bioconda

RSS Feed   channeldata.json

emscripten-wasm32   freebsd-64   linux-32   linux-64   linux-aarch64   linux-armv6l   linux-armv7l   linux-ppc64   linux-ppc64le   linux-riscv64   linux-s390x   noarch   osx-64   osx-arm64   wasi-wasm32   win-32   win-64   win-arm64   zos-z   
Package Latest Version Doc Dev License linux-64osx-64win-64noarch Summary
10x_bamtofastq 1.4.1 doc dev MIT XX 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 doc dev CC-BY-NC-SA-4.0 XX 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 XX 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
aardvark 0.10.3 dev MIT XX A tool for sniffing out the differences in vari-Ants.
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 dev Open XX abawaca is a binning program for metagenomics.
abeona 0.45.0 doc dev Apache XXX A simple transcriptome assembler based on kallisto and Cortex graphs.
abismal 3.3.0 doc dev GPL-3.0-only XX abismal is a fast and memory-efficient mapper for short bisulfite...
abnumber 0.4.4 MIT X AbNumber - Antibody numbering using ANARCI
abpoa 1.5.5 doc dev MIT XX abPOA: fast SIMD-based partial order alignment using adaptive band.
abra2 2.24 MIT X ABRA2 is an updated implementation of ABRA
abricate 1.2.0 GPL-2.0-only XXX Mass screening of contigs for antibiotic resistance genes
abritamr 1.0.20 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 XX 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 doc Copyright XX Abundance-based tool for binning metagenomic sequences.
abyss 2.3.10 doc dev GPL-3.0-only XX 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
accusnv 1.0.0.5 doc dev MIT X High-accuracy SNV calling for bacterial isolates using AccuSNV.
acdc 1.02 doc dev MIT X (a)utomated (c)ontamination (d)etection and (c)onfidence estimation for...
aci 1.45.251125 doc dev 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 0.6.1 BSD-3-Clause-Clear X PacBio utility to align clr to ccs reads
adam 1.0.1 Apache-2.0 XXX 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 dev GPL-3.0-or-later XX The AdapterRemoval v2 tool for merging and clipping reads.
adapterremovalfixprefix 0.0.5 GPLv3 XXX 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...
addeam 1.0.0 GPL-3.0-or-later X A Fast and Scalable Tool for Estimating and Clustering Reference-Level...
addrg 0.2.1 dev MIT XX Add read group to BAM files.
admixtools 8.0.2 doc dev Academic XX ADMIXTOOLS (Patterson et al. 2012) is a software package that supports...
admixture 1.3.0 Free XX 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 dev BSD-3-Clause XX 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 XX Advanced Enumerations (compatible with Python's stdlib Enum),...
aeon 0.1.1 MIT XX Python/Rust library for symbolic manipulation of Boolean networks.
afpdb 0.3.1 doc MIT X A Numpy-based PDB structure manipulation package
afplot 0.2.1 MIT XXX Plot allele frequencies in VCF files
afragmenter 0.0.6 MIT X Schema-free, tunable protein domain segmentation tool for AlphaFold structures
afterqc 0.9.7 MIT XXX Automatic Filtering, Trimming, Error Removing and Quality Control for...
afwdist 1.0.0 GPL-3.0-only XX A lightweight tool to calculate a pairwise distance metric based on...
agat 1.5.1 doc dev GPLv3 X Another Gff Analysis Toolkit (AGAT). Suite of tools to handle gene...
agc 3.2.1 dev MIT XX Assembled Genomes Compressor (AGC) is a tool designed to compress...
age-metasv 2015.01.29.3 CCPL XX optimal alignment of sequences with structural variants (SVs),...
agfusion 1.252 MIT XXX Python package to annotate and visualize gene fusions.
agg 0.3.6 GPL3 XX 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...
agtools 1.0.2 doc dev MIT X agtools: A Software Framework to Manipulate Assembly Graphs
airr 1.5.1 CC X AIRR Community Data Representation Standard reference library for...
akt 0.3.3 dev GPL-3.0-or-later XX Ancestry and Kinship Tools (AKT)
albatradis 1.1.2 dev GPL-3.0-or-later XX Comparative TraDIS analysis.
alcor 1.9 doc dev GPL-3.0-or-later XX Software for alignment-free simulation, mapping, and visualization of...
alder 1.03 Custom XX The ALDER software computes the weighted linkage disequilibrium (LD)...
ale 20180904 NCSA XX ALE: Assembly Likelihood Estimator
ale-core 20220503 NCSA XX ALE: Assembly Likelihood Estimator. Core C implemented scoring...
alen 0.3.2 MIT XX Simple terminal sequence alignment viewer
aletsch 1.1.3 BSD-3-Clause XX Aletsch is an accurate, versatile assembler for multiple RNA-seq samples.
alevin-fry 0.11.2 BSD XX 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 0.5.1 doc dev BSD-3-Clause XX BAM alignment statistics, feature counting and feature annotation
aliceasm 0.6.41 dev AGPL-3.0-only XX Efficient HiFi genome assembler producing haplotype-separated assemblies.
alientrimmer 2.1 AGPL-3.0 X Tool for trimming non-confident bases and alien oligo-nucleotide...
align_it 1.0.4 LGPL X Align-it is a tool to align molecules according to their...
align_trim 1.0.2 doc dev MIT X ARTIC align_trim: A tool for trimming amplicon sequencing primers from...
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 XX Simple wrapper around alignlib C++ library for sequence alignment.
alignment 1.0.10 BSD X Native Python library for generic sequence alignment.
alignoth 1.4.1 doc dev MIT XX A tool for creating alignment plots from bam files.
alignstats 0.11 BSD-3-Clause XX 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 doc INDIVIDUAL XX A fast linkage and haplotype analysis utility making use of MTBDD to...
allelecodes 2.1 GPL-3.0 X Allele Code Assignment Algorithm for cgMLST schemes
allhic 0.9.14 dev BSD-3-Clause XX 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
alloshp 2025.09.12 Apache-2.0 XX From mapped reads to Single Homeologous Polymorphisms (SHPs): pipeline...
alphafill 2.2.0 doc dev BSD-2-Clause XX Transplant missing compounds to the AlphaFold models
altair-mf 1.0.1 GPL X Software for alignment-free and spatial-temporal analysis of multi-FASTA data
altamisa 0.3.1 MIT X Alternative Python API for accessing ISA-tab files.
altex-be 1.0.3 dev MIT X Automatically design sgRNA for exon skipping with many base editors.
alv 1.7.2 GPL-3.0-only X A console-based sequence alignment viewer
amalgkit 0.12.20 BSD-3-Clause X Tools for transcriptome amalgamation
amap 2.2 dev GPL-2 XX AMAP is a multiple sequence alignment program based on sequence annealing.
amaranth-assembler 0.1.0 dev BSD-3-Clause XX Amaranth is a reference-based transcriptome assembler for single-cell RNA-seq.
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 3.0.4 doc dev GPL-3.0-or-later XXX Analysis of Microbial Growth Assays.
aminoextract 0.4.1 dev MIT X Extract amino acid sequences from a fasta file based on a GFF
amira 0.11.0 doc dev Apache-2.0 X A tool to detect acquired AMR genes directly from long read sequencing data.
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 1.0.1 GPL-3 X De novo antimicrobial peptide sequence generation with recurrent neural networks
amplici 2.2 dev BSD XX 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...
ampliconsplitter 1.9.22 dev GPL-3.0-or-later XX Split highly similar collapsed amplicons to obtain all amplicons from a sample.
ampliconsuite 1.5.0 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 2.0.2 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 XXX AMPtk: Amplicon tool kit for processing high throughput amplicon...
amrfior 0.5.0 doc dev GPL-3.0-only X AMRfíor: A customisable and multi-tool approach for antimicrobial...
amulety 2.1 dev GPL-3.0-only X Python package to create embeddings of BCR amino acid sequences.
amused 1.0 GPL-2.0 XXX 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 XX Software for local ancestry inference
ancestry_hmm-s 0.9.0.2 GPL3 XX Inferring adaptive introgression from genomic data using hidden Markov models
anchorwave 1.2.6 doc dev MIT XX Sensitive alignment of genomes with high sequence diversity, extensive...
andi 0.14 GPL-3.0-or-later XX 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 2.0.1 doc dev MIT X A tool for drawing ANI clustermap between all-vs-all microbial genomes
anise_basil 1.2.0 BSD XX 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 2.0 doc dev GPL-3.0-or-later X Convert between AnnData and SingleCellExperiment.
annembed 0.2.6 MIT XX annembed is an ultra-fast and scalable non-linear dimension...
annonars 0.44.1 doc dev Apache-2.0 X Genome annotation based on Rust and RocksDB.
annosine2 2.0.9 doc dev MIT X AnnoSINE_v2 - SINE Annotation Tool for Plant and Animal Genomes.
annotsv 3.5.3 doc dev GPL-3.0-only X Annotation and Ranking of Structural Variation.
annotwg 1.0 CeCILL X Tool for annotating large VCF files
anospp-analysis 0.4.0 MIT X ANOSPP data analysis.
ansible 1.9.4 GPLv3 XX None
ant 1.10.0 Apache XX 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 8.0.4 doc dev AGPL-3.0-or-later XXX antiSMASH - the antibiotics and Secondary Metabolite Analysis SHell.
antismash-lite 8.0.1 doc dev AGPL-3.0-or-later X antiSMASH - the antibiotics and Secondary Metabolite Analysis SHell.
anvio 7 dev GPL-3.0-or-later XXX A platform for integrated multi-omics
anvio-minimal 8 doc dev GPL-3.0-or-later XXX An interactive analysis and visualization platform for omics data
any2fasta 0.8.1 GPL-3.0 XXX 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 XX Large-scale structural comparison of protein pockets
apollo 4.2.13 MIT X WebApollo API library
appspam 1.03 doc GPL3 XX Alignment-free Phylogenetic Placement algorithm based on Spaced-word Matches
aprfinder 1.5 MIT XX Tool for finding aphased repeats.
apscale 4.2.3 doc 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 XX 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 XX ARAGORN, tRNA (and tmRNA) detection
arb-bio 6.0.6 doc dev ARB XX ARB 6 Sequence Analysis Suite
arb-bio-devel 6.0.6 doc dev ARB XX ARB 6 Sequence Analysis Suite
arb-bio-tools 6.0.6 doc dev ARB XX ARB 6 Sequence Analysis Suite
arborator 1.2.0 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
arborist 1.0.0 BSD-3-Clause X Arborist is a tool to rank SNV phylogenies inferred from bulk DNA...
arcas-hla 0.6.0 GPL-3.0-only X high-resolution HLA typing from RNA seq
archer 0.1.1 MIT XX Pre-process amplicon data before running CLIMB workflows.
architeuthis 0.4.0 dev Apache-2.0 XX Tool to analyze and summarize data for Kraken.
arcs 1.2.8 GPL-3.0-or-later XX 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 XXX Aligning Reads by Expectation-Maximization.\nBased on MACS (Model Based...
argh 0.26.1 GNU XX None
argnorm 1.1.0 doc MIT X Normalize antibiotic resistance genes (ARGs) abundance tables (e.g.,...
argo 0.2.1 MIT X Argo: species-resolved profiling of antibiotic resistance genes in...
argparse 1.4.0 Python XX Python command-line parsing library
argparse-tui 0.3.1 doc dev MIT X Present your Argparse CLI as a Textual UI (TUI).
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 XX Functions to build matched argument parsers and config files
aria2 1.34.0 dev GPL-2.0 XX aria2 is a lightweight multi-protocol & multi-source, cross...
ariba 2.14.7 doc dev GPL-3.0-or-later XX ARIBA: Antibiotic Resistance Identification By Assembly.
array-as-vcf 1.1.0 doc dev MIT X Convert SNP array to VCF
arriba 2.5.1 doc dev MIT XX Fast and accurate gene fusion detection from RNA-Seq data.
art 2016.06.05 GPL-3.0-only XX Illumina, 454 and Solid read simulator
art_modern 1.3.2 doc dev GPL-3.0-only XX Modernized ART simulator of diverse Next-Generation Sequencing reads
art_modern-openmpi 1.3.2 doc dev GPL-3.0-only XX Modernized ART simulator of diverse Next-Generation Sequencing reads...
artemis 18.2.0 GPL-3.0 XXX A set of Java genome visualization tools including the Artemis genome...
artex 0.2.0 GPL-3.0 X Artex - Artic pipeline extension
artic 1.8.5 doc dev MIT X ARTIC pipeline - a bioinformatics pipeline for working with virus...
artic-porechop 0.3.2pre GPL3 XX Adapter removal and demultiplexing of Oxford Nanopore reads (fork of...
artic-tools 0.3.1 MIT XX A set of tools for working with the ARTIC bioinformatic pipeline.
arvados-cli 0.1.20151207150126 Apache X None
arvados-cwl-runner 3.1.2 doc dev Apache-2.0 XXX Arvados Common Workflow Language runner.
arvados-python-client 3.2.0 Apache-2.0 XXX Arvados client library.
ascat 3.2.0 doc dev GPL-3.0-or-later XXX ASCAT is a method to derive copy number profiles of tumour cells,...
asciigenome 1.19.0 doc MIT XXX 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 XXX Command line interface for a distant AskOmics
asn2gb 18.2 Public XX 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 XX A combined pipeline for bacterial genome assembly, quality control and...
assemblerflow 1.1.0.post3 doc dev GPL3 XXX A Nextflow pipeline assembler for genomics. Pick your modules. Assemble...
assembly-scan 1.0.0 MIT XXX Assembly summary statistics in JSON format
assembly-stats 1.0.1 dev GPL-3.0-or-later XX Get assembly statistics from FASTA and FASTQ files
assembly_finder 0.9.0 doc dev MIT X Snakemake-powered cli pipeline to download genomes with NCBI datasets
assembly_uploader 1.3.5 doc Apache-2.0 X Python scripts to upload primary metagenome and metatranscriptome...
assemblycomparator2 2.7.1 doc dev GPL-3.0-or-later XX Assemblycomparator2: Genomes to report pipeline
assemblytics 1.2.1 MIT X analyze a genome assembly by comparing it to a reference genome
assemblyutility 20160209 dev MIT XX Tools for DBG2OLC genoome assembler.
astalavista 4.0 BSD XXX AStalavista is a computer program to extract alternative splicing (AS)...
aster 1.23 doc dev AGPL-3.0-or-later XX 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-3.0-or-later XX ATAC is a computational process for comparative mapping between two...
atactk 0.1.9 GPL-3.0-or-later XX A toolkit for working with ATAC-seq data.
ataqv 1.3.1 doc dev GPL-3.0-only XX ataqv is a toolkit for measuring and comparing ATAC-seq results. It was...
athena_meta 1.3 MIT XX Athena read cloud assembler for metagenomes
atlas 2.0.1 MPL-2.0 XX 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 0.1.17 dev GPL-3.0-or-later X Map data from the BPA data portal for AToL's Genome Engine.
atol-genome-launcher 0.1.5 dev GPL-3.0-or-later X Utility code for AToL's Genome Engine. This package provides...
atol-qc-annotation 0.1.4 dev GPL-3.0-or-later X Run QC on GTF and GFF files.
atol-qc-raw-ont 0.1.12 dev GPL-3.0-or-later X Run read QC on ONT reads.
atol-qc-raw-shortread 0.1.7 dev GPL-3.0-or-later X Run short read QC on Hi-C or other Illumina reads.
atropos 1.1.32 doc dev CC0 XX Trim adapters from high-throughput sequencing reads.
attotree 0.1.6 doc MIT X rapid estimation of phylogenetic trees using sketching
augur 32.1.0 doc dev AGPL-3.0-only X Process pathogen genome data for the Nextstrain platform.
augustus 3.5.0 doc dev Artistic XX "AUGUSTUS is a gene prediction program for eukaryotes written by...
auriclass 0.5.4 dev GNU X AuriClass is a tool for quickly predicting the clade of a Candida auris genome.
auspice 2.66.0 doc dev AGPL-3.0-only XX Auspice is an open-source interactive tool for visualising phylogenomic data.
authentict 1.0.1 GPL3 XX Estimates present-day DNA contamination in ancient DNA single-stranded...
autobigs-cli 0.6.5 GPL-3.0-only-or X A CLI tool to rapidly fetch fetch MLST profiles given sequences for...
autobigs-engine 0.14.2 dev GPL-3.0-or-later X A library to rapidly fetch fetch MLST profiles given sequences for...
autocycler 0.5.2 doc dev GPL-3.0-or-later XX A tool for generating consensus long-read assemblies for bacterial genomes.
autodock 4.2.6 GPL-2.0-only XX AutoDock is a suite of automated docking tools.
autodock-vina 1.1.2 Apache XX 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 XX AutoDock is a suite of automated docking tools.
autolog 0.2 GNU XXX quick and easy logging setup
automappa 2.2.1 doc dev AGPL-3.0-or-later 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 0.12.0 doc dev GPL-3.0-only X aviary - Metagenomics pipeline using long and short reads.
avro 1.8.0 Apache XX None
avro-cwl 1.8.9 Apache XXX Avro is a serialization and RPC framework. This package is a fork of...
avro-python2 1.9.0 Apache XXX Avro is a serialization and RPC framework.
avro-python3 1.9.0 Apache XXX Avro is a serialization and RPC framework.
awscli 1.8.3 Apache XX None
axe-demultiplexer 0.3.3 doc dev GPL-3.0-or-later XX Rapid competitive read demulitplexer. Made with tries.
axiome 2.0.4 MIT XXX AXIOME2: Automation Extension and Integration of Microbial Ecology
azure-cli 0.10.3 Apache XX Microsoft Azure Cross Platform Command Line
b2b-utils 0.020 dev GPL-3.0-or-later XX Genomics tools from BASE2BIO
b2btools 3.0.7 doc dev GPL-3.0-or-later XXX The bio2Byte software suite to predict protein biophysical properties.
babappalign 1.1.3 MIT XXX Deep learning–based progressive multiple sequence alignment engine with...
bacgwasim 2.1.1 MIT X BacGWASim is a simulator for Bacterial Machine learning and Genome-wide...
backports.csv 1.0.1 UNKNOWN XX Backport of Python 3 csv module
backports.unittest_mock 1.3 MIT XXX backports.unittest_mock
backspinpy 0.2.1 MIT XXX backSPIN clustering algorythm
bacpage 2025.08.21 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 3.2.0 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 1.7.0 doc dev 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 dev GPL-3.0-or-later XX 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...
bakrep-cli 1.1.0 doc dev GPL-3.0-or-later X BakRep-CLI: a commandline tool for the batch download of BakRep datasets
bakta 1.11.4 doc dev GPL-3.0-or-later X Rapid & standardized annotation of bacterial genomes, MAGs & plasmids.
baktfold 0.0.3 doc MIT X Rapid & standardized annotation of bacterial genomes, MAGs &...
bali-phy 4.1 dev GPL2 XX Phylogenetics - Bayesian estimation of phylogenies and multiple...
balrog 0.5.1 dev MIT XX 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 XX 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 XX Converting and demultiplexing of PacBio BAM files into gzipped fasta...
bam2plot 0.3.7 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 XX lightweight C implementation of name collating BAM file input and BAM...
bamclipper 1.0.0 MIT XXX Remove primer sequence from BAM alignments by soft-clipping.
bamcmp 2.2 dev GPL-3.0-or-later XX Tools for deconvolving host and graft reads using full-length...
bamdam 0.4.2 dev MIT X A post-mapping, post-least-common-ancestor toolkit for ancient DNA analysis.
bamdash 0.4.5 doc dev GPL-3.0-or-later X Aggregate pathogen NGS results into an interactive plot.
bamhash 2.0 dev GPL-3-0-or-later XX 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 doc dev LGPL-3.0-or-later X Metagenomics-focused BAM file manipulation.
bamr 0.2.0 MIT X A lightweight Python3 bam reader library
bamread 0.0.20 dev MIT XX Read bam files quickly into dataframes in Python.
bamrescue 0.3.0 doc dev ISC XX Utility to check BAM files for corruption and repair by skipping...
bamscale 0.0.9 doc dev Public XX BAMscale is a one-step tool for either 1) quantifying and normalizing...
bamslice 0.1.6 doc dev AGPL-3.0-only XX Extract byte ranges from BAM files and convert to interleaved FASTQ...
bamsnap 0.2.19 MIT X A converter from .bam to .png for specific genomic region.
bamstats 0.3.5 BSD-3-Clause XX 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 2.8.0 MIT XX Extract coverage information from BAM files, supporting stranded and...
bamtools 2.5.3 doc dev MIT XX C++ API & command-line toolkit for working with BAM data.
bamutil 1.0.15 doc GPL-3.0-or-later XX Programs that perform operations on SAM/BAM files, all built into a...
bandage 0.9.0 doc dev GPL-3.0-or-later XX Bandage - a Bioinformatics Application for Navigating De novo Assembly...
bandage_ng 2025.12.3 doc dev GPL-3.0-or-later XX Bandage - a Bioinformatics Application for Navigating De novo Assembly...
bandwagon 0.3.4 doc dev MIT X Simulate DNA band patterns for gel migration experiments
banner 0.0.2 MIT X BANNER is a tool that lives inside HULK and aims to make sense of hulk...
barbell 0.3.0 MIT XX Extremely fast and accurate Nanopore demultiplexing
barcode-validator 2.0.10 doc dev Apache-2.0 X A python package for structural and taxonomic validation of DNA barcode data
barcode_splitter 0.18.6 GNU X Split multiple fastq files by matching barcodes in one or more of the...
barcodeforge 1.1.2 doc dev BSD-2-Clause X A CLI tool for generating pathogen-specific barcodes for Freyja.
baredsc 1.1.3 GPL-3.0-or-later X baredSC (Bayesian Approach to Retreive Expression Distribution of...
barriers 1.8.1 dev GPL-3.0-or-later XX Compute local minima and energy barriers of a landscape.
barrnap 0.9 GPLv3 XXX Barrnap predicts the location of ribosomal RNA genes in genomes....
barrnap-python 0.0.5 dev GNU XXX 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 XXX 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 XX Bash automated testing system
batvi 1.04 GPLv3+ XX Detect viral integrations
bax2bam 0.0.11 BSD-3-Clause-Clear XX 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 1.3.4 doc dev MIT XX Mutation-Selection phylogenetic codon models to detect site-specific...
bayestyper 1.5 doc dev MIT XX A method for variant graph genotyping based on exact alignment of k-mers.
baypass 3.1 dev CECILL-B XX 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 dev MIT XXX Batch balanced KNN.
bbmap 39.52 doc dev UC-LBL XXX BBMap is a short read aligner, as well as various other bioinformatic tools.
bbmapy 0.0.51 doc dev Custom X A Python wrapper for BBTools.
bbmix 0.2.2 dev Apache-2.0 X BBMix: inference of beta-binomial mixture model
bcalm 2.2.3 dev MIT XX BCALM 2 is a bioinformatics tool for constructing the compacted de...
bcbio-gff 0.7.1 doc dev Biopython X A Python library to read and write Generic Feature Format (GFF).
bcbio-nextgen 1.2.9 MIT XXX Validated, scalable, community developed variant calling, RNA-seq and...
bcbio-nextgen-vm 0.1.6 MIT XXX Run bcbio-nextgen genomic sequencing analyses using isolated containers...
