL |
X | | | | yaha is an open source, flexible, sensitive and accurate DNA aligner... |
| yahmm |
1.1.3 |
|
|
MIT |
X | X | | | YAHMM is a HMM package for Python, implemented in Cython for speed. |
| yahs |
1.2.2 |
|
dev |
MIT |
X | X | | | YaHS, yet another Hi-C scaffolding tool. |
| yak |
0.1 |
doc |
dev |
MIT |
X | X | | | Yet another k-mer analyzer. |
| yamda |
0.1.00e9c9d |
|
|
MIT |
| | | X | A highly scalable GPU-accelerated de novo motif discovery software package |
| yamllint |
1.2.1 |
|
|
GNU |
X | X | | | A linter for YAML files. |
| yanagiba |
1.0.0 |
|
|
MIT |
X | X | | X | Filter short or low quality Oxford Nanopore reads which have been... |
| yanc |
0.3.3 |
|
|
GNU |
X | X | | X | Yet another nose colorer |
| yapc |
0.1 |
|
|
GPLv3 |
| | | X | Yapc is a (yet another) peak caller for genomic high-throughput sequencing data |
| yara |
1.0.3 |
|
|
https://raw.git |
X | X | | | Yara is an exact tool for aligning DNA sequencing reads to reference genomes. |
| yass |
1.14 |
|
|
CeCILL |
X | X | | | YASS is a genomic similarity search tool, for nucleic (DNA/RNA)... |
| ymp |
0.3.1 |
doc |
dev |
GNU |
| | | X | Create entire NGS pipelines with one command |
| zagros |
1.0.0 |
|
|
GNU |
X | | | | zagros is a motif-discovery tool for CLIP-Seq data. |
| zamp |
1.0.0 |
|
|
MIT |
| | | X | zAMP: bioinformatic pipeline designed for convenient, reproducible and... |
| zarp |
1.0.0 |
doc |
dev |
Apache |
| | | X | User-friendly command-line interface for the ZARP RNA-Seq analysis pipeline |
| zavolan-multiqc-plugins |
1.3 |
|
|
Apache |
| | | X | MultiQC plugins for the Zavolan Lab@ University of Basel, Switzerland |
| zdb |
1.3.4 |
doc |
dev |
MIT |
| | | X | zDB is both a bacterial comparative genomics pipeline and a tool to... |
| zeroc-ice |
3.7.1 |
|
|
GPL |
X | X | | | Ice is a comprehensive RPC framework that helps you network your... |
| zerone |
1.0 |
|
dev |
GPL-3 |
X | X | | | Zerone discretizes several ChIP-seq replicates simultaneously and... |
| zga |
0.1.1 |
|
dev |
BSD-3-Clause |
| | | X | Prokaryotic genome assembly and annotation pipeline |
| zgtf |
0.1.2 |
|
|
Apache |
| | | X | gtf conversion utility. |
| zifa |
0.1.0 |
|
|
MIT |
X | X | | X | Dimensionality reduction for zero-inflated single-cell gene expression analysis |
| zmwfilter |
1.0.0 |
|
|
BSD-3-Clause-Clear |
X | | | X | PacBio utility to filter reads on ZMW ID(s) |
| zol |
1.5.9 |
|
dev |
BSD-3-Clause |
X | X | | | zol (& fai): large-scale targeted detection and evolutionary... |
| zorro |
2011.12.01 |
|
|
Apache |
X | X | | | ZORRO is a probabilistic masking program that assigns confidence scores... |
| zpca |
0.8.3.post1 |
|
|
Apache |
| | | X | PCA analysis for genes or transcripts. |