bcbio-prioritize 0.0.8 MIT XXX Prioritize small variants, structural variants and coverage based on...
bcbio-rnaseq 1.2.0 MIT XX Report generation for bcbio-nextgen RNA-seq runs
bcbio-variation 0.2.6 MIT XXX Toolkit to analyze genomic variation data, built on the GATK with Clojure
bcbio-variation-recall 0.2.6 MIT XXX Parallel merging, squaring off and ensemble calling for genomic variants
bcbio_monitor 1.0.6 MIT XXX bcbio-monitor is an extension of bcbio-nextgen to visualize its progress
bcbiogff 0.6.6 Biopython XXX Read and write Generic Feature Format (GFF) with Biopython integration.
bcbreport 0.99.29 MIT XXX Rmd templates for bcbio-nextgen analysis
bcftools 1.23 GPL XX BCFtools is a set of utilities that manipulate variant calls in the...
bcftools-gtc2vcf-plugin 1.22 MIT X Tools to convert Illumina and Affymetrix array intensity data files...
bcftools-liftover-plugin 1.22 MIT X Tools to work with GWAS-VCF summary statistics files (liftover plugin only)
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 XXX NextSeq .bcl Conversion
bcool 1.0.0 AGPL-3.0 XX BCOOL is a read corrector for NGS sequencing data that align reads on a...
bcov 1.0 doc file XX BCov is a software package designed for predicting protein beta-sheet...
bctools 0.2.2 Apache XXX Tools for handling barcodes in NGS data.
bd2k-python-lib 1.14a1.dev48 Apache XXX 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 2.0.5 Apache-2.0 X Package of tools designed to simplify the population of a Beacon v2...
beagle 5.5_27Feb25.75f doc GPL-3.0-or-later XXX Beagle is a software package for phasing genotypes and for imputing...
beagle-lib 4.0.1 doc dev GPL-3.0-or-later XX A general purpose library for evaluating the likelihood of sequence...
beamspy 1.2.0 GNU X BEAMSpy - Birmingham mEtabolite Annotation for Mass Spectrometry...
beast 10.5.0 doc dev LGPL-2.1-or-later XXX BEAST is a cross-platform program for Bayesian analysis of molecular...
beast2 2.6.3 LGPL-2.1-or-later XXX BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis...
beav 1.4.0 doc dev GPL-3.0-or-later X beav: Bacterial genome and mobile element annotation pipeline.
bed2gff 0.1.5 MIT XX BED-to-GFF3 converter that runs in parallel
bed2gtf 1.9.3 MIT XX A high-performance BED-to-GTF converter written in Rust
bedgovcf 0.1.1 MIT XX A simple tool to convert BED files to VCF files
bedops 2.4.42 doc dev GPL-2.0-or-later XX High-performance genomic feature operations.
bedparse 0.2.3 MIT X A simple library and CLI tool to manipulate BED files
bedtk 1.2 doc dev MIT XX Bedtk is a set of simple tools to process BED files.
bedtools 2.31.1 MIT XX A powerful toolset for genome arithmetic
beem-bio 1.0.1 dev BSD-2-Clause XX Conversion of PDBx/mmCIF files to best effort/minimal PDB files.
behst 3.8 GPLv2 XXX BEHST reads an input dataset of chromosome regions, and intersects them...
bel-resources 0.0.3 MIT X Utilities for BEL resource files.
bellavista 0.0.2 MIT X Python package for interactive visualization of imaging-based spatial...
bellerophon 1.0 MIT X Filter reads that span a mapping junction, retaining the 5'-side.
bellmans-gapc 2024.01.12 doc dev GPL-3.0-or-later XX A language and compiler for algebraic dynamic programming.
berokka 0.2.3 GPL-3.0 XXX Trim, circularise and orient long read bacterial genome assemblies.
besst 2.2.8 GPL-3.0 XXX Scaffolder for genomic assemblies.
bfc r181 dev MIT XX 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
bgen-cpp 1.1.7 Boost X Reference implementation of the BGEN format, written in C++
bgreat 2.0.0 AGPL-3.0 X BGREAT2 is a read mapping tool for NGS sequencing data that align reads...
bgt r283 MIT XX Flexible genotype query among 30,000+ samples whole-genome.
bialign 0.3 doc dev GNU XX 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 XX BICseq2-norm is for normalizing potential biases in the sequencing data.
bicseq2-seg 0.7.2 Custom XX BICseq2-seg is for detecting CNVs based on the normalized data given by...
bifidoannotator 1.0.2 doc dev MIT X Fine-grained annotation of bifidobacterial enzymes involved in...
bifrost 1.3.5 doc dev BSD-2-Clause XX Highly parallel construction and indexing of colored and compacted de...
bifrost-httr 0.5.0 dev LGPL-3.0 X Pre-release version for testing purposes only
bigmag 1.1.0 MIT X BIgMAG: dashboard for extracting insights from MAG quality metrics
bigscape 2.0.0 doc dev 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 2.0.2 doc dev AGPL-3.0-or-later X A highly scalable, user-interactive tool for the large scale analysis...
bigtools 0.5.6 doc dev MIT XX Bigtools provides a high-level, performant API for reading and writing...
bigwig-nim 0.0.3 MIT X Command-line querying+conversion of bigwigs
bin2cell 0.3.4 MIT X Join subcellular Visium HD bins into cells
binchicken 0.13.5 doc dev GPL-3.0-or-later X Targeted recovery of low abundance metagenome assembled genomes through...
bindash 2.6 doc dev Apache-2.0 XX 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 1.2.1 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 XXX Method to cluster contigs based a biphasic method with coverage and composition
binspreader 3.16.0.dev GPL-2.0-only XX BinSPreader is a tool for improving existing binning using assembly...
bio 1.8.1 dev MIT X Command-line utilities to make bioinformatics explorations more enjoyable.
bio-ripser 1.2.1 doc dev MIT XX Ripser: efficient computation of Vietoris–Rips persistence barcodes.
bio-ting 1.1.0 MIT X ting is a tool clustering large scale T cell receptor repertoires by...
bio-unicorn 2.0.0 doc dev MIT XX A tool for computing statistics on short read alignments.
bio-vcf 0.9.5 MIT XX Smart VCF parser
bio2zarr 0.1.6 doc dev Apache-2.0 X Convert bioinformatics data to Zarr
bio_assembly_refinement 0.5.1 GPLv3 XXX Assembly refinement tools, mostly useful for (but not limited to)...
bio_hansel 2.6.1 GNU XXX Subtype Salmonella enterica genomes using 33bp k-mer typing schemes.
bioawk 1.0 Free XX 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 5.1.2 dev Apache-2.0 X Biobb_adapters is the Biobb module collection to use the building...
biobb_amber 5.2.0 doc Apache-2.0 X Biobb_amber is a BioBB category for AMBER MD package.
biobb_analysis 5.2.0 doc Apache-2.0 X Biobb_analysis is the Biobb module collection to perform analysis of...
biobb_chemistry 5.2.0 doc Apache-2.0 X Biobb_chemBiobb_chemistry is the Biobb module collection to perform...
biobb_cmip 5.2.0 doc dev Apache-2.0 X Biobb_cmip is the Biobb module collection to compute classical...
biobb_common 5.2.0 doc dev Apache X Biobb_common is the base package required to use the biobb packages.
biobb_cp2k 5.2.0 doc Apache-2.0 X Biobb_cp2k is a BioBB category for CP2K QM package.
biobb_dna 5.2.0 doc Apache-2.0 X Biobb_dna is a package composed of different analyses for nucleic acid...
biobb_flexdyn 5.2.0 doc dev Apache-2.0 X Biobb_flexdyn is a BioBB category for studies on the conformational...
biobb_flexserv 5.2.0 doc Apache-2.0 X Biobb_flexserv is the Biobb module collection for biomolecular...
biobb_godmd 5.2.0 doc Apache-2.0 X Biobb_godmd is a BioBB category for GOdMD tool (protein conformational...
biobb_gromacs 5.2.0 doc dev Apache-2.0 X biobb_gromacs is the Biobb module collection to perform molecular...
biobb_haddock 5.2.0 doc dev Apache-2.0 X biobb_haddock is the Biobb module collection to compute...
biobb_io 5.2.0 doc Apache-2.0 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 5.2.0 doc dev Apache-2.0 XXX 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 5.2.0 doc Apache-2.0 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 5.2.0 doc Apache-2.0 X Biobb_pdb_tools is a swiss army knife for manipulating and editing PDB files.
biobb_pmx 5.2.1 doc Apache-2.0 X Biobb_pmx is the Biobb module collection to perform PMX...
biobb_pytorch 5.1.0 doc dev Apache-2.0 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 3.15.6 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 5.1.0 doc Apache-2.0 X Biobb_structure_utils is the Biobb module collection to modify or...
biobb_vs 5.1.0 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 1.7.0 doc dev MIT XXX 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 XX An OCaml foundation upon which a number of the bioinformatics tools are built.
biocantor 1.3.0 MIT X Coordinate Maniuplation and Genome Annotation Data Model
biocode 0.12.1 dev MIT X Bioinformatics code libraries and scripts.
biocommons.seqrepo 0.6.11 doc dev Apache-2.0 X Python package for writing and reading a local collection of biological...
bioconda-repodata-patches 20251216 dev CC-PDDC X Generate tweaks to index metadata, hosted separately from anaconda.org index.
bioconda-utils 3.9.1 doc dev MIT XXX 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 XXX 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 XXX Automated Affymetrix Array Analysis Core Package
bioconductor-a4preproc 1.54.0 GPL-3 XXX Automated Affymetrix Array Analysis Preprocessing Package
bioconductor-a4reporting 1.54.0 GPL-3 XXX Automated Affymetrix Array Analysis Reporting Package
bioconductor-abadata 1.24.0 GPL XXX Averaged gene expression in human brain regions from Allen Brain Atlas
bioconductor-abaenrichment 1.24.0 GPL XX 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 XXX ABSSeq: a new RNA-Seq analysis method based on modelling absolute...
bioconductor-acde 1.36.0 GPL-3 XXX 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 XX Classes and functions for Array Comparative Genomic Hybridization data
bioconductor-acme 2.62.0 GPL XX Algorithms for Calculating Microarray Enrichment (ACME)
bioconductor-adacgh2 2.42.0 GPL XX Analysis of big data from aCGH experiments using parallel computing and...
bioconductor-adam 1.22.0 GPL XX 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 XX 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 XX Affymetrix File Parsing SDK
bioconductor-affy 1.84.0 LGPL XX Methods for Affymetrix Oligonucleotide Arrays
bioconductor-affycomp 1.82.0 GPL XXX Graphics Toolbox for Assessment of Affymetrix Expression Measures
bioconductor-affycompatible 1.58.0 Artistic-2.0 XXX Affymetrix GeneChip software compatibility
bioconductor-affycompdata 1.44.0 GPL X affycomp data
bioconductor-affycontam 1.64.0 Artistic-2.0 XXX structured corruption of affymetrix cel file data
bioconductor-affycoretools 1.78.0 Artistic-2.0 XXX Functions useful for those doing repetitive analyses with Affymetrix GeneChips
bioconductor-affydata 1.54.0 GPL XXX Affymetrix Data for Demonstration Purpose
bioconductor-affyexpress 1.56.0 LGPL XXX 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 XXX Linear Model of background subtraction and the Langmuir isotherm
bioconductor-affyio 1.76.0 LGPL XX 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 XXX Probe Dependent Nearest Neighbours (PDNN) for the affy package
bioconductor-affyplm 1.82.0 GPL XX 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 XXX 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 XXX 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 XXX 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 XXX 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 1.6.1 MIT XX 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 1.6.1 MIT XXX 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 1.6.1 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 XXX Analysis Of Differential Abundance Taking Sample and Scale Variation...
bioconductor-alevinqc 1.22.0 MIT XXX Generate QC Reports For Alevin Output
bioconductor-all 1.48.0 Artistic-2.0 XXX 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 XXX alpine
bioconductor-alpinedata 1.26.0 GPL X Data for the alpine package vignette
bioconductor-alps 1.5.0 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 XXX 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 XX Regulatory Network Inference and Driver Gene Evaluation using...
bioconductor-amountain 1.32.0 GPL XX 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 GPL-3 XXX Automated analysis of CRISPR experiments
bioconductor-ampliqueso 1.20.0 GPL-2 X The package provides tools and reports for the analysis of amplicon...
bioconductor-analysispageserver 1.21.0 Artistic-2.0 XX A framework for sharing interactive data and plots from R through the web
bioconductor-anamir 1.13.0 GPL-2 X An integrated analysis package of miRNA and mRNA expression data
bioconductor-anaquin 2.30.0 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 XX Analysis of Copy Number Variation in Single-Cell-Sequencing Data
bioconductor-aneufinderdata 1.34.0 file X WGSCS Data for Demonstration Purposes
bioconductor-anf 1.28.0 GPL-3 X Affinity Network Fusion for Complex Patient Clustering
bioconductor-animalcules 1.22.0 Artistic-2.0 X Interactive microbiome analysis toolkit
bioconductor-annaffy 1.78.0 LGPL XXX Annotation tools for Affymetrix biological metadata
bioconductor-annmap 1.48.0 GPL-2 XXX Genome annotation and visualisation package pertaining to Affymetrix...
bioconductor-annotate 1.84.0 Artistic-2.0 XXX Annotation for microarrays
bioconductor-annotationdbi 1.68.0 Artistic-2.0 XXX Manipulation of SQLite-based annotations in Bioconductor
bioconductor-annotationfilter 1.30.0 Artistic-2.0 XXX Facilities for Filtering Bioconductor Annotation Resources
bioconductor-annotationforge 1.48.0 Artistic-2.0 XXX Tools for building SQLite-based annotation data packages
bioconductor-annotationfuncs 1.40.0 GPL-2 XXX Annotation translation functions
bioconductor-annotationhub 3.14.0 Artistic-2.0 XXX Client to access AnnotationHub resources
bioconductor-annotationhubdata 1.36.0 Artistic-2.0 XXX Transform public data resources into Bioconductor Data Structures
bioconductor-annotationtools 1.80.0 GPL XXX 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 XXX ANalysis Of Translational Activity (ANOTA).
bioconductor-anota2seq 1.28.0 GPL-3 X Generally applicable transcriptome-wide analysis of translational...
bioconductor-antiprofiles 1.46.0 Artistic-2.0 XXX 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 XXX Estimate protein complex membership using AP-MS protein data
bioconductor-apeglm 1.28.0 GPL-2 XX 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 Artistic-2.0 X Base Level Annotation databases for arabidopsis
bioconductor-aracne.networks 1.32.0 file X ARACNe-inferred gene networks from TCGA tumor datasets
bioconductor-aroma.light 3.36.0 GPL XXX Light-Weight Methods for Normalization and Visualization of Microarray...
bioconductor-arrayexpress 1.66.0 Artistic-2.0 XXX Access the ArrayExpress Collection at EMBL-EBI Biostudies and build...
bioconductor-arrayexpresshts 1.44.0 Artistic XX 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 XXX Assessing array quality on spotted arrays
bioconductor-arrayqualitymetrics 3.62.0 LGPL XXX Quality metrics report for microarray data sets
bioconductor-arraytools 1.50.0 LGPL XXX geneChip Analysis Package
bioconductor-arraytv 1.25.0 GPL X Implementation of wave correction for arrays
bioconductor-arrmdata 1.42.0 Artistic-2.0 XXX Example dataset for normalization of Illumina 450k Methylation data
bioconductor-arrmnormalization 1.46.0 Artistic-2.0 XXX 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 XXX Ancestry Specific Allele Frequency Estimation
bioconductor-aseb 1.50.0 GPL XX Predict Acetylated Lysine Sites
bioconductor-asgsca 1.40.0 GPL-3 XXX 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 XXX 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 XX 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 XXX 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 Apache XX Query the Gene Expression Atlas RDF data at the European Bioinformatics...
bioconductor-atsnp 1.22.0 GPL-2 XX 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 XX 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 XXX BaalChIP: Bayesian analysis of allele-specific transcription factor...
bioconductor-bac 1.58.0 Artistic-2.0 XX Bayesian Analysis of Chip-chip experiment
bioconductor-bacon 1.34.0 GPL XX Controlling bias and inflation in association studies using the...
bioconductor-bader 1.44.0 GPL-2 XX Bayesian Analysis of Differential Expression in RNA Sequencing Data
bioconductor-badregionfinder 1.34.0 LGPL-3 XXX BadRegionFinder: an R/Bioconductor package for identifying regions with...
bioconductor-bags 2.46.0 Artistic-2.0 XX A Bayesian Approach for Geneset Selection
bioconductor-ballgown 2.38.0 Artistic-2.0 XXX Flexible, isoform-level differential expression analysis
bioconductor-bambu 3.8.3 GPL-3 XX Context-Aware Transcript Quantification from Long Read RNA-Seq data
bioconductor-bamsignals 1.38.0 GPL-2 XX Extract read count signals from bam files
bioconductor-bandits 1.22.0 GPL XX BANDITS: Bayesian ANalysis of DIfferenTial Splicing
bioconductor-bandle 1.6.0 Artistic-2.0 XX An R package for the Bayesian analysis of differential subcellular...
bioconductor-banocc 1.30.0 MIT XXX 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 XXX Working with Illumina Basecalling and Demultiplexing input and output files
bioconductor-basespacer 1.50.0 Apache XXX R SDK for BaseSpace RESTful API
bioconductor-basic4cseq 1.42.0 LGPL-3 XXX Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data
bioconductor-basics 2.18.0 GPL-3 XX Bayesian Analysis of Single-Cell Sequencing data
bioconductor-basicstan 1.8.0 GPL-3 XX Stan implementation of BASiCS
bioconductor-basicstarrseq 1.34.0 LGPL-3 X Basic peak calling on STARR-seq data
bioconductor-basilisk 1.18.0 GPL-3 X Freezing Python Dependencies Inside Bioconductor Packages
bioconductor-basilisk.utils 1.18.0 GPL-3 X Basilisk Installation Utilities
bioconductor-batchelor 1.22.0 GPL-3 XX Single-Cell Batch Correction Methods
bioconductor-batchqc 2.2.0 MIT XXX 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 XX Bayesian Analysis of ChIP-seq Data
bioconductor-bayesspace 1.12.0 MIT XX Clustering and Resolution Enhancement of Spatial Transcriptomes
bioconductor-baynorm 1.24.0 GPL XX Single-cell RNA sequencing data normalization
bioconductor-bayseq 2.40.0 GPL-3 XXX Empirical Bayesian analysis of patterns of differential expression in count data
bioconductor-bbcanalyzer 1.36.0 LGPL-3 XXX 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 XX Predicting binding site consensus from ranked DNA sequences
bioconductor-bcseq 1.28.0 GPL XX Fast Sequence Mapping in High-Throughput shRNA and CRISPR Screens
bioconductor-bdmmacorrect 1.18.1 GPL XX Meta-analysis for the metagenomic read counts data from different cohorts
bioconductor-beachmat 2.22.0 GPL-3 XX Compiling Bioconductor to Handle Each Matrix Type
bioconductor-beachmat.hdf5 1.4.0 GPL-3 XX beachmat bindings for HDF5-backed matrices
bioconductor-beadarray 2.56.0 MIT XX 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 XXX 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 XX Compression of Illumina BeadArray data
bioconductor-beadsorted.saliva.epic 1.14.0 GPL-3 X Illumina EPIC data on BeadSorted child saliva cells
bioconductor-bearscc 1.22.0 GPL-3 X BEARscc (Bayesian ERCC Assesstment of Robustness of Single Cell Clusters)
bioconductor-beat 1.44.0 LGPL XXX BEAT - BS-Seq Epimutation Analysis Toolkit
bioconductor-beclear 2.22.0 GPL-3 XXX 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 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 GPL-3 X Performs Bayesian GWAS analysis for non-Gaussian data using BG2
bioconductor-bgafun 1.49.0 Artistic-2.0 XXX BGAfun A method to identify specifity determining residues in protein families
bioconductor-bgeecall 1.22.0 GPL-3 X Automatic RNA-Seq present/absent gene expression calls generation
bioconductor-bgeedb 2.28.0 GPL-3 XXX Annotation and gene expression data retrieval from Bgee database....
bioconductor-bgmix 1.59.0 GPL-2 XX Bayesian models for differential gene expression
bioconductor-bgx 1.68.0 GPL-2 XX Bayesian Gene eXpression
bioconductor-bhc 1.54.0 GPL-3 XX Bayesian Hierarchical Clustering
bioconductor-bicare 1.64.0 GPL-2 XX Biclustering Analysis and Results Exploration
bioconductor-bifet 1.26.0 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 GPL-3 X Illumina methylation array analysis for large experiments
bioconductor-bigmemoryextras 1.38.0 Artistic-2.0 X An extension of the bigmemory package with added safety, convenience,...
bioconductor-bigpint 1.15.0 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 Artistic-2.0 X Cross-target analysis of small molecule bioactivity
bioconductor-biobase 2.66.0 Artistic-2.0 XX Biobase: Base functions for Bioconductor
bioconductor-biobroom 1.38.0 LGPL X Turn Bioconductor objects into tidy data frames
bioconductor-biobtreer 1.18.0 MIT X Using biobtree tool from R
bioconductor-biocancer 1.34.0 AGPL-3 X Interactive Multi-Omics Cancers Data Visualization and Analysis
bioconductor-biocartaimage 1.4.0 MIT X BioCarta Pathway Images
bioconductor-biocbaseutils 1.8.0 Artistic-2.0 X General utility functions for developing Bioconductor packages
bioconductor-biocbook 1.4.0 MIT X Write, containerize, publish and version Quarto books with Bioconductor
bioconductor-bioccasestudies 1.52.0 Artistic-2.0 X BiocCaseStudies: Support for the Case Studies Monograph
bioconductor-bioccheck 1.42.0 Artistic-2.0 X Bioconductor-specific package checks
bioconductor-biocdockermanager 1.11.0 Artistic-2.0 X Access Bioconductor docker images
bioconductor-biocfhir 1.8.0 Artistic-2.0 X Illustration of FHIR ingestion and transformation using R
bioconductor-biocfilecache 2.14.0 Artistic-2.0 XXX Manage Files Across Sessions
bioconductor-biocgenerics 0.56.0 Artistic-2.0 XXX S4 generic functions used in Bioconductor
bioconductor-biocgraph 1.68.0 Artistic-2.0 XXX Graph examples and use cases in Bioinformatics
bioconductor-biochail 1.2.0 Artistic-2.0 X basilisk and hail
bioconductor-biochubsshiny 1.6.0 Artistic-2.0 X View AnnotationHub and ExperimentHub Resources Interactively
bioconductor-biocinstaller 1.32.1 Artistic-2.0 XXX This package is used to install and update Bioconductor, CRAN, and...
bioconductor-biocio 1.16.0 Artistic-2.0 X Standard Input and Output for Bioconductor Packages
bioconductor-biocneighbors 2.0.0 GPL-3 XX Nearest Neighbor Detection for Bioconductor Packages
bioconductor-bioconcotk 1.22.0 Artistic-2.0 X Bioconductor components for general cancer genomics
bioconductor-biocor 1.30.0 MIT X Functional similarities
bioconductor-biocparallel 1.40.0 GPL-2 XX Bioconductor facilities for parallel evaluation
bioconductor-biocpkgtools 1.24.0 MIT X Collection of simple tools for learning about Bioconductor Packages
bioconductor-biocroxytest 1.2.0 GPL X Handle Long Tests in Bioconductor Packages
bioconductor-biocset 1.20.0 Artistic-2.0 X Representing Different Biological Sets
bioconductor-biocsingular 1.22.0 GPL-3 XX Singular Value Decomposition for Bioconductor Packages
bioconductor-biocsklearn 1.28.0 Artistic-2.0 XXX interface to python sklearn via Rstudio reticulate
bioconductor-biocstyle 2.34.0 Artistic-2.0 XXX Standard styles for vignettes and other Bioconductor documents
bioconductor-biocthis 1.16.0 Artistic-2.0 X Automate package and project setup for Bioconductor packages
bioconductor-biocversion 3.20.0 Artistic-2.0 X Set the appropriate version of Bioconductor packages
bioconductor-biocviews 1.74.0 Artistic-2.0 XXX Categorized views of R package repositories
bioconductor-biocworkflowtools 1.32.0 MIT XXX Tools to aid the development of Bioconductor Workflow packages
bioconductor-biodb 1.14.0 AGPL-3 XX biodb, a library and a development framework for connecting to chemical...
bioconductor-biodbchebi 1.12.0 AGPL-3 X biodbChebi, a library for connecting to the ChEBI Database
bioconductor-biodbexpasy 1.6.0 AGPL-3 X biodbExpasy, a library for connecting to Expasy ENZYME database.
bioconductor-biodbhmdb 1.12.0 AGPL-3 XX biodbHmdb, a library for connecting to the HMDB Database
bioconductor-biodbkegg 1.8.0 AGPL-3 X biodbKegg, a library for connecting to the KEGG Database
bioconductor-biodblipidmaps 1.8.0 AGPL-3 X biodbLipidmaps, a library for connecting to the Lipidmaps Structure database
bioconductor-biodbmirbase 1.5.0 AGPL-3 X biodbMirbase, a library for connecting to miRBase mature database
bioconductor-biodbncbi 1.10.0 AGPL-3 X biodbNcbi, a library for connecting to NCBI Databases.
bioconductor-biodbnci 1.10.0 AGPL-3 XX biodbNci, a library for connecting to biodbNci, a library for...
bioconductor-biodbuniprot 1.12.0 AGPL-3 X biodbUniprot, a library for connecting to the Uniprot Database
bioconductor-biodist 1.78.0 Artistic-2.0 XXX Different distance measures
bioconductor-bioga 1.0.0 MIT X Bioinformatics Genetic Algorithm (BioGA)
bioconductor-bioimagedbs 1.14.0 Artistic-2.0 X Bio- and biomedical imaging dataset for machine learning and deep...
bioconductor-biomart 2.62.0 Artistic-2.0 XXX Interface to BioMart databases (i.e. Ensembl)
bioconductor-biomartgogenesets 0.99.11 MIT X Gene Ontology Gene Sets from BioMart
bioconductor-biomformat 1.34.0 GPL-2 XXX An interface package for the BIOM file format
bioconductor-biomm 1.15.0 GPL-3 X BioMM: Biological-informed Multi-stage Machine learning framework for...
bioconductor-biomvcclass 1.74.0 LGPL XXX Model-View-Controller (MVC) Classes That Use Biobase
bioconductor-biomvrcns 1.46.0 GPL XX Copy Number study and Segmentation for multivariate biological data
bioconductor-bionar 1.8.0 Artistic-2.0 X Biological Network Analysis in R
bioconductor-bionero 1.14.0 GPL-3 X Biological Network Reconstruction Omnibus
bioconductor-bionet 1.66.0 GPL XXX Routines for the functional analysis of biological networks
bioconductor-bionetstat 1.22.0 GPL X Biological Network Analysis
bioconductor-bioplex 1.12.0 Artistic-2.0 X R-side access to BioPlex protein-protein interaction data
bioconductor-bioqc 1.34.0 GPL XX Detect tissue heterogeneity in expression profiles with gene sets
bioconductor-bioseqclass 1.45.0 LGPL X Classification for Biological Sequences
bioconductor-biosigner 1.34.0 CeCILL XXX Signature discovery from omics data
bioconductor-biostrings 2.74.0 Artistic-2.0 XX Efficient manipulation of biological strings
bioconductor-biosvd 2.23.0 Artistic-2.0 XXX Package for high-throughput data processing, outlier detection, noise...
bioconductor-biotip 1.20.0 GPL-2 X BioTIP: An R package for characterization of Biological Tipping-Point
bioconductor-biotmle 1.30.0 MIT X Targeted Learning with Moderated Statistics for Biomarker Discovery
bioconductor-biotmledata 1.30.0 file X Example experimental microarray data set for the "biotmle" R package
bioconductor-biovizbase 1.54.0 Artistic-2.0 XX Basic graphic utilities for visualization of genomic data.
bioconductor-birewire 3.38.0 GPL-3 XX High-performing routines for the randomization of a bipartite graph (or...
bioconductor-birta 1.31.0 GPL XX Bayesian Inference of Regulation of Transcriptional Activity
bioconductor-birte 1.18.0 GPL XX Expression levels of mRNA molecules are regulated by different...
bioconductor-biscuiteer 1.20.0 GPL-3 X Convenience Functions for Biscuit
bioconductor-biscuiteerdata 1.20.0 GPL-3 X Data Package for Biscuiteer
bioconductor-biseq 1.46.0 LGPL-3 XXX Processing and analyzing bisulfite sequencing data
bioconductor-bitseq 1.38.0 Artistic-2.0 XX Transcript expression inference and differential expression analysis...
bioconductor-blacksheepr 1.20.0 MIT X Outlier Analysis for pairwise differential comparison
bioconductor-bladderbatch 1.44.0 Artistic-2.0 XXX Bladder gene expression data illustrating batch effects
bioconductor-blima 1.40.0 GPL-3 XX Tools for the preprocessing and analysis of the Illumina microarrays on...
bioconductor-blimatestingdata 1.26.0 GPL-3 X Data for testing of the package blima.
bioconductor-blma 1.30.0 GPL X BLMA: A package for bi-level meta-analysis
bioconductor-bloodcancermultiomics2017 1.26.0 LGPL X "Drug-perturbation-based stratification of blood cancer" by...
bioconductor-bloodgen3module 1.14.0 GPL-2 X This R package for performing module repertoire analyses and generating...
bioconductor-bluster 1.16.0 GPL-3 XX Clustering Algorithms for Bioconductor
bioconductor-bnbc 1.28.0 Artistic-2.0 XX Bandwise normalization and batch correction of Hi-C data
bioconductor-bnem 1.10.0 GPL-3 X Training of logical models from indirect measurements of perturbation...
bioconductor-bobafit 1.10.0 GPL X Refitting diploid region profiles using a clustering procedure
bioconductor-bodymaprat 1.22.0 CC X Experimental dataset from the rat BodyMap project
bioconductor-borealis 1.10.0 GPL-3 X Bisulfite-seq OutlieR mEthylation At singLe-sIte reSolution
bioconductor-bovine.db 3.13.0 Artistic-2.0 X Affymetrix Affymetrix Bovine Array annotation data (chip bovine)
bioconductor-bovine.db0 3.20.0 Artistic-2.0 X Base Level Annotation databases for bovine
bioconductor-bovinecdf 2.18.0 LGPL X bovinecdf
bioconductor-bovineprobe 2.18.0 LGPL X Probe sequence data for microarrays of type bovine
bioconductor-bprmeth 1.32.0 GPL-3 XX Model higher-order methylation profiles
bioconductor-brain 1.52.0 GPL-2 XXX Baffling Recursive Algorithm for Isotope distributioN calculations
bioconductor-brainflowprobes 1.16.0 Artistic-2.0 X Plots and annotation for choosing BrainFlow target probe sequence
bioconductor-brainimager 1.1.0 CC X BrainImageR is a package that provides the user with information of...
bioconductor-brainimagerdata 1.12.0 CC X Image masks and expression data for use with BrainImageR
bioconductor-brainsaber 1.8.0 Artistic-2.0 X Brain Span Atlas in Biobase Expressionset R toolset
bioconductor-brainstars 1.34.0 Artistic-2.0 XXX query gene expression data and plots from BrainStars (B*)
bioconductor-branchpointer 1.32.0 BSD_3_clause X Prediction of intronic splicing branchpoints
bioconductor-breakpointr 1.24.0 file X Find breakpoints in Strand-seq data
bioconductor-breakpointrdata 1.24.0 file X Strand-seq data for demonstration purposes
bioconductor-breastcancermainz 1.44.0 Artistic-2.0 X Gene expression dataset published by Schmidt et al. [2008] (MAINZ).
bioconductor-breastcancernki 1.44.0 Artistic-2.0 X Genexpression dataset published by van't Veer et al. [2002] and van...
bioconductor-breastcancertransbig 1.44.0 Artistic-2.0 X Gene expression dataset published by Desmedt et al. [2007] (TRANSBIG).
bioconductor-breastcancerunt 1.44.0 Artistic-2.0 X Gene expression dataset published by Sotiriou et al. [2007] (UNT).
bioconductor-breastcancerupp 1.44.0 Artistic-2.0 X Gene expression dataset published by Miller et al. [2005] (UPP).
bioconductor-breastcancervdx 1.44.0 Artistic-2.0 X Gene expression datasets published by Wang et al. [2005] and Minn et...
bioconductor-brendadb 1.20.0 MIT XX The BRENDA Enzyme Database
bioconductor-brew3r.r 1.2.0 GPL-3 X R package associated to BREW3R
bioconductor-brgedata 1.28.0 MIT X Exposures, Gene Expression and Methylation data for ilustration purpouses
bioconductor-brgenomics 1.13.0 Artistic-2.0 X Tools for the Efficient Analysis of High-Resolution Genomics Data
bioconductor-bridge 1.62.0 GPL XX Bayesian Robust Inference for Differential Gene Expression
bioconductor-bridgedbr 2.16.0 AGPL-3 X Code for using BridgeDb identifier mapping framework from within R
bioconductor-broadseq 1.0.0 MIT X broadSeq : for streamlined exploration of RNA-seq data
bioconductor-bronchialil13 1.44.0 GPL-2 X time course experiment involving il13
bioconductor-browserviz 2.28.0 GPL-2 XXX BrowserViz: interactive R/browser graphics using websockets and JSON
bioconductor-browservizdemo 1.11.0 GPL-2 XX A BrowserViz subclassing example, xy plotting in the browser using d3.
bioconductor-bsgenome 1.74.0 Artistic-2.0 XXX Software infrastructure for efficient representation of full genomes...
bioconductor-bsgenome.alyrata.jgi.v1 1.0.1 Artistic-2.0 X Arabidopsis lyrata full genome (JGI version V1.0)
bioconductor-bsgenome.amellifera.beebase.assembly4 1.4.0 Artistic-2.0 X Full genome sequences for Apis mellifera (BeeBase assembly4)
bioconductor-bsgenome.amellifera.ncbi.amelhav3.1 1.5.0 Artistic-2.0 X Full genome sequences for Apis mellifera (Amel_HAv3.1)
bioconductor-bsgenome.amellifera.ucsc.apimel2 1.4.0 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 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 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 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 Artistic-2.0 X Full genome sequences for Bos taurus (UCSC version bosTau9)
bioconductor-bsgenome.btaurus.ucsc.bostau9.masked 1.4.4 Artistic-2.0 X Full masked genome sequences for Bos taurus (UCSC version bosTau9)
bioconductor-bsgenome.carietinum.ncbi.v1 1.0.0 GPL-3 X Cicer arietinum (Chickpea) full genome (NCBI version ASM33114v1)
bioconductor-bsgenome.celegans.ucsc.ce10 1.4.0 Artistic-2.0 XXX 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 Artistic-2.0 X Full genome sequences for Caenorhabditis elegans (UCSC version ce2)
bioconductor-bsgenome.celegans.ucsc.ce6 1.4.0 Artistic-2.0 XXX 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 Artistic-2.0 X Full genome sequences for Callithrix jacchus (UCSC version calJac3)
bioconductor-bsgenome.cjacchus.ucsc.caljac4 1.5.0 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 XXX 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 XXX 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 XXX 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 XXX 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 XXX 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 XXX 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 XXX 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 XXX 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 XX 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 XXX BubbleTree: an intuitive visualization to elucidate tumoral aneuploidy...
bioconductor-bufferedmatrix 1.70.0 LGPL XX A matrix data storage object held in temporary files
bioconductor-bufferedmatrixmethods 1.70.0 GPL XX 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 XXX Bump Hunter
bioconductor-bumpymatrix 1.14.0 MIT X Bumpy Matrix of Non-Scalar Objects
bioconductor-bus 1.62.0 GPL-3 XX Gene network reconstruction
bioconductor-buscorrect 1.24.0 GPL XX Batch Effects Correction with Unknown Subtypes
bioconductor-busparse 1.20.0 BSD_2_clause XX kallisto | bustools R utilities
bioconductor-busseq 1.12.0 Artistic-2.0 XX 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 XX 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 XXX Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for...
bioconductor-calib 1.52.0 LGPL XX 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 XX 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 XX 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 XX An R interface for computational modeling of tumor progression
bioconductor-cancermutationanalysis 1.32.0 GPL XX Cancer mutation analysis
bioconductor-cancersubtypes 1.26.0 GPL XXX Cancer subtypes identification, validation and visualization based on...
bioconductor-cand 1.26.0 Artistic-2.0 XXX 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 XXX A mass spectrometry imaging toolbox for statistical analysis
bioconductor-cardinalio 1.4.0 Artistic-2.0 XX 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 XX 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 XXX 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 XXX 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 XX 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 XX Cancer Clone Finder
bioconductor-ccimpute 1.8.0 GPL-3 XX 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 XX 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 XX Data structures, clustering and testing for single cell immune receptor...
bioconductor-cellbarcode 1.12.0 Artistic-2.0 XX 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 XXX 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 XXX Analysis of cell-based screens - revised version of cellHTS
bioconductor-cellid 1.14.0 GPL-3 XX 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 XXX 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 XX 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 XXX 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 XXX An R package to uncover high-resolution protein-DNA interactions in...
bioconductor-cfassay 1.40.0 LGPL XXX 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 XX 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 XX An R package for analysis of case-control studies in genetic epidemiology
bioconductor-cghbase 1.66.0 GPL XXX CGHbase: Base functions and classes for arrayCGH data analysis.
bioconductor-cghcall 2.68.0 GPL XXX Calling aberrations for array CGH tumor profiles.
bioconductor-cghmcr 1.64.0 LGPL XXX Find chromosome regions showing common gains/losses
bioconductor-cghnormaliter 1.60.0 GPL XXX Normalization of array CGH data with imbalanced aberrations.
bioconductor-cghregions 1.64.0 GPL XXX 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 XX R interface to a subset of OpenBabel functionalities
bioconductor-chemminer 3.58.0 Artistic-2.0 XX 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 XXX 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 XX Save Delayed Operations to a HDF5 File
bioconductor-chimera 1.32.0 Artistic-2.0 XX A package for secondary analysis of fusion products
bioconductor-chimeraviz 1.32.0 Artistic-2.0 XXX 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 XX 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 XXX Batch annotation of the peaks identified from either ChIP-seq,...
bioconductor-chipqc 1.42.0 GPL XXX Quality metrics for ChIPseq data
bioconductor-chipseeker 1.42.0 Artistic-2.0 XXX ChIPseeker for ChIP peak Annotation, Comparison, and Visualization
bioconductor-chipseq 1.56.0 Artistic-2.0 XX 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 XX 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 XXX Simulation of ChIP-seq experiments
bioconductor-chipxpress 1.42.0 GPL(>=2) XXX ChIPXpress: enhanced transcription factor target gene identification...
bioconductor-chipxpressdata 1.36.0 GPL XXX ChIPXpress Pre-built Databases
bioconductor-chopsticks 1.72.0 GPL-3 XX 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 XX chromDraw is a R package for drawing the schemes of karyotypes in the...
bioconductor-chromheatmap 1.60.0 Artistic-2.0 XXX 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 XXX Global visualization tool of genomic data
bioconductor-chromscape 1.16.0 GPL-3 XXX Analysis of single-cell epigenomics datasets with a Shiny App
bioconductor-chromstar 1.28.0 Artistic-2.0 XX Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data
bioconductor-chromstardata 1.32.0 GPL-3 XXX 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 1.30.1 doc dev MIT XX Chromatin Variation Across Regions.
bioconductor-chronos 1.34.0 GPL-2 XXX 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 XXX 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 XX Visualization and management of the protein-protein interaction networks.
bioconductor-citefuse 1.18.0 GPL-3 XXX 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 XXX A framework for cross-validated classification problems, with...
bioconductor-cleanupdtseq 1.44.0 GPL-2 XXX 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 XXX 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 XX 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 XX 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 XXX Infers clonal composition of a tumor
bioconductor-clonality 1.47.0 GPL-3 XXX Clonality testing
bioconductor-clonotyper 1.32.1 file XXX High throughput analysis of T cell antigen receptor sequences
bioconductor-clst 1.54.0 GPL-3 XXX Classification by local similarity threshold
bioconductor-clstutils 1.54.0 GPL-3 XXX 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 XXX Clustering Comparison Package
bioconductor-clusterexperiment 2.26.0 Artistic-2.0 XX 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 XXX 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 XXX The ClusterSignificance package provides tools to assess if class...
bioconductor-clusterstab 1.78.0 Artistic-2.0 XXX 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 XXX Clustering of immune receptor repertoires
bioconductor-cma 1.64.0 GPL XXX Synthesis of microarray-based classification
bioconductor-cmap 1.15.1 LGPL XXX A data package containing annotation data for cMAP
bioconductor-cmap2data 1.42.0 GPL-3 XXX Connectivity Map (version 2) Data
bioconductor-cmapr 1.18.0 file X CMap Tools in R
bioconductor-cn.farms 1.54.0 LGPL XX cn.FARMS - factor analysis for copy number estimation
bioconductor-cn.mops 1.52.0 LGPL XX cn.mops - Mixture of Poissons for CNV detection in NGS data
bioconductor-cnanorm 1.52.0 GPL-2 XX A normalization method for Copy Number Aberration in cancer samples
bioconductor-cner 1.43.0 doc GPL-2.0-or-later XX CNE Detection and Visualization.
bioconductor-cnordt 1.48.0 GPL-2 XX 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 XX Addon to CellNOptR: Fuzzy Logic
bioconductor-cnorode 1.48.0 GPL-2 XX ODE add-on to CellNOptR
bioconductor-cnpbayes 1.13.5 Artistic-2.0 XX Bayesian hierarchical mixture models for batch effects and copy number.
bioconductor-cntools 1.62.0 LGPL XX 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 XXX 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 XXX 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 XX 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 XXX Manipulation of Codelink microarray data
bioconductor-codex 1.38.0 GPL-2 XXX 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 XX Coordinated Gene Activity in Pattern Sets
bioconductor-cogena 1.40.0 LGPL-3 XXX 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 XXX cancer outlier Gene Profile Sets
bioconductor-cohcap 1.48.0 GPL-3.0-only XX CpG Island Analysis Pipeline for Illumina Methylation Array and...
bioconductor-cohcapanno 1.42.0 GPL-3 XXX Annotations for City of Hope CpG Island Analysis Pipeline
bioconductor-cola 2.12.0 MIT XX 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 XX 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 XXX 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 XXX 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 XXX ConsensusClusterPlus
bioconductor-consensusde 1.24.0 GPL-3 X RNA-seq analysis using multiple algorithms
bioconductor-consensusov 1.24.0 Artistic-2.0 XXX Gene expression-based subtype classification for high-grade serous...
bioconductor-consensusseeker 1.34.0 Artistic-2.0 XXX 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 XX 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 XXX Convert Microarray Data Objects
bioconductor-copa 1.74.0 Artistic-2.0 XX 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 XXX 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 XXX 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 XXX 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 XX 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 XXX 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 XXX 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 XX 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 XX 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 XXX 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 XXX Multivariate Analysis of Transcriptomic Data
bioconductor-cpvsnp 1.38.0 Artistic-2.0 XXX Gene set analysis methods for SNP association p-values that lie in...
bioconductor-cqn 1.52.0 Artistic-2.0 XXX Conditional quantile normalization
bioconductor-crcl18 1.26.0 GPL-2 X CRC cell line dataset
bioconductor-crimage 1.54.0 Artistic-2.0 XXX 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 XXX Design of target-specific guide RNAs in CRISPR-Cas9, genome-editing systems
bioconductor-crisprseekplus 1.26.0 GPL-3 XXX crisprseekplus
bioconductor-crisprshiny 1.2.0 MIT X Exploring curated CRISPR gRNAs via Shiny
bioconductor-crisprvariants 1.34.0 GPL-2 XXX 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 XX 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 XX Statistical tools for the analysis of ChIP-seq data
bioconductor-csaw 1.40.0 GPL-3 XX ChIP-Seq Analysis with Windows
bioconductor-csdr 1.12.0 GPL-3 XX Differential gene co-expression
bioconductor-cssp 1.37.0 GPL-2 XX 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 XXX 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 XXX 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 XXX 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 XXX Curated Metagenomic Data of the Human Microbiome
bioconductor-curatedovariandata 1.44.0 Artistic-2.0 XXX 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 XXX Generate customized protein database from NGS data, with a focus on...
bioconductor-cve 1.11.2 GPL-3 XXX 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 XX 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 XX Differential expression using kernel-based score test
bioconductor-cytolib 2.18.0 AGPL-3.0-only XXX 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 XXX 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 XX 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 XX 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 XXX 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 20250625 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 XXX 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 XXX Distance-correlation based Gene Set Analysis for longitudinal gene...
bioconductor-dchiprep 1.18.0 MIT XXX DChIPRep - Analysis of chromatin modification ChIP-Seq data with replication
bioconductor-ddct 1.62.0 LGPL-3 XXX 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 XX 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 XX 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 XX 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 XX Differential Expression via Distance Summary for Microarray Data
bioconductor-deepbluer 1.24.0 GPL XXX 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 XX 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 XXX 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 XX DegNorm: degradation normalization for RNA-seq data
bioconductor-degraph 1.58.0 GPL-3 XXX Two-sample tests on a graph
bioconductor-degreport 1.42.0 MIT XXX Report of DEG analysis
bioconductor-degseq 1.60.0 LGPL XX Identify Differentially Expressed Genes from RNA-seq data
bioconductor-delayedarray 0.32.0 Artistic-2.0 XX 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 XXX Functions that Apply to Rows and Columns of 'DelayedMatrix' Objects
bioconductor-delayedrandomarray 1.14.0 GPL-3 XX 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 XXX DeMAND
bioconductor-demixt 1.22.0 GPL-3 XX 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 XX 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 XX 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 XXX a tool to perform statistical analysis of differential protein...
bioconductor-derfinder 1.40.0 Artistic-2.0 XXX 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 XXX derfinder helper package
bioconductor-derfinderplot 1.40.0 Artistic-2.0 XXX Plotting functions for derfinder
bioconductor-descan2 1.26.0 Artistic-2.0 XX Differential Enrichment Scan 2
bioconductor-deseq 1.39.0 GPL XX Differential gene expression analysis based on the negative binomial...
bioconductor-deseq2 1.46.0 LGPL XX 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 XX 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 XXX Inference of differential exon usage in RNA-Seq
bioconductor-dexus 1.30.0 LGPL XX DEXUS - Identifying Differential Expression in RNA-Seq Studies with...
bioconductor-dfp 1.64.0 GPL-2 XXX Gene Selection
bioconductor-dfplyr 1.0.0 GPL-3 X A `DataFrame` (`S4Vectors`) backend for `dplyr`
bioconductor-dialignr 2.10.0 GPL-3 XX Dynamic Programming Based Alignment of MS2 Chromatograms
bioconductor-diffbind 3.16.0 Artistic-2.0 XX 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 XX Differentially regulated genes from scRNA-seq data
bioconductor-diffgeneanalysis 1.88.0 GPL XXX Performs differential gene expression Analysis
bioconductor-diffhic 1.38.0 GPL-3 XX 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 XXX 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 XX 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 XXX A dynamic visualization tool of multi-level data
bioconductor-dirichletmultinomial 1.48.0 LGPL-3 XX Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data
bioconductor-discordant 1.30.0 GPL-3 XX 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 XX 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 XX Differentially Methylated Regions caller
bioconductor-dmrcate 3.2.1 file XXX Methylation array and sequencing spatial analysis methods
bioconductor-dmrcatedata 2.20.0 GPL-3 XXX 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 XXX A Tool for Optimizing Combinations of DNA Barcodes Used in Multiplexed...
bioconductor-dnabarcodes 1.36.0 GPL-2 XX A tool for creating and analysing DNA barcodes used in Next Generation...
bioconductor-dnacopy 1.80.0 GPL XX 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 XX 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 XXX 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 XXX Identify likely duplicate samples from genomic or meta-data
bioconductor-doqtl 1.19.0 GPL-3 XX 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 XXX 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 XX 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-dreamlet 1.6.0 Artistic-2.0 XX Cohort-scale differential expression analysis of single cell data using...
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 XXX Differential transcript usage and tuQTL analyses with...
bioconductor-drivernet 1.46.0 GPL-3 XXX 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 XX 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 XXX Comparison of disease and drug profiles using Gene set Enrichment Analysis
bioconductor-drugvsdiseasedata 1.42.0 GPL-3 XXX Drug versus Disease Data
bioconductor-dsimer 1.8.0 GPL XX 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 XX 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 XXX 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 XXX 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 1.38.0 GPL-3 XXX 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 XXX 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 XXX 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 XXX 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 XX Unified Approach for Simultaneous Gene Clustering and Differential...
bioconductor-ebcoexpress 1.50.0 GPL XX EBcoexpress for Differential Co-Expression Analysis
bioconductor-ebimage 4.48.0 LGPL XX Image processing and analysis toolbox for R
bioconductor-ebsea 1.34.0 GPL-2 XXX Exon Based Strategy for Expression Analysis of genes
bioconductor-ebseq 2.4.0 Artistic-2.0 XXX 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 XXX Exploratory Data Analysis and Normalization for RNA-Seq
bioconductor-edda 1.26.0 GPL XX Experimental Design in Differential Abundance analysis
bioconductor-edge 2.38.0 MIT XX Extraction of Differential Gene Expression
bioconductor-edger 4.4.0 GPL XX 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 XX 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 XXX Ensemble of Gene Set Enrichment Analyses
bioconductor-egseadata 1.34.0 file XXX Gene set collections for the EGSEA package
bioconductor-eir 1.46.0 Artistic-2.0 XX 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 XXX Inferring Regulatory Element Landscapes and Transcription Factor...
bioconductor-elmer.data 2.30.0 GPL-3 XXX 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 XXX 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 XXX 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 XX 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 XX Making Enriched Heatmaps
bioconductor-enrichmentbrowser 2.36.0 Artistic-2.0 XX Seamless navigation through combined results of set-based and...
bioconductor-enrichplot 1.26.1 Artistic-2.0 XXX 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 XXX 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 XXX Utilities to create and use Ensembl-based annotation databases
bioconductor-ensemblvep 1.44.0 Artistic-2.0 XXX 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 XX 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 XXX Epigenetic and gene transcription data normalization and integration...
bioconductor-epigrahmm 1.14.0 MIT XX 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 XX 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 XX 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 XXX 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 XXX Data Management API for epiviz interactive visualization app
bioconductor-epivizrserver 1.34.0 MIT XXX WebSocket server infrastructure for epivizr apps and packages
bioconductor-epivizrstandalone 1.34.0 MIT XXX 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 XX 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 XXX 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 XXX 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 XXX 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 XXX R functions for the normalization of Exiqon miRNA array data
bioconductor-exomecopy 1.48.0 GPL-3.0-or-later XX Copy number variant detection from exome sequencing read depth
bioconductor-exomepeak 2.17.0 GPL-2 XXX 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 XXX 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 XX Gene Expression Normalization Workflow
bioconductor-expressionview 1.42.0 GPL XX Visualize biclusters identified in gene expression data
bioconductor-extrachips 1.10.0 GPL-3 XXX Additional functions for working with ChIP-Seq data
bioconductor-faahko 1.46.0 LGPL XXX Saghatelian et al. (2004) FAAH knockout LC/MS data
bioconductor-fabia 2.52.0 LGPL XX 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 XXX 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 XX 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 XX 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 XXX 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 XXX 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 XX FDR adjustments of Microarray Experiments (FDR-AME)
bioconductor-feast 1.14.0 GPL-2 XX 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 XXX 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 XX 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 XX Microbial Comparative Genomics in R
bioconductor-fis 1.34.0 GPL-3 XXX Human Functional Interactions (FIs) for splineTimeR package
bioconductor-fishalyser 1.40.0 Artistic-2.0 XXX FISHalyseR a package for automated FISH quantification
bioconductor-fishpond 2.12.0 GPL-2 XXX 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 XX Confidence estimation for intra-chromosomal contact maps
bioconductor-flagme 1.62.0 LGPL XX Analysis of Metabolomics GC/MS Data
bioconductor-flames 1.8.0 GPL XX 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 GPL X Master regulators of FGFR2 signalling and breast cancer risk
bioconductor-flipflop 1.18.0 GPL-3 XX Flipflop discovers which isoforms of a gene are expressed in a given...
bioconductor-flowai 1.36.0 GPL XXX Automatic and interactive quality control for flow cytometry data
bioconductor-flowbeads 1.44.0 Artistic-2.0 XXX 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 XXX Semantic labelling of flow cytometric cell populations
bioconductor-flowclean 1.44.0 Artistic-2.0 XXX flowClean
bioconductor-flowclust 3.44.0 MIT XX Clustering for Flow Cytometry
bioconductor-flowcore 2.18.0 Artistic-2.0 XX 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 XXX 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 XX 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 XXX Mapping cell populations in flow cytometry data for cross-sample...
bioconductor-flowmatch 1.42.0 Artistic-2.0 XX 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 XX An R package for flow data clustering
bioconductor-flowploidy 1.32.0 GPL-3 XXX 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 XX 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 XXX FlowRepository R Interface
bioconductor-flowsom 2.14.0 GPL XX Using self-organizing maps for visualization and interpretation of...
bioconductor-flowsorted.blood.450k 1.44.0 Artistic-2.0 XXX 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 XX 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 XXX Utilities for flow cytometry
bioconductor-flowviz 1.70.0 Artistic-2.0 XXX 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 XX 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 XX Mismatch Tolerant Maximum Common Substructure Searching
bioconductor-fmrs 1.16.0 GPL-3 XX 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 XXX 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 XXX Package analyse 4C sequencing data
bioconductor-fourdndata 1.6.0 MIT X 4DN data package
bioconductor-fraser 2.4.6 dev MIT XX 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 XXX Frozen RMA and Barcode
bioconductor-frmaexampledata 1.42.0 GPL X Frma Example Data
bioconductor-frmatools 1.58.0 GPL XXX 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 XX 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 XX 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 XX GaGa hierarchical model for high-throughput data analysis
bioconductor-gage 2.56.0 GPL XXX Generally Applicable Gene-set Enrichment for Pathway Analysis
bioconductor-gagedata 2.44.0 GPL XXX 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 XXX Prediction of gestational age with Illumina HumanMethylation450 data
bioconductor-garfield 1.34.0 GPL-3 XX 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 XX 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 XXX 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 XXX Suite of Functions for Pooled Crispr Screen QC and Analysis
bioconductor-gcrma 2.78.0 LGPL XX Background Adjustment Using Sequence Information
bioconductor-gcsconnection 1.6.0 GPL XX 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 XXX 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 XX 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 XX R Interface to CoreArray Genomic Data Structure (GDS) Files
bioconductor-geecc 1.21.0 GPL XX 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 XXX 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 XXX Identification of candidate genes associated with genetic variation
bioconductor-genebreak 1.36.0 GPL-2 XXX 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 XX genefilter: methods for filtering genes from high-throughput experiments
bioconductor-genefu 2.34.0 Artistic-2.0 XXX Computation of Gene Expression-Based Signatures in Breast Cancer
bioconductor-genega 1.56.0 GPL XXX Design gene based on both mRNA secondary structure and codon usage bias...
bioconductor-genegeneinter 1.32.0 GPL XXX Tools for Testing Gene-Gene Interaction at the Gene Level
bioconductor-genelendatabase 1.42.0 LGPL XXX Lengths of mRNA transcripts for a number of genomes
bioconductor-genemeta 1.78.0 Artistic-2.0 XXX MetaAnalysis for High Throughput Experiments
bioconductor-genenetworkbuilder 1.48.0 GPL XX GeneNetworkBuilder: a bioconductor package for building regulatory...
bioconductor-geneoverlap 1.42.0 GPL-3 XXX Test and visualize gene overlaps
bioconductor-geneplast 1.32.0 GPL XXX 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 XXX Graphics related functions for Bioconductor
bioconductor-generecommender 1.78.0 GPL XXX A gene recommender algorithm to identify genes coexpressed with a query...
bioconductor-generegionscan 1.62.0 GPL XXX GeneRegionScan
bioconductor-generxcluster 1.42.0 GPL XX gRx Differential Clustering
bioconductor-geneselectmmd 2.50.0 GPL XX Gene selection based on the marginal distributions of gene profiles...
bioconductor-geneselector 2.32.0 GPL XX The term 'GeneSelector' refers to a filter selecting those...
bioconductor-genesis 2.36.0 GPL-3 XXX 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 XXX Classify diseases and build associated gene networks using gene...
bioconductor-geneticsdesign 1.55.0 GPL-2 XXX Functions for designing genetics studies
bioconductor-geneticsped 1.68.0 LGPL XX 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 XX Optimized Functional Annotation Of ChIP-seq Data
bioconductor-genie3 1.28.0 GPL XX GEne Network Inference with Ensemble of trees
bioconductor-genocn 1.58.0 GPL XX genotyping and copy number study tools
bioconductor-genogam 2.11.0 GPL-2 XX A GAM based framework for analysis of ChIP-Seq data
bioconductor-genomation 1.38.0 Artistic-2.0 XX 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 XXX Plotting genomic information from Ensembl
bioconductor-genomeinfodb 1.42.0 Artistic-2.0 XXX Utilities for manipulating chromosome names, including modifying them...
bioconductor-genomeinfodbdata 1.2.13 Artistic-2.0 XXX Species and taxonomy ID look up tables used by GenomeInfoDb
bioconductor-genomeintervals 1.62.0 Artistic-2.0 XXX 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 XX Representation and manipulation of short genomic alignments
bioconductor-genomicdatacommons 1.30.0 Artistic-2.0 XXX 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 XXX Query the gene models of a given organism/assembly
bioconductor-genomicfiles 1.42.0 Artistic-2.0 XXX 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 XXX 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 XX Representation and manipulation of genomic intervals
bioconductor-genomicscores 2.18.0 Artistic-2.0 XXX 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 XX Representation and Manipulation of Genomic Tuples
bioconductor-genominator 1.40.0 Artistic-2.0 XXX Analyze, manage and store genomic data
bioconductor-genoset 1.45.1 Artistic-2.0 XX 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 XX 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 XXX Candidate gene prioritization based on convergent evidence
bioconductor-genvisr 1.38.0 GPL-3 XXX Genomic Visualizations in R
bioconductor-geodiff 1.12.0 MIT XX 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 1.68.1 Artistic-2.0 XXX A compilation of metadata from NCBI GEO
bioconductor-geomxtools 3.10.0 MIT X NanoString GeoMx Tools
bioconductor-geoquery 2.74.0 MIT XXX Get data from NCBI Gene Expression Omnibus (GEO)
bioconductor-geosubmission 1.58.0 GPL XXX 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 XXX 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 XXX GGBase infrastructure for genetics of gene expression package GGtools
bioconductor-ggbio 1.54.0 Artistic-2.0 XXX Visualization tools for genomic data
bioconductor-ggcyto 1.34.0 file XXX 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 XX graph-GPA: A graphical model for prioritizing GWAS results and...
bioconductor-ggsc 1.4.0 Artistic-2.0 XX 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 XXX software and data for analyses in genetics of gene expression
bioconductor-ggtree 3.14.0 Artistic-2.0 XXX 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 XX 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 XX 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 XXX Interactive visualizations for gene expression analysis
bioconductor-glmgampoi 1.18.0 GPL-3 XX 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 XX Global test for groups of variables via model comparisons
bioconductor-globalseq 1.34.0 GPL-3 XXX Global Test for Counts
bioconductor-globaltest 5.60.0 GPL XXX 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 XX 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 XXX GWAS-based Mendelian Randomization and Path Analyses
bioconductor-gnet2 1.18.0 Apache XX 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 XXX 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 XX Gene ontology enrichment using FUNC
bioconductor-gofunction 1.35.0 GPL XXX GO-function: deriving biologcially relevant functions from...
bioconductor-golubesets 1.48.0 LGPL XXX exprSets for golub leukemia data
bioconductor-googlegenomics 2.4.0 Apache XX Provides an R package to interact with the Google Genomics API.
bioconductor-gopro 1.32.0 GPL-3 XX 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 XX GO-terms Semantic Similarity Measures
bioconductor-goseq 1.58.0 LGPL XXX Gene Ontology analyser for RNA-seq and other length biased data
bioconductor-gosim 1.40.0 GPL XX 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 XXX Tools for manipulating GO and microarrays
bioconductor-gosummaries 2.37.0 GPL XX Word cloud summaries of GO enrichment analysis
bioconductor-gothic 1.42.0 GPL-3 XXX Binomial test for Hi-C data analysis
bioconductor-gotools 1.80.0 GPL-2 XXX Functions for Gene Ontology database
bioconductor-gp53cdf 2.18.0 LGPL X gp53cdf
bioconductor-gpa 1.18.0 GPL XX 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 XX Human genome partitioning of dense sequencing data by identifying...
bioconductor-gpls 1.78.0 Artistic-2.0 XXX 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 XX 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 XX Adaptive penalization in high-dimensional regression and classification...
bioconductor-graph 1.84.0 Artistic-2.0 XX graph: A package to handle graph data structures
bioconductor-graphalignment 1.70.0 file XX GraphAlignment
bioconductor-graphat 1.78.0 LGPL XXX Graph Theoretic Association Tests
bioconductor-graphite 1.52.0 AGPL-3 XXX GRAPH Interaction from pathway Topological Environment
bioconductor-graphpac 1.44.0 GPL-2 XXX 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 XX 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 XXX 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 XX 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 XXX 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) XXX 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 XXX 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 XXX 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 XXX 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 XX Gene Set Regulation (GS-Reg)
bioconductor-gsri 2.54.0 GPL-3 XXX Gene Set Regulation Index
bioconductor-gsva 2.0.0 GPL XX 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 XXX Genome Level Trellis Layout
bioconductor-guideseq 1.36.0 GPL XXX GUIDE-seq and PEtag-seq analysis pipeline
bioconductor-guitar 2.22.0 GPL-2 X Guitar
bioconductor-gviz 1.50.0 Artistic-2.0 XXX Plotting data and annotation information along genomic coordinates
bioconductor-gwas.bayes 1.16.0 GPL-3 XXX 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 XX 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 XX 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 XX 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 XX 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 XXX 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 XX 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 XXX Flexible Heatmaps for Functional Genomics and Sequence Features
bioconductor-heatplus 3.14.0 GPL XXX 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 XXX Introduce *Ranges to bedtools users
bioconductor-hellorangesdata 1.32.0 GPL X Data for the HelloRanges tutorial vignette
bioconductor-help 1.64.0 GPL XXX Tools for HELP data analysis
bioconductor-hem 1.78.0 GPL XX 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 XX 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 XXX Affymetrix Affymetrix HG-U133A Array annotation data (chip hgu133a)
bioconductor-hgu133a2.db 3.13.0 Artistic-2.0 XXX 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 XXX 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 XXX 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 XXX Functions for annotating GRanges objects
bioconductor-hibag 1.42.0 GPL-3 XX 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 XXX 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 XX Hi-C Direct Caller Plus
bioconductor-hicdoc 1.8.0 LGPL-3 XX 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 XXX 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 XXX Making 2D Hilbert Curve
bioconductor-hilbertvis 1.64.0 GPL XX Hilbert curve visualization
bioconductor-hilda 1.20.0 GPL-3 XX 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 XX Detection of cell-type-specific risk-CpG sites in epigenome-wide...
bioconductor-hitc 1.50.0 Artistic-2.0 XXX 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 LGPL X hivprtplus2cdf
bioconductor-hmdbquery 1.26.0 Artistic-2.0 X utilities for exploration of human metabolome database
bioconductor-hmmcopy 1.48.0 GPL-3 XX Copy number prediction with correction for GC and mappability bias for HTS data
bioconductor-hmp16sdata 1.26.0 Artistic-2.0 X 16S rRNA Sequencing Data from the Human Microbiome Project
bioconductor-hmp2data 1.20.0 Artistic-2.0 X 16s rRNA sequencing data from the Human Microbiome Project 2
bioconductor-hmyrib36 1.26.0 Artistic-2.0 X YRI hapmap + expression (GENEVAR), Build 36, r23a genotypes
bioconductor-holofoodr 1.0.0 Artistic-2.0 X R interface to EBI HoloFood resource
bioconductor-hom.at.inp.db 3.1.3 Artistic-2.0 X Homology information for Arabidopsis thaliana from Inparanoid
bioconductor-hom.ce.inp.db 3.1.3 Artistic-2.0 X Homology information for Caenorhabditis elegans from Inparanoid
bioconductor-hom.dm.inp.db 3.1.3 Artistic-2.0 X Homology information for Drosophila melanogaster from Inparanoid
bioconductor-hom.dr.inp.db 3.1.3 Artistic-2.0 X Homology information for Danio rerio from Inparanoid
bioconductor-hom.hs.inp.db 3.1.3 Artistic-2.0 XXX Homology information for Homo Sapiens from Inparanoid
bioconductor-hom.mm.inp.db 3.1.3 Artistic-2.0 X Homology information for Mus musculus from Inparanoid
bioconductor-hom.rn.inp.db 3.1.3 Artistic-2.0 X Homology information for Rattus norvegicus from Inparanoid
bioconductor-hom.sc.inp.db 3.1.3 Artistic-2.0 X Homology information for Saccharomyces cerevisiae from Inparanoid
bioconductor-homo.sapiens 1.3.1 Artistic-2.0 XXX Annotation package for the Homo.sapiens object
bioconductor-hoodscanr 1.4.0 GPL-3 XX Spatial cellular neighbourhood scanning in R
bioconductor-hopach 2.66.0 GPL XX Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)
bioconductor-hpaanalyze 1.24.0 GPL-3 X Retrieve and analyze data from the Human Protein Atlas
bioconductor-hpannot 1.1.0 GPL-2 X Anotation package for Hipathia package
bioconductor-hpar 1.48.0 Artistic-2.0 XXX 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 Artistic-2.0 X A set of annotation maps describing the entire Human Phenotype Ontology
bioconductor-hs25kresogen.db 2.5.0 Artistic-2.0 X RNG_MRC Human Pangenomic 25k Set annotation data (chip hs25kresogen)
bioconductor-hs6ug171.db 3.2.3 Artistic-2.0 X A package containing metadata for Hs6UG171 arrays
bioconductor-hsagilentdesign026652.db 3.2.3 Artistic-2.0 X Agilent Chips that use Agilent design number 026652 annotation data...
bioconductor-hsmmsinglecell 1.26.0 Artistic-2.0 XXX Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)
bioconductor-hspec 0.99.1 LGPL X Hspec
bioconductor-hspeccdf 0.99.1 LGPL X hspeccdf
bioconductor-hta20probeset.db 8.8.0 Artistic-2.0 X Affymetrix hta20 annotation data (chip hta20probeset)
bioconductor-hta20transcriptcluster.db 8.8.0 Artistic-2.0 X Affymetrix hta20 annotation data (chip hta20transcriptcluster)
bioconductor-hthgu133a.db 3.13.0 Artistic-2.0 X Affymetrix Affymetrix HT_HG-U133A Array annotation data (chip hthgu133a)
bioconductor-hthgu133acdf 2.18.0 LGPL X hthgu133acdf
bioconductor-hthgu133afrmavecs 1.3.0 GPL X Vectors used by frma for microarrays of type hthgu133a
bioconductor-hthgu133aprobe 2.18.0 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 LGPL X hthgu133pluspmcdf
bioconductor-hthgu133pluspmprobe 2.18.0 LGPL X Probe sequence data for microarrays of type hthgu133pluspm
bioconductor-htmg430a.db 3.13.0 Artistic-2.0 X Affymetrix Affymetrix HT_MG-430A Array annotation data (chip htmg430a)
bioconductor-htmg430acdf 2.18.0 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 XXX 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 XXX We provide efficient, easy-to-use tools for High-Throughput Sequencing...
bioconductor-htsfilter 1.46.0 Artistic-2.0 XXX 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 Artistic-2.0 X Interface to 'HuBMAP'
bioconductor-hubpub 1.14.0 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 Artistic-2.0 X Affymetrix huex10 annotation data (chip huex10stprobeset)
bioconductor-huex10sttranscriptcluster.db 8.8.0 Artistic-2.0 X Affymetrix huex10 annotation data (chip huex10sttranscriptcluster)
bioconductor-huexexonprobesetlocation 1.15.0 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 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 Artistic-2.0 X Affymetrix hugene10 annotation data (chip hugene10stprobeset)
bioconductor-hugene10sttranscriptcluster.db 8.8.0 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 Artistic-2.0 X Affymetrix hugene11 annotation data (chip hugene11stprobeset)
bioconductor-hugene11sttranscriptcluster.db 8.8.0 Artistic-2.0 X Affymetrix hugene11 annotation data (chip hugene11sttranscriptcluster)
bioconductor-hugene20stprobeset.db 8.8.0 Artistic-2.0 X Affymetrix hugene20 annotation data (chip hugene20stprobeset)
bioconductor-hugene20sttranscriptcluster.db 8.8.0 Artistic-2.0 X Affymetrix hugene20 annotation data (chip hugene20sttranscriptcluster)
bioconductor-hugene21stprobeset.db 8.8.0 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 Artistic-2.0 X Base Level Annotation databases for human
bioconductor-human1mduov3bcrlmm 1.0.4 Artistic-2.0 X Metadata for fast genotyping with the 'crlmm' package
bioconductor-human1mv1ccrlmm 1.0.3 Artistic-2.0 X Metadata for fast genotyping with the 'crlmm' package
bioconductor-human370quadv3ccrlmm 1.0.3 Artistic-2.0 X Metadata for fast genotyping with the 'crlmm' package
bioconductor-human370v1ccrlmm 1.0.2 Artistic-2.0 X Metadata for fast genotyping with the 'crlmm' package
bioconductor-human550v3bcrlmm 1.0.4 Artistic-2.0 X Metadata for fast genotyping with the 'crlmm' package
bioconductor-human610quadv1bcrlmm 1.0.3 Artistic-2.0 X Metadata for fast genotyping with the 'crlmm' package
bioconductor-human650v3acrlmm 1.0.3 Artistic-2.0 X Metadata for fast genotyping with the 'crlmm' package
bioconductor-human660quadv1acrlmm 1.0.3 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 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 Artistic-2.0 X Human Stem Cells time course experiment
bioconductor-humantranscriptomecompendium 1.17.0 Artistic-2.0 X Tools to work with a Compendium of 181000 human transcriptome sequencing studies
bioconductor-hummingbird 1.16.0 GPL XX Bayesian Hidden Markov Model for the detection of differentially...
bioconductor-huo22.db 3.2.3 Artistic-2.0 X FHCRC Genomics Shared Resource HuO22 Annotation Data (HuO22)
bioconductor-hwgcod.db 3.4.0 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 XXX Hybrid Multiple Testing
bioconductor-hyper 2.4.0 GPL-3 X An R Package For Geneset Enrichment Workflows
bioconductor-hyperdraw 1.58.0 GPL XXX Visualizing Hypergaphs
bioconductor-hypergraph 1.78.0 Artistic-2.0 XXX A package providing hypergraph data structures
bioconductor-iaseq 1.50.0 GPL-2 XXX iASeq: integrating multiple sequencing datasets for detecting...
bioconductor-iasva 1.24.0 GPL-2 X Iteratively Adjusted Surrogate Variable Analysis
bioconductor-ibbig 1.50.0 Artistic-2.0 XX Iterative Binary Biclustering of Genesets
bioconductor-ibh 1.54.0 GPL XXX Interaction Based Homogeneity for Evaluating Gene Lists
bioconductor-ibmq 1.46.0 Artistic-2.0 XX integrated Bayesian Modeling of eQTL data
bioconductor-icare 1.34.0 GPL-3 XX Individualized Coherent Absolute Risk Estimation (iCARE)
bioconductor-icens 1.78.0 Artistic-2.0 XXX NPMLE for Censored and Truncated Data
bioconductor-icetea 1.24.0 GPL-3 X Integrating Cap Enrichment with Transcript Expression Analysis
bioconductor-icheck 1.36.0 GPL X QC Pipeline and Data Analysis Tools for High-Dimensional Illumina mRNA...
bioconductor-ichip 1.60.0 GPL XX Bayesian Modeling of ChIP-chip Data Through Hidden Ising Models
bioconductor-iclusterplus 1.38.0 GPL XX Integrative clustering of multi-type genomic data
bioconductor-icnv 1.26.0 GPL-2 X Integrated Copy Number Variation detection
bioconductor-icobra 1.34.0 GPL XXX Comparison and Visualization of Ranking and Assignment Methods
bioconductor-ideal 2.0.0 MIT XXX Interactive Differential Expression AnaLysis
bioconductor-ideoviz 1.42.0 GPL-2 XXX Plots data (continuous/discrete) along chromosomal ideogram
bioconductor-idiogram 1.82.0 GPL-2 XXX idiogram
bioconductor-idmappinganalysis 1.30.0 GPL-2 X ID Mapping Analysis
bioconductor-idmappingretrieval 1.34.0 GPL-2 X ID Mapping Data Retrieval
bioconductor-idpr 1.16.0 LGPL X Profiling and Analyzing Intrinsically Disordered Proteins in R
bioconductor-idr2d 1.20.0 MIT X Irreproducible Discovery Rate for Genomic Interactions Data
bioconductor-ifaa 1.8.0 GPL-2 X Robust Inference for Absolute Abundance in Microbiome Analysis
bioconductor-igc 1.36.0 GPL-2 X An integrated analysis package of Gene expression and Copy number alteration
bioconductor-iggeneusage 1.20.0 MIT XX Differential gene usage in immune repertoires
bioconductor-igvr 1.26.0 MIT X igvR: integrative genomics viewer
bioconductor-ihw 1.34.0 Artistic-2.0 XXX Independent Hypothesis Weighting
bioconductor-ihwpaper 1.34.0 Artistic-2.0 XX Reproduce figures in IHW paper
bioconductor-illumina450probevariants.db 1.42.0 GPL-3 X Annotation Package combining variant data from 1000 Genomes Project for...
bioconductor-illuminadatatestfiles 1.44.0 Artistic-2.0 X Illumina microarray files (IDAT) for testing
bioconductor-illuminahumanmethylation27k.db 1.4.8 Artistic-2.0 X Illumina Illumina Human Methylation 27k annotation data (chip...
bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19 0.6.0 Artistic-2.0 X Annotation for Illumina's 27k methylation arrays
bioconductor-illuminahumanmethylation27kmanifest 0.4.0 Artistic-2.0 X Annotation for Illumina's 27k methylation arrays
bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 0.6.1 Artistic-2.0 XXX Annotation for Illumina's 450k methylation arrays
bioconductor-illuminahumanmethylation450kmanifest 0.4.0 Artistic-2.0 XXX Annotation for Illumina's 450k methylation arrays
bioconductor-illuminahumanmethylation450kprobe 2.0.6 LGPL X Probe sequence data for microarrays of type IlluminaHumanMethylation450k
bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 0.6.0 Artistic-2.0 XXX Annotation for Illumina's EPIC methylation arrays
bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19 0.6.0 Artistic-2.0 XXX Annotation for Illumina's EPIC methylation arrays
bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 0.6.0 Artistic-2.0 XXX Annotation for Illumina's EPIC methylation arrays
bioconductor-illuminahumanmethylationepicmanifest 0.3.0 Artistic-2.0 XXX Manifest for Illumina's EPIC methylation arrays
bioconductor-illuminahumanmethylationepicv2anno.20a1.hg38 1.0.0 Artistic-2.0 X Annotation for Illumina's EPIC v2.0 methylation arrays
bioconductor-illuminahumanmethylationepicv2manifest 1.0.0 Artistic-2.0 X Manifest for Illumina's EPIC v2.0 methylation arrays
bioconductor-illuminahumanv1.db 1.26.0 Artistic-2.0 X Illumina HumanWG6v1 annotation data (chip illuminaHumanv1)
bioconductor-illuminahumanv2.db 1.26.0 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 Artistic-2.0 X Illumina HumanHT12v3 annotation data (chip illuminaHumanv3)
bioconductor-illuminahumanv4.db 1.26.0 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 GPL-2 XX Parsing Illumina Microarray Output Files
bioconductor-illuminamousev1.db 1.26.0 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 XXX 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 GPL-3 X ILoReg: a tool for high-resolution cell population identification from...
bioconductor-imagehts 1.48.0 LGPL-2.1 XXX Analysis of high-throughput microscopy-based screens
bioconductor-imas 1.30.0 GPL-2 XXX Integrative analysis of Multi-omics data for Alternative Splicing
bioconductor-imcdatasets 1.14.0 GPL-3 X Collection of publicly available imaging mass cytometry (IMC) datasets
bioconductor-imcrtools 1.12.0 GPL-3 X Methods for imaging mass cytometry data analysis
bioconductor-imetagene 1.18.0 Artistic-2.0 X A graphical interface for the metagene package
bioconductor-imman 1.26.0 Artistic-2.0 X Interlog protein network reconstruction by Mapping and Mining ANalysis
bioconductor-immunespacer 1.30.0 GPL-2 X A Thin Wrapper around the ImmuneSpace Data and Tools Portal
bioconductor-immunoclust 1.38.0 Artistic-2.0 XX immunoClust - Automated Pipeline for Population Detection in Flow Cytometry
bioconductor-immunogenviewer 1.0.0 Apache X Visualization and evaluation of protein immunogens
bioconductor-immunotation 1.14.0 GPL-3 X Tools for working with diverse immune genes
bioconductor-impcdata 1.42.0 file X Retrieves data from IMPC database
bioconductor-impulsede 1.13.0 GPL-3 XXX Detection of DE genes in time series data using impulse models
bioconductor-impulsede2 1.11.0 Artistic-2.0 X Differential expression analysis of longitudinal count data sets
bioconductor-impute 1.80.0 GPL-2 XX impute: Imputation for microarray data
bioconductor-indac.db 3.2.3 Artistic-2.0 X INDAC FlyChip_long_oligonucleotide_002 (FL002) annotation data (chip indac)
bioconductor-indeed 2.20.0 Artistic-2.0 X Interactive Visualization of Integrated Differential Expression and...
bioconductor-inetgrate 1.4.0 GPL-3 X Integrates DNA methylation data with gene expression in a single gene network
bioconductor-infercnv 1.22.0 BSD_3_clause X Infer Copy Number Variation from Single-Cell RNA-Seq Data
bioconductor-infinityflow 1.12.0 GPL-3 X Augmenting Massively Parallel Cytometry Experiments Using Multivariate...
bioconductor-informeasure 1.16.0 Artistic-2.0 X R implementation of information measures
bioconductor-inpas 2.14.0 GPL X Identify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data
bioconductor-inpower 1.42.0 GPL-2 XXX An R package for computing the number of susceptibility SNPs
bioconductor-inspect 1.36.0 GPL-2 XXX Modeling RNA synthesis, processing and degradation with RNA-seq data
bioconductor-intact 1.6.0 GPL-3 X Integrate TWAS and Colocalization Analysis for Gene Set Enrichment Analysis
bioconductor-intad 1.26.0 GPL X Search for correlation between epigenetic signals and gene expression in TADs
bioconductor-intansv 1.46.0 MIT X Integrative analysis of structural variations
bioconductor-interaccircos 1.16.0 GPL-3 X The Generation of Interactive Circos Plot
bioconductor-interactionset 1.34.0 GPL-3 XX Base Classes for Storing Genomic Interaction Data
bioconductor-interactivecomplexheatmap 1.14.0 MIT X Make Interactive Complex Heatmaps
bioconductor-interactivedisplay 1.38.0 Artistic-2.0 XXX Package for enabling powerful shiny web displays of Bioconductor objects
bioconductor-interactivedisplaybase 1.44.0 Artistic-2.0 XXX Base package for enabling powerful shiny web displays of Bioconductor objects
bioconductor-intercellar 2.12.0 MIT X InterCellar: an R-Shiny app for interactive analysis and exploration of...
bioconductor-interest 1.30.0 GPL-2 XXX Intron-Exon Retention Estimator
bioconductor-interminer 1.24.0 LGPL XXX R Interface with InterMine-Powered Databases
bioconductor-intomics 1.2.0 GPL-3 X Integrative analysis of multi-omics data to infer regulatory networks
bioconductor-intramirexplorer 1.28.0 GPL-2 X Predicting Targets for Drosophila Intragenic miRNAs
bioconductor-inversion 1.42.0 GPL XX Inversions in genotype data
bioconductor-ioniser 2.30.0 MIT XXX Quality Assessment Tools for Oxford Nanopore MinION data
bioconductor-iontreedata 1.18.0 GPL-2 X Raw MS2, MS3 scans from direct infusion mass spectrometry (DIMS) and a...
bioconductor-ipac 1.46.0 GPL-2 XXX Identification of Protein Amino acid Clustering
bioconductor-ipath 1.12.0 GPL-2 XX iPath pipeline for detecting perturbed pathways at individual level
bioconductor-ipddb 1.24.0 Artistic-2.0 X IPD IMGT/HLA and IPD KIR database for Homo sapiens
bioconductor-ipo 1.32.0 GPL XXX Automated Optimization of XCMS Data Processing parameters
bioconductor-ippd 1.35.0 GPL XX Isotopic peak pattern deconvolution for Protein Mass Spectrometry by...
bioconductor-iranges 2.40.0 Artistic-2.0 XX Foundation of integer range manipulation in Bioconductor
bioconductor-irisfgm 1.8.0 GPL-2 XX Comprehensive Analysis of Gene Interactivity Networks Based on...
bioconductor-isanalytics 1.12.0 CC X Analyze gene therapy vector insertion sites data identified from...
bioconductor-isee 2.18.0 MIT XXX Interactive SummarizedExperiment Explorer
bioconductor-iseede 1.4.0 Artistic-2.0 X iSEE extension for panels related to differential expression analysis
bioconductor-iseefier 1.2.0 MIT X Streamlining the creation of initial states for starting an iSEE instance
bioconductor-iseehex 1.8.0 Artistic-2.0 X iSEE extension for summarising data points in hexagonal bins
bioconductor-iseehub 1.8.0 Artistic-2.0 X iSEE for the Bioconductor ExperimentHub
bioconductor-iseeindex 1.4.0 Artistic-2.0 X iSEE extension for a landing page to a custom collection of data sets
bioconductor-iseepathways 1.4.0 Artistic-2.0 X iSEE extension for panels related to pathway analysis
bioconductor-iseetree 1.0.0 Artistic-2.0 X Interactive visualisation for microbiome data
bioconductor-iseeu 1.18.0 MIT X iSEE Universe
bioconductor-iseq 1.58.0 GPL XX Bayesian Hierarchical Modeling of ChIP-seq Data Through Hidden Ising Models
bioconductor-islet 1.8.0 GPL-2 X Individual-Specific ceLl typE referencing Tool
bioconductor-isobar 1.52.0 LGPL-2 X Analysis and quantitation of isobarically tagged MSMS proteomics data
bioconductor-isobayes 1.4.0 GPL-3 XX IsoBayes: Single Isoform protein inference Method via Bayesian Analyses
bioconductor-isocorrector 1.24.0 GPL-3 X Correction for natural isotope abundance and tracer purity in MS and...
bioconductor-isocorrectorgui 1.22.0 GPL-3 X Graphical User Interface for IsoCorrectoR
bioconductor-isoformswitchanalyzer 2.6.0 GPL XX Identify, Annotate and Visualize Isoform Switches with Functional...
bioconductor-isogenegui 2.30.0 GPL-2 XX A graphical user interface to conduct a dose-response analysis of...
bioconductor-isolde 1.34.0 GPL XX Integrative Statistics of alleLe Dependent Expression
bioconductor-isomirs 1.34.0 MIT XXX Analyze isomiRs and miRNAs from small RNA-seq
bioconductor-italics 2.62.0 GPL-2 X ITALICS
bioconductor-italicsdata 2.44.0 GPL X ITALICSData
bioconductor-iterativebma 1.64.0 GPL XXX The Iterative Bayesian Model Averaging (BMA) algorithm
bioconductor-iterativebmasurv 1.64.0 GPL XXX The Iterative Bayesian Model Averaging (BMA) Algorithm For Survival Analysis
bioconductor-iterclust 1.24.0 file X Iterative Clustering
bioconductor-iteremoval 1.14.0 GPL-2 X Iteration removal method for feature selection
bioconductor-ivas 2.26.0 GPL-2 XXX Identification of genetic Variants affecting Alternative Splicing
bioconductor-ivygapse 1.28.0 Artistic-2.0 X A SummarizedExperiment for Ivy-GAP data
bioconductor-iwtomics 1.30.0 GPL XXX Interval-Wise Testing for Omics Data
bioconductor-iyer517 1.48.0 Artistic-2.0 X exprSets for Iyer, Eisen et all 1999 Science paper
bioconductor-jaspar2014 1.42.0 GPL-2 XXX Data package for JASPAR
bioconductor-jaspar2016 1.34.0 GPL-2 XXX Data package for JASPAR 2016
bioconductor-jaspar2018 1.1.1 GPL-2 XXX Data package for JASPAR 2018
bioconductor-jaspar2020 0.99.10 GPL-2 X Data package for JASPAR database (version 2020)
bioconductor-jaspar2022 0.99.8 GPL-2 X Data package for JASPAR database (version 2022)
bioconductor-jaspar2024 0.99.6 GPL-2 X Data package for JASPAR database (version 2024)
bioconductor-jazaerimetadata.db 3.2.3 Artistic-2.0 X A data package containing annotation data for JazaeriMetaData
bioconductor-jctseqdata 1.20.0 file X Example Junction Count data for use with JunctionSeq
bioconductor-jmosaics 1.10.0 GPL XX jmosaics detects enriched regions of ChIP-seq data sets jointly.
bioconductor-joda 1.35.0 GPL X JODA algorithm for quantifying gene deregulation using knowledge
bioconductor-junctionseq 1.17.0 file XX JunctionSeq: A Utility for Detection of Differential Exon and...
bioconductor-karyoploter 1.32.0 Artistic-2.0 X Plot customizable linear genomes displaying arbitrary data
bioconductor-katdetectr 1.8.0 GPL-3 X Detection, Characterization and Visualization of Kataegis in Sequencing Data
bioconductor-kboost 1.14.0 GPL-2 X Inference of gene regulatory networks from gene expression data
bioconductor-kcsmart 2.64.0 GPL-3 XXX Multi sample aCGH analysis package using kernel convolution
bioconductor-kebabs 1.40.0 GPL XX Kernel-Based Analysis of Biological Sequences
bioconductor-kegg.db 3.2.4 file XXX A set of annotation maps for KEGG
bioconductor-keggandmetacoredzpathwaysgeo 1.26.0 GPL-2 X Disease Datasets from GEO
bioconductor-keggdzpathwaysgeo 1.44.0 GPL-2 XXX KEGG Disease Datasets from GEO
bioconductor-kegggraph 1.66.0 GPL XXX KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor
bioconductor-kegglincs 1.32.0 GPL-3 XXX Visualize all edges within a KEGG pathway and overlay LINCS data
bioconductor-keggorthology 2.58.0 Artistic-2.0 XXX graph support for KO, KEGG Orthology
bioconductor-keggprofile 1.32.0 GPL X An annotation and visualization package for multi-types and...
bioconductor-keggrest 1.46.0 Artistic-2.0 XXX Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG)
bioconductor-kidpack 1.48.0 GPL-2 X DKFZ kidney package
bioconductor-kimod 1.15.0 GPL XXX A k-tables approach to integrate multiple Omics-Data
bioconductor-kinswingr 1.24.0 GPL-3 X KinSwingR: network-based kinase activity prediction
bioconductor-kissde 1.20.0 GPL X Retrieves Condition-Specific Variants in RNA-Seq Data
bioconductor-kmcut 1.0.0 Artistic-2.0 X Optimized Kaplan Meier analysis and identification and validation of...
bioconductor-knowseq 1.20.0 GPL X KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline
bioconductor-knowyourcg 1.2.0 MIT X Functional analysis of DNA methylome datasets
bioconductor-kodata 1.32.0 MIT XXX LINCS Knock-Out Data Package
bioconductor-koinar 1.0.0 Apache X KoinaR - Remote machine learning inference using Koina
bioconductor-lace 2.10.0 file X Longitudinal Analysis of Cancer Evolution (LACE)
bioconductor-lapmix 1.72.0 GPL XXX Laplace Mixture Model in Microarray Experiments
bioconductor-lapointe.db 3.2.3 Artistic-2.0 X A package containing metadata for LAPOINTE arrays
bioconductor-lbe 1.74.0 GPL-2 XXX Estimation of the false discovery rate
bioconductor-ldblock 1.36.0 Artistic-2.0 X data structures for linkage disequilibrium measures in populations
bioconductor-lea 3.18.0 GPL-3 XX LEA: an R package for Landscape and Ecological Association Studies
bioconductor-ledpred 1.40.0 MIT X Learning from DNA to Predict Enhancers
bioconductor-leebamviews 1.42.0 Artistic X leeBamViews -- multiple yeast RNAseq samples excerpted from Lee 2009
bioconductor-lefser 1.16.0 Artistic-2.0 X R implementation of the LEfSE method for microbiome biomarker discovery
bioconductor-lemur 1.4.0 MIT XX Latent Embedding Multivariate Regression
bioconductor-les 1.56.0 GPL-3 XXX Identifying Differential Effects in Tiling Microarray Data
bioconductor-leukemiaseset 1.42.0 GPL X Leukemia's microarray gene expression data (expressionSet).
bioconductor-levi 1.24.0 GPL XX Landscape Expression Visualization Interface
bioconductor-lfa 2.6.0 GPL XX Logistic Factor Analysis for Categorical Data
bioconductor-liebermanaidenhic2009 0.44.0 LGPL X Selected data from the HiC paper of E. Lieberman-Aiden et al. in Science (2009)
bioconductor-limma 3.62.1 GPL XX 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 Artistic-2.0 X An R package for the linear modeling of high-dimensional designed data...
bioconductor-linc 1.15.0 Artistic-2.0 XX co-expression of lincRNAs and protein-coding genes
bioconductor-lineagepulse 1.21.0 Artistic-2.0 X Differential expression analysis and model fitting for single-cell RNA-seq data
bioconductor-lineagespot 1.10.0 MIT X Detection of SARS-CoV-2 lineages in wastewater samples using...
bioconductor-linkhd 1.20.0 GPL-3 X LinkHD: a versatile framework to explore and integrate heterogeneous data
bioconductor-linnorm 2.30.0 MIT XX Linear model and normality based normalization and transformation...
bioconductor-lintind 1.10.0 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 XXX LiquidAssociation
bioconductor-lisaclust 1.14.0 GPL X lisaClust: Clustering of Local Indicators of Spatial Association
bioconductor-listeretalbsseq 1.38.0 Artistic X BS-seq data of H1 and IMR90 cell line excerpted from Lister et al. 2009
bioconductor-lmdme 1.48.0 GPL XXX Linear Model decomposition for Designed Multivariate Experiments
bioconductor-lmgene 2.43.0 LGPL XXX LMGene Software for Data Transformation and Identification of...
bioconductor-lobstahs 1.32.0 GPL XXX Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences
bioconductor-loci2path 1.26.0 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 XX 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 XXX Lots Of Lasso
bioconductor-lola 1.36.0 GPL-3 XXX Locus overlap analysis for enrichment of genomic ranges
bioconductor-loomexperiment 1.24.0 Artistic-2.0 X LoomExperiment container
bioconductor-lowmaca 1.28.0 GPL-3 X LowMACA - Low frequency Mutation Analysis via Consensus Alignment
bioconductor-lowmacaannotation 0.99.3 GPL-3 X LowMACAAnnotation
bioconductor-lpe 1.80.0 LGPL XXX Methods for analyzing microarray data using Local Pooled Error (LPE) method
bioconductor-lpeadj 1.62.0 LGPL XXX A correction of the local pooled error (LPE) method to replace the...
bioconductor-lpnet 2.38.0 Artistic XXX Linear Programming Model for Network Inference
bioconductor-lpsymphony 1.34.0 EPL XX Symphony integer linear programming solver in R
bioconductor-lrbase.ath.eg.db 2.0.0 Artistic-2.0 X Ligand-Receptor list for Arabidopsis thaliana (Ath, Thale cress,...
bioconductor-lrbase.bta.eg.db 2.0.0 Artistic-2.0 X Ligand-Receptor list for Bos taurus (Bta, Cow, Taxonomy ID: 9913)
bioconductor-lrbase.cel.eg.db 2.0.0 Artistic-2.0 X Ligand-Receptor list for Caenorhabditis elegans (Cel, Worm, Taxonomy ID: 6239)
bioconductor-lrbase.dme.eg.db 2.0.0 Artistic-2.0 X Ligand-Receptor list for Drosophila melanogaster (Dme, Fruit fly,...
bioconductor-lrbase.dre.eg.db 2.0.0 Artistic-2.0 X Ligand-Receptor list for Danio rerio (Dre, Zebrafish, Taxonomy ID: 7955)
bioconductor-lrbase.gga.eg.db 2.0.0 Artistic-2.0 X Ligand-Receptor list for Gallus gallus (Gga, Chicken, Taxonomy ID: 9031)
bioconductor-lrbase.hsa.eg.db 2.0.0 Artistic-2.0 X Ligand-Receptor list for Homo sapiens (Hsa, Human, Taxonomy ID: 9606)
bioconductor-lrbase.mmu.eg.db 2.0.0 Artistic-2.0 X Ligand-Receptor list for Mus musculus (Mmu, Mouse, Taxonomy ID: 10090)
bioconductor-lrbase.pab.eg.db 2.0.0 Artistic-2.0 X Ligand-Receptor list for Pongo abelii (Pab, Orangutan, Taxonomy ID: 9601)
bioconductor-lrbase.rno.eg.db 2.0.0 Artistic-2.0 X Ligand-Receptor list for Rattus norvegicus (Rno, Rat, Taxonomy ID: 10116)
bioconductor-lrbase.ssc.eg.db 2.0.0 Artistic-2.0 X Ligand-Receptor list for Sus scrofa (Ssc, Pig, Taxonomy ID: 9823)
bioconductor-lrbase.xtr.eg.db 2.0.0 Artistic-2.0 X Ligand-Receptor list for Xenopus tropicalis (Xtr, Tropical clawed frog,...
bioconductor-lrbasedbi 2.16.0 Artistic-2.0 X DBI to construct LRBase-related package
bioconductor-lrcell 1.14.0 MIT X Differential cell type change analysis using Logistic/linear Regression
bioconductor-lrcelltypemarkers 1.14.0 MIT X Marker gene information for LRcell R Bioconductor package
bioconductor-lumi 2.58.0 LGPL XXX 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 XXX Illumina Human Illumina expression annotation data (chip lumiHumanAll)
bioconductor-lumihumanidmapping 1.10.1 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 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 The X Illumina Identifier mapping for Rat
bioconductor-lungcanceracvssccgeo 1.42.0 GPL-2 XXX 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 GPL X ExpressionSets for Parmigiani et al., 2004 Clinical Cancer Research paper
bioconductor-lute 1.2.0 Artistic-2.0 X Framework for cell size scale factor normalized bulk transcriptomics...
bioconductor-lvsmirna 1.36.0 GPL-2 XX LVS normalization for Agilent miRNA data
bioconductor-lydata 1.32.0 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 XX Identifies differentially methylated regions across testing groups
bioconductor-m3dexampledata 1.32.0 GPL X M3Drop Example Data
bioconductor-m3drop 1.32.0 GPL XXX 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 XX 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 XXX MicroArray Chromosome Analysis Tool
bioconductor-macorrplot 1.76.0 GPL XXX Visualize artificial correlation in microarray data
bioconductor-macpet 1.14.0 GPL-3 XX Model based analysis for paired-end data
bioconductor-macrophage 1.22.0 GPL X Human macrophage immune response
bioconductor-macsdata 1.14.0 file X Test datasets for the MACSr package
bioconductor-macsquantifyr 1.20.0 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 XXX Multivariate analysis of microarray data using ADE4
bioconductor-madseq 1.32.0 GPL(>=2) XXX 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 XXX 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 XX Functions to handle cDNA microarray data, including several methods of...
bioconductor-mait 1.40.0 GPL-2 XX 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 XX 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 XX CGH Micro-Array NORmalization
bioconductor-manta 1.32.0 Artistic-2.0 XXX Microbial Assemblage Normalized Transcript Analysis
bioconductor-mantelcorr 1.76.0 GPL XXX Compute Mantel Cluster Correlations
bioconductor-mapkl 1.28.0 GPL XX 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 XXX 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 XX Maximum rank reproducibility
bioconductor-marray 1.84.0 LGPL XXX Exploratory analysis for two-color spotted microarray data
bioconductor-martini 1.26.0 GPL-3 XX GWAS Incorporating Networks
bioconductor-maser 1.24.0 MIT X Mapping Alternative Splicing Events to pRoteins
bioconductor-masigpro 1.78.0 GPL XXX Significant Gene Expression Profile Differences in Time Course Gene...
bioconductor-maskbad 1.50.0 GPL XXX Masking probes with binding affinity differences
bioconductor-massarray 1.58.0 GPL XXX Analytical Tools for MassArray Data
bioconductor-massir 1.42.0 GPL-3 XXX massiR: MicroArray Sample Sex Identifier
bioconductor-massspecwavelet 1.72.0 LGPL XX Peak Detection for Mass Spectrometry data using wavelet-based algorithms
bioconductor-mast 1.32.0 GPL(>= XXX 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 XX Obtain total affinity and occupancies for binding site matrices on a...
bioconductor-matter 2.8.0 Artistic-2.0 XX 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 XXX Model-based analysis of DNA methylation data
bioconductor-mbased 1.40.0 Artistic-2.0 XXX 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 XX 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 XXX 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 XXX 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 XXX 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 XXX 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 XXX 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 XXX 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 XX 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 XXX 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 XXX Merge Maid
bioconductor-mergeomics 1.34.0 GPL XXX 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 XXX 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 XXX DBI to construct MeSH-related package from sqlite file
bioconductor-meshes 1.32.0 Artistic-2.0 XXX 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 XX 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 XX Single-gene classifiers and outlier-resistant detection of differential...
bioconductor-metaarray 1.66.0 LGPL-2 XX Integration of Microarray Data for Meta-analysis
bioconductor-metab 1.33.0 GPL XXX Metab: An R Package for a High-Throughput Analysis of Metabolomics Data...
bioconductor-metabcombiner 1.16.0 GPL-3 XX 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 XXX MetaboSignal: a network-based approach to overlay and explore metabolic...
bioconductor-metacca 1.34.0 MIT XXX 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 XXX 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 XX Hierarchical Dependence in Meta-Analysis
bioconductor-metams 1.42.0 GPL XXX 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 XXX 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 XX 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 XX 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 XXX An R package for the analysis and result reporting of RNA-Seq data by...
bioconductor-metavizr 1.21.0 MIT XXX 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 XXX 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 XX 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 XXX 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 XXX 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 XXX 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 XX 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 XX 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 XX detect different methylation level (DMR)
bioconductor-methylpipe 1.40.0 GPL(>=2) XX Base resolution DNA methylation data analysis
bioconductor-methylscaper 1.14.0 GPL-2 X Visualization of Methylation Data
bioconductor-methylseekr 1.46.0 GPL XXX 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 XXX 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 XX 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 XXX Marker Gene Finder in Microarray gene expression data
bioconductor-mgfr 1.32.0 GPL-3 XXX 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 XX 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 XXX 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 XXX MiChip Parsing and Summarizing Functions
bioconductor-microbiome 1.28.0 BSD_2_clause XXX 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 XX 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 XXX Differential neighbourhood abundance testing on a graph
bioconductor-mimager 1.30.0 MIT X mimager: The Microarray Imager
bioconductor-mimosa 1.37.0 MIT XX Mixture Models for Single-Cell Assays
bioconductor-mina 1.14.0 GPL XX Microbial community dIversity and Network Analysis
bioconductor-mineica 1.46.0 GPL-2 XXX Analysis of an ICA decomposition obtained on genomics data
bioconductor-minet 3.64.0 Artistic-2.0 XX Mutual Information NETworks
bioconductor-minfi 1.52.0 Artistic-2.0 XXX 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 XXX 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 XXX 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 XXX 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 XXX 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 XXX 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 XXX Convert miRNA Names to Different miRBase Versions
bioconductor-mirnapath 1.66.0 LGPL-2.1 XXX miRNApath: Pathway Enrichment for miRNA Expression Data
bioconductor-mirnatap 1.40.0 GPL-2 XXX miRNAtap: microRNA Targets - Aggregated Predictions
bioconductor-mirnatap.db 0.99.10 GPL-2 XXX 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 XX Inferring miRNA sponge modules in heterogeneous data
bioconductor-mirsponge 1.10.0 GPL-3 XX The name of the miRsponge package has been changed into...
bioconductor-mirsponger 2.10.0 GPL-3 XX Identification and analysis of miRNA sponge regulation
bioconductor-mirsynergy 1.23.0 GPL-2 XXX Mirsynergy
bioconductor-mirtarrnaseq 1.14.0 MIT X mirTarRnaSeq
bioconductor-missmethyl 1.40.0 GPL-2 XXX 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 XX Clonal Population Identification in Single-Cell RNA-Seq Data using...
bioconductor-mitoode 1.25.0 LGPL XX 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 XXX Uniform interfaces to R machine learning procedures for data in...
bioconductor-mlm4omics 1.2.0 GPL-3 XX To conduct Bayesian inference regression for responses with multilevel...
bioconductor-mlp 1.54.0 GPL-3 XXX Mean Log P Analysis
bioconductor-mlseq 2.24.0 GPL(>=2) XXX 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 XXX 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 XX 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 XX 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 XX 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 XX 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 XXX MoPS - Model-based Periodicity Screening
bioconductor-mosaics 2.44.0 GPL XX 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 XX 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 XXX 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 XXX A Package For Predicting The Disruptiveness Of Single Nucleotide...
bioconductor-motifcounter 1.30.0 GPL-2 XX R package for analysing TFBSs in DNA sequences
bioconductor-motifdb 1.48.0 Artistic-2.0 XXX An Annotated Collection of Protein-DNA Binding Sequence Motifs
bioconductor-motifmatchr 1.30.0 GPL-3.0-or-later XX Fast Motif Matching in R.
bioconductor-motifrg 1.31.0 Artistic-2.0 XXX A package for discriminative motif discovery, designed for high...
bioconductor-motifstack 1.50.0 GPL XXX 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 XX 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 XXX 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 XX mQTL.NMR provides a complete mQTL analysis pipeline for 1H NMR data....
bioconductor-msa 1.38.0 GPL XX Multiple Sequence Alignment
bioconductor-msa2dist 1.10.0 GPL-3 XX 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 XX 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 XXX 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 XX Base Functions and Classes for Mass Spectrometry and Proteomics
bioconductor-msnid 1.40.0 Artistic-2.0 XX 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 XX Automated Evaluation of Precursor Ion Purity for Mass Spectrometry...
bioconductor-mspuritydata 1.34.0 GPL XXX 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 XXX 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 XX LiP Significance Analysis in shotgun mass spectrometry-based proteomic...
bioconductor-msstatslobd 1.14.0 Artistic-2.0 XX Assay characterization: estimation of limit of blanc(LoB) and limit of...
bioconductor-msstatsptm 2.4.1 Artistic-2.0 XXX 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 XXX 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 XX 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 XXX 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 XXX 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 XXX 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 XXX 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 XXX 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 XX 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 XX 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 XX Multiple Sequence Alignment with MUSCLE
bioconductor-musicatk 1.12.0 LGPL-3 X Mutational Signature Comprehensive Analysis Toolkit
bioconductor-mutationalpatterns 3.16.0 MIT XXX Comprehensive genome-wide analysis of mutational processes
bioconductor-mvcclass 1.80.0 LGPL XXX Model-View-Controller (MVC) Classes
bioconductor-mvgst 1.12.0 GPL-3 XX 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 XXX 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 XXX Access MyGene.Info_ services
bioconductor-myvariant 1.36.0 Artistic-2.0 XXX Accesses MyVariant.info variant query and annotation services
bioconductor-mzid 1.44.0 GPL XXX An mzIdentML parser for R
bioconductor-mzr 2.40.0 Artistic-2.0 XX parser for netCDF, mzXML and mzML and mzIdentML files (mass spectrometry data)
bioconductor-nadfinder 1.30.0 GPL XXX Call wide peaks for sequencing data
bioconductor-nanomethviz 3.2.0 Apache XX 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 XX 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 XX 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 XX ncdfFlow: A package that provides HDF5 based storage for flow cytometry data.
bioconductor-ncgtw 1.20.0 GPL-2 XX Alignment of LC-MS Profiles by Neighbor-wise Compound-specific...
bioconductor-ncigraph 1.54.0 GPL-3 XXX 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 XXX 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 XX (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 XX Benchmarking of several gene network inference methods
bioconductor-netbiov 1.31.0 GPL XXX A package for visualizing complex biological network
bioconductor-netboost 2.6.0 GPL-3 XX 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 XX 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 XX 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 XX Network-Regularized Regression Models
bioconductor-netresponse 1.66.0 GPL XX 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 XX 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 XXX 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 XXX Exploratory analysis and differential expression for RNA-seq data
bioconductor-nondetects 2.32.0 GPL-3 XXX 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 XX 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 XXX Permutation approximation methods for gene set enrichment analysis...
bioconductor-ntw 1.56.0 GPL-2 XXX Predict gene network using an Ordinary Differential Equation (ODE) based method
bioconductor-nucleosim 1.34.0 Artistic-2.0 XXX Generate synthetic nucleosome maps
bioconductor-nucler 2.38.0 LGPL XXX Nucleosome positioning package for R
bioconductor-nucpos 1.24.0 GPL-2 XXX An R package for prediction of nucleosome positions
bioconductor-nudge 1.46.0 GPL-2 XX 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 XX An R package for nucleosome positioning prediction
bioconductor-nxtirfcore 1.6.0 MIT XX 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 XXX 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 XXX Outlier Gene Set Analysis
bioconductor-oligo 1.70.0 LGPL XX Preprocessing tools for oligonucleotide arrays
bioconductor-oligoclasses 1.68.0 GPL XXX 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 XXX 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 XX 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 XXX Multiple co-inertia analysis of omics datasets
bioconductor-omiccircos 1.44.0 GPL-2 XXX 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 XX 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 XX 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 XXX 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 XX 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 XX Comprehensive analysis of transcriptome data
bioconductor-oppar 1.34.0 GPL-2 XX 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 XXX Similarities of Ordered Gene Lists
bioconductor-orfhunter 1.14.0 MIT XX Predict open reading frames in nucleotide sequences
bioconductor-orfik 1.26.0 MIT XX 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 XXX Genome wide annotation for Bovine
bioconductor-org.ce.eg.db 3.20.0 Artistic-2.0 XXX Genome wide annotation for Worm
bioconductor-org.cf.eg.db 3.20.0 Artistic-2.0 XXX Genome wide annotation for Canine
bioconductor-org.dm.eg.db 3.20.0 Artistic-2.0 XXX Genome wide annotation for Fly
bioconductor-org.dr.eg.db 3.20.0 Artistic-2.0 XXX 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 XXX Genome wide annotation for Chicken
bioconductor-org.hs.eg.db 3.20.0 Artistic-2.0 XXX Genome wide annotation for Human
bioconductor-org.mm.eg.db 3.20.0 Artistic-2.0 XXX 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 XXX Genome wide annotation for Rat
bioconductor-org.sc.sgd.db 3.20.0 Artistic-2.0 XXX Genome wide annotation for Yeast
bioconductor-org.ss.eg.db 3.20.0 Artistic-2.0 XXX 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 XXX 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 XXX OSAT: Optimal Sample Assignment Tool
bioconductor-oscope 1.36.0 Artistic-2.0 XXX Oscope - A statistical pipeline for identifying oscillatory genes in...
bioconductor-otubase 1.56.0 Artistic-2.0 XXX Provides structure and functions for the analysis of OTU data
bioconductor-outlierd 1.53.0 GPL XXX Outlier detection using quantile regression on the M-A scatterplots of...
bioconductor-outrider 1.26.3 MIT XX 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 XX OVESEG-test to detect tissue/cell-specific markers
bioconductor-paa 1.40.0 BSD_3_clause XX 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 XXX 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 XXX 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 XXX PANDA Algorithm
bioconductor-panelcn.mops 1.28.0 LGPL X CNV detection tool for targeted NGS panel data
bioconductor-pannbuilder 1.43.0 LGPL XX 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 XXX Presence-Absence Calls from Negative Strand Matching Probesets
bioconductor-panr 1.52.0 Artistic-2.0 XXX Posterior association networks and functional modules inferred from...
bioconductor-panther.db 1.0.12 Artistic-2.0 XXX 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(>= XXX 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 XXX 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 XXX Prediction of pathway-related protein-protein interaction networks
bioconductor-pathifier 1.44.0 Artistic-1.0 XXX Quantify deregulation of pathways in cancer
bioconductor-pathnet 1.46.0 GPL-3 XXX 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 XXX PathoStat Statistical Microbiome Analysis Package
bioconductor-pathprint 1.17.0 GPL XXX 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 XXX Render molecular pathways
bioconductor-pathvar 1.30.0 LGPL XXX Methods to Find Pathways with Significantly Different Variability
bioconductor-pathview 1.46.0 GPL XXX 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 XX Manipulating and exploring protein and proteomics data
bioconductor-pbcmc 1.8.0 GPL XX The pbcmc package characterizes uncertainty assessment on gene...
bioconductor-pcaexplorer 3.0.0 MIT XXX Interactive Visualization of RNA-seq Data Using a Principal Components Approach
bioconductor-pcagopromoter 1.30.0 GPL XXX 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 XX A collection of PCA methods
bioconductor-pcan 1.34.0 CC XXX Phenotype Consensus ANalysis (PCAN)
bioconductor-pcatools 2.18.0 GPL-3 XXX PCAtools: Everything Principal Components Analysis
bioconductor-pchicdata 1.34.0 Artistic-2.0 XXX Promoter Capture Hi-C data
bioconductor-pcot2 1.58.0 GPL XXX Principal Coordinates and Hotelling's T-Square method
bioconductor-pcpheno 1.50.0 Artistic-2.0 XXX 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 XX 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 XXX 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 XXX Statistical analysis of peptide microarrays
bioconductor-pepxmltab 1.40.0 Artistic-2.0 XXX 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 XXX 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 XXX 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 XXX Analysis of Large-Scale Pharmacogenomic Data
bioconductor-phastcons100way.ucsc.hg19 3.7.2 Artistic-2.0 XXX 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 XX 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 XX 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 XXX Statistical analysis of phenotypic data
bioconductor-philr 1.32.0 GPL-3 XXX 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 XXX 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 XXX 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 XXX Platform for integrative analysis of omics data
bioconductor-pickgene 1.78.0 GPL XXX Adaptive Gene Picking for Microarray Expression Data Analysis
bioconductor-pics 2.50.0 Artistic-2.0 XX 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 XX Probabilistic inference for Nucleosome Positioning with MNase-based or...
bioconductor-pint 1.36.0 BSD_2_clause XXX 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 XXX 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 XXX R framework for exploration and analysis of respirometry data
bioconductor-plgem 1.78.0 GPL-2 XXX Detect differential expression in microarray and proteomics datasets...
bioconductor-plier 1.76.0 GPL XX 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 XX 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 XXX 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 XX 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 XXX 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 XX 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 XXX 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 XX Probabilistic Outlier Identification for RNA Sequencing Generalized...
bioconductor-ppidata 0.32.0 Artistic-2.0 XXX A package that contains the bait to prey directed graphs for...
bioconductor-ppinfer 1.32.0 Artistic-2.0 XXX Inferring functionally related proteins using protein interaction networks
bioconductor-ppistats 1.60.0 Artistic-2.0 XXX Protein-Protein Interaction Statistical Package
bioconductor-pqsfinder 2.22.0 BSD_2_clause XX Identification of potential quadruplex forming sequences
bioconductor-prada 1.63.0 LGPL XX 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 XXX 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 XXX 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 XX Inference for predictive networks designed for (but not limited to) genomic data
bioconductor-preprocesscore 1.68.0 LGPL XX 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 XXX 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 XXX 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 XXX Ciphergen SELDI-TOF Processing
bioconductor-procoil 2.34.0 GPL XXX 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 XX 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 XX 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 XX 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 XXX Interactive visualisation of spatial proteomics data
bioconductor-promise 1.58.0 GPL XXX PRojection Onto the Most Interesting Statistical Evidence
bioconductor-prone 1.0.0 GPL X The PROteomics Normalization Evaluator
bioconductor-proper 1.38.0 GPL XXX 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 XXX 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 XXX 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 XXX Generic infrastructure for Bioconductor mass spectrometry packages
bioconductor-psea 1.36.0 Artistic-2.0 XXX Population-Specific Expression Analysis.
bioconductor-psichomics 1.32.0 MIT XX Graphical Interface for Alternative Splicing Quantification, Analysis...
bioconductor-psicquic 1.32.0 Apache XXX 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 XXX 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 XX 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 XX 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 XXX Copy number calling and SNV classification using targeted short read sequencing
bioconductor-pvac 1.54.0 LGPL XXX PCA-based gene filtering for Affymetrix arrays
bioconductor-pvca 1.46.0 LGPL XXX Principal Variance Component Analysis (PVCA)
bioconductor-pviz 1.40.0 Artistic-2.0 XXX Peptide Annotation and Data Visualization using Gviz
bioconductor-pwalign 1.2.0 Artistic-2.0 XX Perform pairwise sequence alignments
bioconductor-pwmenrich 4.42.0 LGPL XXX 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 XXX 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 XX FASTQ Quality Control
bioconductor-qcmetrics 1.44.0 GPL-2 XXX A Framework for Quality Control
bioconductor-qdnaseq 1.42.0 GPL XXX 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 XXX 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 XXX Data-driven normalization strategies for high-throughput qPCR data.
bioconductor-qpgraph 2.40.0 GPL XX 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 XX Quick Read Quality Control
bioconductor-qsea 1.32.0 GPL-2 XX 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 XXX 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 XXX A test for when to use quantile normalization
bioconductor-quantsmooth 1.72.0 GPL-2 XXX Quantile smoothing and genomic visualization of array data
bioconductor-quartpac 1.34.0 GPL-2 XXX Identification of mutational clusters in protein quaternary structures.
bioconductor-quasr 1.46.0 GPL-2 XX Quantify and Annotate Short Reads in R
bioconductor-quaternaryprod 1.40.0 GPL XX Computes the Quaternary Dot Product Scoring Statistic for Signed and...
bioconductor-qubic 1.34.0 CC XX 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 XXX qusage: Quantitative Set Analysis for Gene Expression
bioconductor-qvalue 2.38.0 LGPL XXX 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 XX 3CPET: Finding Co-factor Complexes in Chia-PET experiment using a...
bioconductor-r3cseq 1.52.0 GPL-3 XXX Analysis of Chromosome Conformation Capture and Next-generation...
bioconductor-r453plus1toolbox 1.56.0 LGPL-3 XX A package for importing and analyzing data from Roche's Genome...
bioconductor-r4rna 1.34.0 GPL-3 XXX 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 XX 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 XXX 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 XXX Rhythmicity Analysis Incorporating Non-parametric Methods
bioconductor-rama 1.72.0 GPL XX Robust Analysis of MicroArrays
bioconductor-ramigo 1.28.0 Artistic-2.0 XX 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 XX 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 XXX 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 XXX 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 XXX A suite for analysis of rare genomic variants in whole genome sequencing data
bioconductor-rariant 1.25.0 GPL-3 XXX Identification and Assessment of Single Nucleotide Variants through...
bioconductor-rarr 1.6.0 MIT XX 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 XXX Support for Springer monograph on Bioconductor
bioconductor-rbec 1.14.0 LGPL-3 XX Rbec: a tool for analysis of amplicon sequencing data from synthetic...
bioconductor-rbgl 1.82.0 Artistic-2.0 XX 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 XX RBioinf
bioconductor-rbiopaxparser 2.46.0 GPL XXX 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 XXX RBM: a R package for microarray and RNA-Seq data analysis
bioconductor-rbowtie 1.46.0 Artistic-2.0 XX R bowtie wrapper
bioconductor-rbowtie2 2.12.3 GPL XX An R Wrapper for Bowtie2 and AdapterRemoval
bioconductor-rbsurv 2.64.0 GPL XXX Robust likelihood-based survival modeling with microarray data
bioconductor-rbwa 1.10.0 MIT XX 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 XXX RNA Centric Annotation System
bioconductor-rcaspar 1.52.0 GPL XXX 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 XXX Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data
bioconductor-rchemcpp 2.21.1 GPL XX 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 XXX 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 XXX 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 XX 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 XXX R Wrapper for DGIdb
bioconductor-rdisop 1.66.0 GPL-2 XX 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 XXX 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 XXX 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 XXX Read qPCR data
bioconductor-reb 1.65.0 GPL-2 XX Regional Expression Biases
bioconductor-rebet 1.24.0 GPL-2 XX 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 XXX 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 XXX An R package for the creation of complex genomic profile plots
bioconductor-reder 3.2.0 GPL-3 XXX 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 XXX A queryable collection of molecular interactions, from many sources
bioconductor-refplus 1.70.0 GPL XXX 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 XXX 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 XXX 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 XX Epigenomic tools
bioconductor-reportingtools 2.46.0 Artistic-2.0 XXX 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 GPL-3 XX 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 GPL-3 X An R interface to the Rfam database
bioconductor-rfastp 1.16.0 GPL-3 XX 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 XX Assign rfPred functional prediction scores to a missense variants list
bioconductor-rgadem 2.54.0 Artistic-2.0 XX de novo motif discovery
bioconductor-rgalaxy 1.37.1 Artistic-2.0 XXX Make an R function available in the Galaxy web platform
bioconductor-rgenometracks 1.12.0 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 XX 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 MIT XX Lipid Shorthand Name Parsing and Normalization
bioconductor-rgraph2js 1.34.0 GPL-2 XXX Convert a Graph into a D3js Script
bioconductor-rgraphviz 2.50.0 EPL XX Provides plotting capabilities for R graph objects
bioconductor-rgreat 2.8.0 MIT XXX GREAT Analysis - Functional Enrichment on Genomic Regions
bioconductor-rgsea 1.40.0 GPL(>=3) XXX Random Gene Set Enrichment Analysis
bioconductor-rgsepd 1.38.0 GPL-3 XXX 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 XX R Interface to HDF5
bioconductor-rhdf5client 1.28.0 Artistic-2.0 XX Access HDF5 content from HDF Scalable Data Service
bioconductor-rhdf5filters 1.18.0 BSD_2_clause XX HDF5 Compression Filters
bioconductor-rhdf5lib 1.28.0 Artistic-2.0 XX 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-3.0-or-later XX R Wrapper for HISAT2 Aligner.
bioconductor-rhtslib 3.2.0 LGPL XX 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 XX Differential pattern analysis for Ribo-seq data
bioconductor-riboprofiling 1.36.0 GPL-3 XXX 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 XXX 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 XXX RImmPort: Enabling Ready-for-analysis Immunology Research Data
bioconductor-ringo 1.66.0 Artistic-2.0 XX 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 XXX 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 XX 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 XX 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 XXX 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 XX 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 XX 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 XXX Package to work with miRNAs and miRNA targets with R
bioconductor-rmir.hs.mirna 1.0.7 The XXX 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 XX 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 XX 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 XXX 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 XXX 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 XXX 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 XXX 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 XX rnaSeq secondary analyses
bioconductor-rnaseqpower 1.46.0 LGPL XXX 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 XX RnaSeqSampleSize
bioconductor-rnaseqsamplesizedata 1.38.0 GPL XXX RnaSeqSampleSizeData
bioconductor-rnbeads 2.24.0 GPL-3 XXX RnBeads
bioconductor-rnbeads.hg19 1.38.0 GPL-3 XXX RnBeads.hg19
bioconductor-rnbeads.hg38 1.38.1 GPL-3 X RnBeads.hg38
bioconductor-rnbeads.mm10 2.14.0 GPL-3 XXX RnBeads.mm10
bioconductor-rnbeads.mm9 1.38.0 GPL-3 XXX RnBeads.mm9
bioconductor-rnbeads.rn5 1.38.0 GPL-3 XXX RnBeads.rn5
bioconductor-rnits 1.40.0 GPL-3 XXX 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 XXX 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 XX 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 XXX Infer miRNA-mRNA interactions using paired expression data from a single sample
bioconductor-rols 3.2.0 GPL-2 XXX An R interface to the Ontology Lookup Service
bioconductor-rontotools 2.34.0 CC XXX R Onto-Tools suite
bioconductor-ropls 1.38.0 CeCILL XXX 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 XX Reproducibility-Optimized Test Statistic
bioconductor-rpa 1.62.0 BSD_2_clause XXX 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 XX C++ headers and static libraries of Protocol buffers
bioconductor-rpsixml 2.36.0 LGPL-3 XXX R interface to PSI-MI 2.5 files
bioconductor-rpx 2.14.0 GPL-2 XXX R Interface to the ProteomeXchange Repository
bioconductor-rqc 1.40.0 GPL XX 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 XX 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 XXX 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 XXX 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 XX Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
bioconductor-rsbml 2.60.0 Artistic-2.0 XX 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 XXX R SeqAn
bioconductor-rsffreader 0.31.0 Artistic-2.0 XX rSFFreader reads sequence, qualities and clip point values from sff...
bioconductor-rsubread 2.20.0 GPL XX Mapping, quantification and variant analysis of sequencing data
bioconductor-rsvsim 1.46.0 LGPL-3 XXX 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 XX Interfaces the tandem protein identification algorithm in R
bioconductor-rtca 1.58.0 LGPL-3 XXX Open-source toolkit to analyse data from xCELLigence System (RTCA)
bioconductor-rtcga 1.36.0 GPL-2 XXX 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 XXX mRNA datasets from The Cancer Genome Atlas Project
bioconductor-rtcga.mutations 20151101.36.0 GPL-2 X Mutations datasets from The Cancer Genome Atlas Project
bioconductor-rtcga.pancan12 1.34.0 GPL-2 X PanCan 12 from Genome Cancer Browser
bioconductor-rtcga.rnaseq 20151101.36.0 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 XXX 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 XXX 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 XX R interface to genome annotation files and the UCSC genome browser
bioconductor-rtreemix 1.68.0 LGPL XX Rtreemix: Mutagenetic trees mixture models.
bioconductor-rtrm 1.44.0 GPL-3 XXX Identification of Transcriptional Regulatory Modules from...
bioconductor-rtrmui 1.44.0 GPL-3 XXX 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 XX 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 XXX RUV for normalization of expression array data
bioconductor-ruvnormalizedata 1.26.0 GPL-3 XXX Gender data for the RUVnormalize package
bioconductor-ruvseq 1.40.0 Artistic-2.0 XXX 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 1.30.0 MIT X rWikiPathways - R client library for the WikiPathways API
bioconductor-s4arrays 1.6.0 Artistic-2.0 XX Foundation of array-like containers in Bioconductor
bioconductor-s4vectors 0.44.0 Artistic-2.0 XX Foundation of vector-like and list-like containers in Bioconductor
bioconductor-safe 3.46.0 GPL XXX Significance Analysis of Function and Expression
bioconductor-sagenhaft 1.76.0 GPL XXX Collection of functions for reading and comparing SAGE libraries
bioconductor-sagx 1.64.0 GPL-3 XX Statistical Analysis of the GeneChip
bioconductor-saigegds 2.6.0 GPL-3 XX 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 XX 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 XXX Tools for Sanger Sequencing Data in R
bioconductor-santa 2.42.0 GPL XX Spatial Analysis of Network Associations
bioconductor-sapfinder 1.26.0 GPL-2 XX 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 XXX 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 XX 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 XXX 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 XXX 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 1.34.1 GPL-3 XXX 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 XX 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 1.23.4 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 XX A compositional model to assess expression changes from single-cell rna-seq data
bioconductor-scde 2.34.0 GPL-2 XX 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 1.22.0 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 XX A search tool for single cell RNA-seq data by gene lists
bioconductor-scgps 1.20.0 GPL-3 XX 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 XXX 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 XX A tool for unsupervised projection of single cell RNA-seq data
bioconductor-scmerge 1.22.0 GPL-3 XXX scMerge: Merging multiple batches of scRNA-seq data
bioconductor-scmet 1.8.0 GPL-3 XX 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 XX 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 XXX 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 XX Pipeline for single cell multi-omic data pre-processing
bioconductor-scran 1.34.0 GPL-3 XX 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 XX 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 XX A toolkit for single-cell immune receptor profiling
bioconductor-scrnaseq 2.20.0 CC0 XXX 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 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 XX Cell type annotation for unannotated single-cell RNA-Seq data
bioconductor-scthi 1.18.0 GPL-2 X Indentification of significantly activated ligand-receptor interactions...
bioconductor-scthi.data 1.18.0 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 XX 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 Artistic-2.0 X Seahtrue revives XF data for structured data analysis
bioconductor-sechm 1.14.0 GPL-3 X sechm: Complex Heatmaps from a SummarizedExperiment
bioconductor-segmenter 1.12.0 GPL-3 X Perform Chromatin Segmentation Analysis in R by Calling ChromHMM
bioconductor-segmentseq 2.40.0 GPL-3 XXX Methods for identifying small RNA loci from high-throughput sequencing data
bioconductor-selectksigs 1.18.0 GPL-3 XX 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 XXX Information Accretion-based Function Predictor Evaluation
bioconductor-semisup 1.30.0 GPL-3 XXX Semi-Supervised Mixture Model
bioconductor-sepa 1.13.0 GPL(>=2) XXX Given single-cell RNA-seq data and true experiment time of cells or...
bioconductor-sepira 1.20.0 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 XXX a novel tool for functional gene-set (or termed as pathway) analysis of...
bioconductor-seq2pathway.data 1.38.0 GPL XXX 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 XX Data Management of Large-Scale Whole-Genome Sequence Variant Calls
bioconductor-seqbias 1.50.0 LGPL-3 XX 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 XX 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 XXX Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating...
bioconductor-seqlogo 1.72.0 LGPL XXX Sequence logos for DNA sequence alignments
bioconductor-seqpattern 1.38.0 GPL-3 XXX Visualising oligonucleotide patterns and motif occurrences across a set...
bioconductor-seqplots 1.27.0 GPL-3 X An interactive tool for visualizing NGS signals and sequence motif...
bioconductor-seqsetvis 1.26.0 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 XX Analysis of nucleotide, sequence and quality content on fastq files
bioconductor-seqvartools 1.44.0 GPL-3 X Tools for variant data
bioconductor-serumstimulation 1.42.0 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 GPL X SEtools: tools for working with SummarizedExperiment
bioconductor-sevenbridges 1.36.0 Apache X Seven Bridges Platform API Client and Common Workflow Language Tool Builder in R
bioconductor-sevenc 1.26.0 GPL-3 X Computational Chromosome Conformation Capture by Correlation of...
bioconductor-seventygenedata 1.42.0 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 Artistic-2.0 XXX Splice event prediction and quantification from RNA-seq data
bioconductor-sharedobject 1.20.0 GPL-3 XX 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 XXX 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 XX 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 XX 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 XXX 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 XXX SigFuge
bioconductor-siggenes 1.80.0 LGPL XXX Multiple Testing using SAM and Efron's Empirical Bayes Approaches
bioconductor-sights 1.32.0 GPL-3 XXX Statistics and dIagnostic Graphs for HTS
bioconductor-signaturesearch 1.20.0 Artistic-2.0 XX 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 XX 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 XX 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 XX Integrated Analysis on two human genomic datasets
bioconductor-simat 1.38.0 GPL-2 XX 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 XXX 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 XX 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 XXX Metrics to estimate a level of similarity between two ChIP-Seq profiles
bioconductor-simlr 1.32.0 file XX Single-cell Interpretation via Multi-kernel LeaRning (SIMLR)
bioconductor-simona 1.4.0 MIT XX 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 XXX The package contains BioGRID interactions for various organisms in a...
bioconductor-simpleaffy 2.66.0 GPL XX 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 XX Simulator for Collections of Independent Genomic Data Sets
bioconductor-sincell 1.38.0 GPL XX 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 XXX 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 2.16.0 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 XX 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 XXX 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 XX Phylogeny-based sequence clustering with site polymorphism
bioconductor-sizepower 1.76.0 LGPL XXX 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 XX Factorial Latent Variable Modeling of Single-Cell RNA-Seq Data
bioconductor-slgi 1.54.0 Artistic-2.0 XXX 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 XXX Functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH
bioconductor-smad 1.22.0 MIT XX Statistical Modelling of AP-MS Data (SMAD)
bioconductor-smap 1.66.0 GPL-2 XX 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 XXX 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 XXX Signal-to-Noise applied to Gene Expression Experiments
bioconductor-snageedata 1.42.0 Artistic-2.0 XXX SNAGEE data
bioconductor-snapcgh 1.72.0 GPL XX 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 XXX Supervised Normalization of Microarrays
bioconductor-snpchip 2.32.0 LGPL XXX Visualizations for copy number alterations
bioconductor-snpediar 1.32.0 GPL-2 XXX Query data from SNPedia
bioconductor-snphood 1.36.0 LGPL XXX 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 XXX 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 XX Parallel Computing Toolset for Relatedness and Principal Component...
bioconductor-snpstats 1.56.0 GPL-3 XX SnpMatrix and XSnpMatrix classes and methods
bioconductor-soggi 1.38.0 GPL XXX Visualise ChIP-seq, MNase-seq and motif occurrence as aggregate plots...
bioconductor-sojourner 1.11.0 Artistic-2.0 XX 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 XXX 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 XXX 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 XX 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 XX 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 XXX specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics
bioconductor-specond 1.60.0 LGPL XXX 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 XXX S-system parameter estimation method
bioconductor-spia 2.58.0 file XXX 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 XXX 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 XXX 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 XXX Methods for Spike-in Arrays
bioconductor-splatter 1.30.0 GPL-3 XXX Simple Simulation of Single-cell RNA Sequencing Data
bioconductor-splicegear 1.58.0 LGPL XXX splicegear
bioconductor-splicer 1.22.0 GPL XX An R package for classification of alternative splicing and prediction...
bioconductor-splicesites 1.31.0 GPL-2 XX Performs splice centered analysis on RNA-seq data.
bioconductor-splicewiz 1.8.0 MIT XX 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 XXX Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them
bioconductor-splinetimer 1.34.0 GPL-3 XXX Time-course differential gene expression data analysis using spline...
bioconductor-splinter 1.28.0 GPL-2 XXX Splice Interpreter of Transcripts
bioconductor-splots 1.72.0 LGPL XXX 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 XXX 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 XXX Add-on of the SQUAD Software
bioconductor-sracipe 1.22.0 MIT XX Systems biology tool to simulate gene regulatory circuits
bioconductor-sradb 1.64.0 Artistic-2.0 XXX A compilation of metadata from NCBI SRA and tools
bioconductor-srap 1.27.0 GPL-3 XXX 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 XX Finding differentially expressed unannotated genomic regions from RNA-seq data
bioconductor-sscore 1.72.0 GPL XXX S-Score Algorithm for Affymetrix Oligonucleotide Microarrays
bioconductor-sscu 2.36.0 GPL XXX Strength of Selected Codon Usage
bioconductor-sseq 1.44.0 GPL XXX Shrinkage estimation of dispersion in Negative Binomial models for...
bioconductor-ssize 1.80.0 LGPL XXX Estimate Microarray Sample Size
bioconductor-ssnappy 1.10.0 GPL-3 XXX Single Sample directioNAl Pathway Perturbation analYsis
bioconductor-sspa 2.30.0 GPL XX 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 XXX 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 XX 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 XXX Stability Ranking
bioconductor-starbiotrek 1.28.0 GPL XXX StarBioTrek
bioconductor-starr 1.43.0 Artistic-2.0 XX Simple tiling array analysis of Affymetrix ChIP-chip data
bioconductor-stategra 1.42.0 GPL-2 XXX 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 XXX Differentiation of Human Embryonic Stem Cells under Hypoxia gene...
bioconductor-stepnorm 1.78.0 LGPL XXX 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 XX Enabling stream processing of large files
bioconductor-stringdb 2.18.0 GPL-2 XXX 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 XX Implementation of the dot bracket annotations with Biostrings
bioconductor-structtoolbox 1.18.2 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 XXX 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 XX 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 XXX 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 XXX 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 XX Identification Of Clinically Relevant Genomic Subtypes Using Outcome...
bioconductor-survcomp 1.56.0 Artistic-2.0 XX 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 XXX Tools for visualizing genomics data
bioconductor-sva 3.54.0 Artistic-2.0 XX Surrogate Variable Analysis
bioconductor-svanumt 1.12.0 GPL-3 X NUMT detection from structural variant calls
bioconductor-svaplsseq 1.13.0 GPL-3 XXX 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 XXX Transform and Filter SWATH Data for Statistical Packages
bioconductor-swathxtend 2.28.0 GPL-2 XXX 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 XXX SwimR: A Suite of Analytical Tools for Quantification of C. elegans...
bioconductor-switchbox 1.42.0 GPL-2 XX Utilities to train and validate classifiers based on pair switching...
bioconductor-switchde 1.32.0 GPL XXX 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 XXX 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 XXX Calculate and Visualize Synergy Scores for Drug Combinations
bioconductor-synextend 1.18.0 GPL-3 XXX Tools for Working With Synteny Objects
bioconductor-synlet 2.6.0 GPL-3 XXX 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 XX Inference And Analysis Of Synteny Networks
bioconductor-systempiper 2.12.0 Artistic-2.0 XXX 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 XXX 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 XXX TargetScore: Infer microRNA targets using microRNA-overexpression data...
bioconductor-targetscoredata 1.42.0 GPL-2 X TargetScoreData
bioconductor-targetsearch 2.8.0 GPL XX 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 XXX 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 XXX TCC: Differential expression analysis for tag count data with robust...
bioconductor-tcgabiolinks 2.34.0 GPL XXX 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 XXX 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 XX 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 XXX Quality control for target capture experiments
bioconductor-ternarynet 1.50.0 GPL XX 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 1.46.0 doc GPL-2.0-or-later XX 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 XX Analyze High-dimensional Cytometry Data Using Tidy Data Principles
bioconductor-tigre 1.60.0 AGPL-3 XX Transcription factor Inference through Gaussian process Reconstruction...
bioconductor-tiledbarray 1.16.0 MIT XXX Using TileDB as a DelayedArray Backend
bioconductor-tilingarray 1.84.0 Artistic-2.0 XX Transcript mapping with high-density oligonucleotide tiling arrays
bioconductor-timecourse 1.78.0 LGPL XXX 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 XXX 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 XX 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 XX 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 XX 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 XX 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 XXX 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 XXX Build IGV tracks and HTML reports
bioconductor-trackviewer 1.42.0 GPL XXX 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 XXX An Integrative Tool for ChIP- And RNA-Seq Based Primary Transcripts...
bioconductor-transformgampoi 1.12.0 GPL-3 XXX Variance Stabilizing Transformation for Gamma-Poisson Models
bioconductor-transite 1.24.0 MIT XX RNA-binding protein motif analysis
bioconductor-translatome 1.44.0 GPL-3 XXX 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 XX Read density map construction and accession. Visualization of ChIPSeq...
bioconductor-trare 1.5.0 MIT X Transcriptional Rewiring
bioconductor-traser 1.36.0 GPL XXX 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 XXX 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 XXX Triform finds enriched regions (peaks) in transcription factor...
bioconductor-trigger 1.52.0 GPL-3 XX Transcriptional Regulatory Inference from Genetics of Gene ExpRession
bioconductor-trio 3.44.0 LGPL-2 XXX Testing of SNPs and SNP Interactions in Case-Parent Trio Studies
bioconductor-triplex 1.46.0 BSD_2_clause XX 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) XXX 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 XX 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 XX 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 XX A fast scatterplot smoother suitable for microarray normalization
bioconductor-tvtb 1.32.0 Artistic-2.0 XXX TVTB: The VCF Tool Box
bioconductor-tweedeseq 1.52.0 GPL XX 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 XX 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 XXX Annotation package for TxDb object(s)
bioconductor-txdb.celegans.ucsc.ce6.ensgene 3.2.2 Artistic-2.0 XXX 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 XXX Annotation package for TxDb object(s)
bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene 3.12.0 Artistic-2.0 XXX Annotation package for TxDb object(s)
bioconductor-txdb.drerio.ucsc.danrer10.refgene 3.4.6 Artistic-2.0 XXX 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 XXX Annotation package for TxDb object(s)
bioconductor-txdb.hsapiens.ucsc.hg19.knowngene 3.2.2 Artistic-2.0 XXX Annotation package for TxDb object(s)
bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts 3.2.2 Artistic-2.0 XXX Annotation package for TxDb object(s)
bioconductor-txdb.hsapiens.ucsc.hg38.knowngene 3.20.0 Artistic-2.0 XXX 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 XXX Annotation package for TxDb object(s)
bioconductor-txdb.mmusculus.ucsc.mm10.knowngene 3.10.0 Artistic-2.0 XXX 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 XXX 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 XXX Annotation package for TxDb object(s)
bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene 3.12.0 Artistic-2.0 XXX 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 XXX 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 XXX Annotation package for TxDb object(s)
bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene 3.2.2 Artistic-2.0 XXX 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 XXX 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 XXX 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 XXX Unsupervised Deconvolution of Tumor-Stromal Mixed Expressions
bioconductor-unifiedwmwqpcr 1.42.0 GPL XXX Unified Wilcoxon-Mann Whitney Test for testing differential expression...
bioconductor-uniprot.ws 2.46.0 Artistic-2.0 XXX 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 XXX Identification of cancer cell lines based on their weighted mutational/...
bioconductor-universalmotif 1.24.0 GPL-3 XX Import, Modify, and Export Motifs with R
bioconductor-updateobject 1.10.0 Artistic-2.0 X Find/fix old serialized S4 instances
bioconductor-updhmm 1.6.0 MIT X Detecting Uniparental Disomy through NGS trio data
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 XX 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 XXX Quantify and interpret drivers of variation in multilevel gene...
bioconductor-variantannotation 1.52.0 Artistic-2.0 XX 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 XX Filtering of coding and non-coding genetic variants
bioconductor-varianttools 1.48.0 Artistic-2.0 XXX 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 XXX 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 XXX 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 XX An R package for copy number data segmentation
bioconductor-vegamc 3.44.0 GPL-2 XX 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 XX 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 XXX 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 XX Feature-based variance-sensitive quantitative clustering
bioconductor-vsn 3.74.0 Artistic-2.0 XX 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 XX Statistical tests for detecting differential distributions based on the...
bioconductor-watermelon 2.12.0 GPL-3 XXX Illumina DNA methylation array normalization and metrics
bioconductor-wavcluster 2.40.0 GPL-2 XXX Sensitive and highly resolved identification of RNA-protein interaction...
bioconductor-wavetiling 1.28.0 GPL XX 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 XXX Tools and extensions for processing Sweave documents
bioconductor-webbioc 1.78.0 GPL XXX 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 XXX 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 XXX Test for differential expression for RNA-seq data
bioconductor-xcir 1.7.0 GPL-2 X XCI-inference
bioconductor-xcms 4.4.0 GPL XX 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 XX 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 XXX Export plotting files to the xmapBridge for visualisation in X:Map
bioconductor-xnastring 1.14.0 GPL-2 XX 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 XX Foundation of external vector representation and manipulation in Bioconductor
bioconductor-yamss 1.32.0 Artistic-2.0 XXX Tools for high-throughput metabolomics
bioconductor-yapsa 1.28.0 GPL-3 XXX Yet Another Package for Signature Analysis
bioconductor-yaqcaffy 1.50.0 Artistic-2.0 XXX Affymetrix expression data quality control and reproducibility analysis
bioconductor-yarn 1.32.0 Artistic-2.0 XXX 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 XXX Spellman et al. (1998) and Pramila/Breeden (2006) yeast cell cycle...
bioconductor-yeastexpdata 0.52.0 GPL XXX 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 XXX A suite of functions to facilitate zFPKM transformations
bioconductor-zinbwave 1.28.0 Artistic-2.0 XX 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 XX 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-or-later XXX Convert between bioinformatics formats.
biodiff 0.2.2 GPLv3+ XX 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...
bioemu 1.2.0 Apache-2.0 X Biomolecular emulator for scalable emulation of protein equilibrium...
bioepic 0.1.6 GNU XX Chip-Seq broad peak/domain finder.
bioexcel_seqqc 0.6 Apache X Sequence Quality Control pipeline/modules
biofluff 3.0.4 doc dev MIT XXX Exploratory analysis and visualization of high-throughput sequencing data.
bioformats 0.1.15 MIT XXX A collection of Python classes to handle bioinformatics data.
bioframe 0.8.0 doc MIT X Pandas utilities for tab-delimited and other genomic files
biogridpy 0.1.1 MIT XXX 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 XXX Set of visualisation and analysis tools for biological data sets
biolib 0.1.9 GPL3 XXX Package for common tasks in bioinformatics.
biolite 1.2.0 GPLv3 XX A lightweight bioinformatics framework with automated tracking of...
biolite-tools 0.4.0 GPLv3 XX C++ tools for biolite, a lightweight bioinformatics framework with...
biom-format 2.1.7 BSD XX Biological Observation Matrix (BIOM) format
biomaj 3.0.19 GNU XX 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 1.0.14 doc dev MIT X Library for working with biological sequence data as numpy arrays.
biopet 0.9.0 https://github. XXX 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 XXX 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 XXX #### 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 XXX 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 XXX 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 XXX Vcfstats is a tool that can generate metrics from a vcf file.
biophi 1.0.11 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 XX 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 XXX 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 XX 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
biovalid 0.4.0 AGPL-3.0-or-later X Quick validation of common bioinformatics files in pure Python
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 0.6.0 dev GPL-3.0-or-later X Python utilities used as part of the bird suite of bioinformatic tools.
bis-snp 1.0.1 MIT XXX Bisulfite-seq/NOMe-seq SNPs & cytosine methylation caller
bis-snp-utils 0.0.1 MIT XXX bis-snp-utils are support tools for Bis-SNP
biscot 2.3.3 LGPL-2.1 X Bionano SCaffolding Correction Tool
biscuit 1.7.1.20250908 doc dev MIT XX A utility for analyzing sodium bisulfite conversion-based DNA...
biskit 3.0.1 doc dev GPL-3.0-or-later XXX A Python platform for structural bioinformatics.
bismark 0.25.1 GNU XXX 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 XX 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 XX BLASR - The PacBio long read aligner
blasr_libcpp 5.3.4 BSD-3-Clause-Clear XX blasr_libcpp is a support library used by blasr and other PacBio tools
blast 2.17.0 NCBI-PD XX BLAST+ is a new suite of BLAST tools that utilizes the NCBI C++ Toolkit.
blast-legacy 2.2.26 Public XX 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 1.2.0 dev MIT XXX Rapid discovery of reciprocal best blast pairs from BLAST output files.
blastmining 1.2.0 doc dev GNU X blastMining: Mining NCBI BLAST outputs
blastn2dotplots 1.1.2 dev MIT X A script for visualizing multiple dot-plot alignments from BLASTN output.
blat 36 Free XX 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 XX An easy whitelist-based HTML-sanitizing tool.
blend-bio 1.0.0 MIT XX 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
blobtk 0.7.1 doc dev MIT XX Core functionality shared across BlobToolKit tools.
blobtoolkit 4.5.0 doc dev MIT X Interactive quality assessment of genome assemblies.
blobtools 1.1.1 GPLv3 XX Modular command-line solution for visualisation, quality control and...
blockbuster 0.0.1.1 The XX 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 XX Bloocoo is a k-mer spectrum-based read error corrector, designed to...
bloomfiltertrie 0.8.7 MIT XX An alignment-free, reference-free and incremental data structure for...
blosum 2.2.0 doc dev GPL-3.0-or-later X A small module for easy access to BLOSUM matrices without dependencies.
blue-crab 0.4.0 doc dev MIT X lossless nanopore pod5 <=> s/blow5 file conversion
bmfilter 3.101 Public XX 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 XX BMTagger aka Best Match Tagger is for removing human reads from...
bmtool 3.101 Public XX bmtool is part of BMTagger aka Best Match Tagger, for removing human...
bohra 3.0.6 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 XX A variant caller for short-read sequencing data
bolt-lmm 2.5 GPL-3+ XX Efficient large cohorts genome-wide Bayesian mixed-model association testing
boltons 16.4.1 XX None
boms 1.1.0 MIT X Cell Segmentation for Spatial Transcriptomics Data using BOMS
booster 0.1.2 GPL-2.0 XX 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 XX None
boutroslabplottinggeneral 5.3.4 GPL-2extra XX None
bowtie 1.3.1 Artistic-2.0-only XX An ultrafast memory-efficient short read aligner
bowtie2 2.5.4 doc dev GPL-3.0-or-later XX A fast and sensitive gapped read aligner.
bpipe 0.9.13 BSD-3-Clause XXX Bpipe - a tool for running and managing bioinformatics pipelines
bpp-core 2.4.1 CeCILL XX Bio++ is a set of C++ libraries for Bioinformatics.
bpp-phyl 2.4.1 CeCILL XX Bio++ is a set of C++ libraries for Bioinformatics.
bpp-popgen 2.4.1 CeCILL XX Bio++ is a set of C++ libraries for Bioinformatics.
bpp-seq 2.4.1 CeCILL XX Bio++ is a set of C++ libraries for Bioinformatics.
bracken 3.1 doc dev GPL-3.0-or-later XXX 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 XX BRAKER1: Unsupervised RNA-Seq-based genome annotation with GeneMark-ET...
braker2 2.1.6 Artistic XXX 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 XXX BPI uses Manta’s variant calls to re-analyse BAM files and precisely...
breakdancer 1.4.5 GPLv3 XX SV detection from paired end reads mapping
breakfast 0.4.6 dev MIT X breakfast: fast putative outbreak cluster and infection chain detection...
breakinator 1.1.1 dev MIT X Detection of foldback and chimeric read artifacts in PAF files.
breakseq2 2.2 BSD-2-Clause XX BreakSeq2: Ultrafast and accurate nucleotide-resolution analysis of...
breseq 0.39.0 doc dev GPL-2.0-or-later XX A computational pipeline for finding mutations relative to a reference...
brockman-pipeline 1.0 GPL-3.0 XXX Brockman Representation Of Chromatin by K-mers in Mark-Associated Nucleotides
bronko 0.1.0 doc dev MIT XX bronko is an ultra-rapid mapping free variant caller for viral amplicon...
brooklyn_plot 0.0.4 doc dev MIT X Gene co-expression and transcriptional bursting pattern recognition...
bs-seeker2 2.1.7 MIT XXX BS Seeker 2 is a seamless and versatile pipeline for accurately and...
bs_call 2.02 GPL-3.0 XX DNA methylation and variant Caller for Bisulfite Sequencing Data.
bsmap 2.90 GNU XX BSMAP is a short reads mapping software for bisulfite sequencing reads.
bte 0.9.3 doc dev MIT XX Cython wrapper enabling use of the MAT library in Python.
btllib 1.7.5 doc dev GPL-3.0-or-later XX Bioinformatics common code library in C++ with Python wrappers, from...
btrim 1.0.1 dev AGPL-3.0-or-later XX 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...
bubblefinder 1.0.1 MIT XX BubbleFinder - detecting superbubbles/snarls in graphs
bubblegun 1.1.10 doc dev MIT X BubbleGun is a tool for detecting bubbles and superbubbles in GFA...
bucketcache 0.12.0 MIT XX Versatile persisent file cache.
bufet 1.0 file XX Tool that performs the unbiased miRNA functional enrichment analysis...
bugseq-porechop 0.3.4pre GPL3 XX 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 XXX Framework for wrapping and controlling command-line applications.
burrito-fillings 0.1.1 BSD XXX 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 6.0.0 doc dev MIT XXX Assessment of assembly completeness using Universal Single Copy Orthologs.
busco_phylogenomics 20240919 MIT X Utility script to construct species phylogenies using BUSCO proteins.
buscolite 25.4.24 dev BSD-2-Clause X buscolite: busco analysis for gene predictions.
bustools 0.45.1 doc dev BSD-2-Clause XX bustools is a program for manipulating BUS files for single cell...
bwa 0.7.19 doc dev GPL-3.0-or-later XX The BWA read mapper.
bwa-aln-interactive 0.7.18 GPL-3.0-only XX Version of the BWA aln read mapper for interactive alignment.
bwa-mem2 2.3 doc dev MIT XX 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 XXX A self-consistent installation-free package of scripts and precompiled...
bwameth 0.2.9 dev MIT XXX A fast and accurate aligner of BS-seq reads.
bwapy 0.1.4 Mozilla XX 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 XX Read bigwig files quickly into PyRanges or DataFrames
bwtk 1.8.1 doc dev GPL-3.0-only XX A bigWig toolkit.
bx-python 0.14.0 doc dev MIT XX Tools for manipulating biological data, particularly multiple sequence...
bxtools 0.1.0 GPLv3 XX Tools for analyzing 10X Genomics data
bygul 1.0.6 dev BSD-2-Clause X Bygul is an amplicon read simulating tool that can generate different...
byobu 5.98 GPLv3 X Byobu is a GPLv3 open source text-based window manager and terminal multiplexer.
c-ares 1.11.0 MIT XX 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 doc dev https://github. XX Cactus is a reference-free whole-genome multiple alignment program...
cactus-gfa-tools 0.1 doc dev MIT XX Command-line utilitites required for the Cactus Pangenome Pipeline.
cadd-scripts 1.7.3 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
cagecleaner 1.4.5 doc dev MIT X Genomic redundancy removal tool for cblaster hit sets.
cagee 1.2 doc dev ECL XX 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 XX Clustering without alignment using (locality sensitive hashing) LSH and...
calisp 3.1.4 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 dev MIT XX 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 1.1.3 doc dev 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 XXX Distributed execution of bioinformatics tools on Apache Spark
canopy 0.25 GPL-2.0-or-later XX Canopy - Metagenomics Canopy Clustering Implementation
cansam 3489bc1 BSD-3-Clause XX C++ binding for SAM/BAM files
cansnper 1.0.10 GPLv3 XXX 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 XX 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 XX DNA sequence assembly program.
capc-map 1.1.3 GNU XX 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 1.6.1 doc dev GPL-3.0-only 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 XX Constraint-based Alignment of RNA Ensembles
carnac-lr 1.0.0 GNU XX Clustering coefficient-based Acquisition of RNA Communities in Long Read
carp 0.1.1 dev MIT XX carp - quantify the rearrangement complexity of pangenomes and their graphs.
carpedeam 1.0.1 doc dev GPL-3.0-only XX 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 1.6.6 doc dev Apache-2.0 X CarveMe: automated genome-scale metabolic model reconstruction
cas-offinder 2.4.1 doc dev BSD-3-Clause XX 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.
cascade-reg 0.5.1 doc dev MIT X Causal discovery of gene regulatory programs from single-cell genomics
caspeak 1.1.5 GPL-3.0-or-later X A pipeline for finding non-reference mobile element insertions
cassiopee 1.0.9 GPL-3+ XX scan an input genomic sequence (dna/rna/protein) and search for a...
cassiopeia 2.0.0 dev MIT XX 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 XXX CAT/BAT: tool for taxonomic classification of contigs and...
catch 1.5.2 MIT XXX 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 XX Protein structure comparison tools such as SSAP, as used by the Orengo...
cats-rb 1.0.3 doc MIT X Reference-based transcriptome assembly quality assessment tool.
cats-rf 1.0.4 doc MIT X Reference-free transcriptome assembly quality assessment tool.
cawlign 0.1.15 dev MIT XX A tool for aligning consensus sequences to reference genomes.
cayman 0.10.2 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 1.4.0 doc dev MIT X Find clustered hits from a BLAST search.
ccat 3.0 unknown XX 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
ccp4srs 2024.06.14 doc dev LGPL-3.0 XX CCP4 Storage, Retrieval and Search framework for small-molecule data
ccphylo 0.8.2 Apache-2.0 XX 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.
cctyper 1.8.0 dev MIT X CRISPRCasTyper: Automatic detection and subtyping of CRISPR-Cas operons
cd-hit 4.8.1 doc dev GPL-2.0-or-later XX Clusters and compares protein or nucleotide sequences.
cd-hit-auxtools 4.8.1 GPLv2 XX Clusters and compares protein or nucleotide sequences
cdbtools 0.99 Public XX 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 XX cDNA_Cupcake is a miscellaneous collection of Python and R scripts used...
cdskit 0.14.5 BSD-3-Clause X A toolkit for processing protein-coding sequences (CDS).
cdst 0.2.1 dev GPL-3.0-only X CoDing Sequence Typer (CDST): MD5 hash-based genome typing and clustering.
ceas 1.0.2 Artistic XX 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 0.8.4 doc dev BSD-3-Clause XXX 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 XXX 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 0.1.0 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 XX Efficient genotyping bi-allelic SNPs on single cells.
celltypist 1.7.1 doc 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
cenmap 1.1.1 doc dev MIT X A centromere mapping and annotation pipeline for T2T human and primate...
cenote-taker3 3.4.3 doc dev MIT X Cenote-Taker 3: Discover and annotate the virome.
cenplot 0.1.5 MIT X Centromere plotting library.
censtats 0.1.3 MIT X Centromere statistics toolkit.
centreseq 0.3.8 dev MIT X Fast generation of core genome from bacterial strains
centrifuge 1.0.4.2 GPL-3.0-only XX Classifier for metagenomic sequences. Supports classifier scripts
centrifuge-core 1.0.4.2 doc dev GPL-3.0-only XX Classifier for metagenomic sequences. Does not include evaluation scripts
centrifuger 1.0.12 MIT XX 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 1.3.2 BSD XX An open source image processing library. Dependency for CellProfiler
cerberus-x 1.5.0 doc dev BSD-3-Clause X Versatile Functional Ontology Assignments via Hidden Markov Model (HMM)...
cesar 1.01 MIT XX 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 XX Tools for applying Competitive Fragmentation Modeling (CFM) to spectrum...
cgat-apps 0.7.10 doc dev MIT XX 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 XXX A report generator in python based on sphinx
cgat-scripts 0.3.2 BSD XX Computational Genomics Analysis Toolkit
cgat-scripts-nosetests 0.0.4 BSD X Computational Genomics Analysis Toolkit
cgatcore 0.6.16 MIT XXX CGAT : the Computational Genomics Analysis Toolkit
cgcloud-lib 1.6.0 Apache XXX Components shared between cgcloud-core and cgcloud-agent
cgecore 2.0.1 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 XX 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 XX cgranges is a small C library for genomic interval overlap queries
cgt 1.0.0 Apache-2.0 XX Calculate a core genome threshold (cgt) from metagenome data
cgview 1.0 GNU XXX 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 XX convert CHAIN format to PAF format
chainmap 1.0.3 Python XXX Backport/clone of ChainMap for py26, py32, and pypy3.
chamois 0.2.0 dev GPL-3.0-or-later X Chemical Hierarchy Approximation for secondary Metabolism clusters...
changeo 1.3.4 doc dev AGPL-3.0-only X A bioinformatics toolkit for processing high-throughput lymphocyte...
chanjo 3.3.0 MIT XX 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 XX check sort-order of genomic files according to a genomefile
checkatlas 0.7.1 doc dev BSD X One liner tool to check the quality of your single-cell atlases.
checkm-genome 1.2.4 doc dev GPL-3.0-or-later XXX 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 4.0.7 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 3.5.0 doc GPL-3.0-or-later XXX 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 XX A package for measuring reproducibility of ChIA-PET data.
chicagotools 1.2.0 artistic XXX 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 XX ChIPs is a tool for simulating ChIP-sequencing experiments.
chipseq-greylist 1.0.2 MIT XXX 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 0.12.0 doc dev MIT XX A rust command line for filtering and trimming long reads.
chorus2 2.01 doc dev MIT XXX A pipeline to select oligonucleotides for fluorescence in situ...
chromap 0.3.2 doc MIT XX 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 XX An ultra fast, heuristic approach to detect conserved signals in...
chromhmm 1.27 GPLv3 XXX 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 XX 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 XXX A reference-assisted assembly tool for producing draft chromosome sequences.
chromsize 0.0.32 MIT XX 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
cif-tools 1.0.12 doc dev BSD-2-Clause XX A suite of programs to manipulate and examine mmCIF files
cigar 0.1.3 MIT X manipulate SAM cigar strings
circexplorer 1.1.10 MIT XXX A combined strategy to identify circular RNAs (circRNAs and ciRNAs)
circexplorer2 2.3.8 MIT XXX Circular RNA analysis toolkits
circlator 1.5.5 GNU XXX circlator: a tool to circularise genome assemblies
circle-map 1.1.4 dev MIT X Circular DNA analysis tools.
circle-map-cpp 1.0.0 dev GPL-3.0-only XX Circle-Map-cpp is the C++ version of Circle-Map.
circminer 0.4.2 GPLv3 XX Sensitive and fast computational tool for detecting circular RNAs...
circos 0.69.9 GNU XXX Circos is a software package for visualizing data and information. It...
circos-tools 0.23 GNU XXX 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 2.0.3 doc dev GPL-3.0-or-later X circtools - a circular RNA toolbox.
circularmapper 1.93.5 GPLv3 XXX 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 1.1.3 doc dev 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 XX Fast ISO8601 date time parser for Python written in C
cistrome-ceas 1.0.2b1 doc dev Artistic XXX Cistrome-CEAS -- Cis-regulatory Element Annotation System
cistrome_beta 1.0.7 dev This XX 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 XX Python-bindings for CityHash, a fast non-cryptographic hash algorithm
civicpy 5.1.0 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 1.2.0 BSD-3-Clause XX Clair3 is a small variant caller for long-reads. Compare to PEPPER...
clair3-illumina 1.2.0 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 XX Identifying the variants of DNA sequences sensitively and accurately is...
clam 0.2.2 dev MIT X clam is a tool for classification of callable loci intervals, and...
clame 1.0 dev GPL-3.0-or-later X CLAME is a binning software for metagenomic reads. It immplements a...
clan 0.05 Creative X CLAN - the CrossLinked reads ANalysis tool
clark 1.3.0.0 doc dev GPL-3.0-or-later XX Fast, accurate and versatile k-mer based classification system.
classpro 1.0.2 https://github. X A K-mer classifier for HiFi reads .
cleanifier 1.2.0 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).
cleaverna 1.0.0 doc dev MIT X Computational tool for scoring candidate cleavage sites of DNAzyme
clermontyping 24.02 GPL-3.0-only X determine the Clermont E coli phylotype
clever-toolkit 2.4 doc dev GPL-3.0-only XX The CLEVER Toolkit.
cligv 0.1.0 dev MIT X command line Interactive Genome Viewer
clincnv 1.19.1 MIT X Copy number variation detection for clinical sequencing.
clinker 1.33 MIT XX Clinker is a bioinformatics pipeline that generates a...
clinker-py 0.0.32 doc dev MIT X Gene cluster comparison figure generator
clinod 1.3 Apache XX 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 XXX 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 2.7.0 doc MIT X Alignment trimming software for phylogenetics.
clipper 2.1.20180802 GPL-2.0-only XX Crystallographic automation and complex data manipulation libraries.
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 0.4.0 dev AGPL-3.0-only X Co-occurrence Locus and Orthologous Cluster Identifier.
clonalframeml 1.13 doc dev GPL-3.0-or-later XX 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 XXX CLOVE: Classification of genomic fusions into structural variation events.
clsify 0.1.1 MIT X Haplotyping of C. Liberibacter solanacearum from Sanger data.
clumppling 2.0.6 doc dev MIT X Cluster matching and permutation program with integer linear programming.
clust 1.18.0 LGPL-3.0 XXX Optimised consensus clustering of multiple heterogeneous datasets.
clustalo 1.2.4 doc GPL-2.0-or-later XX Latest version of Clustal: a multiple sequence alignment program for...
clustalw 2.1 doc LGPL-3.0-or-later XX ClustalW2 is a general purpose multiple sequence alignment program for...
cluster-picker 1.2.3 GPLv3 XX 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 XXX 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 1.2.2 doc dev GPL-3.0-or-later XX Clusty is a tool for large-scale data clustering.
cmaple 1.1.0 doc dev GPL-2.0 XX MAximum Parsimonious Likelihood Estimation in C/C++.
cmappy 4.0.1 BSD XX 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 3.4.2 doc dev Apache-2.0 X ClinVar Mapping and Annotation Toolkit.
cmfinder 0.4.1.9 GPL3 XX CMfinder - A Covariance Model Based RNA Motif Finding Algorithm
cmip 2.7.0 Apache XX CMIP Classical Molecular Interaction Potentials
cmph 2.0 LGPL XX 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 1.3.5 GPL-3.0-only X Improved simulation of single-cell copy number profiles and DNA-seq...
cnmf 1.7.0 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 XXX Copy number variant detection from high-throughput sequencing.
cnvnator 0.4.1 MIT X Tool for calling copy number variations.
cnvpytor 1.3.2 doc dev MIT XXX 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 XX Coalescent tree simulation along a transmission network
cobra 0.21.0 GNU XXX 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 XX 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 XXX CoCoScore: context-aware co-occurrence scores for biomedical text...
codan 1.2 doc GPLv3 XXX 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 XX CodingQuarry: highly accurate hidden Markov model gene prediction in...
codoff 1.2.3 doc dev BSD-3-Clause XX codoff: program to measure the irregularity of the codon usage for a...
codon-bias 0.3.5 MIT X codon usage bias analysis tools
codonw 1.4.4 GPLv2 XX 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 2.0.0 doc dev MIT X Classify prokaryote protein sequences into COG functional category.
cogent 1.9 GNU XX COmparative GENomics Toolkit
cogent3 2025.12.10a3 doc dev BSD-3-Clause X COmparative GENomics Toolkit 3: genomic sequence analysis within...
cogtriangles 2012.04 Public XX 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 XX A generalized profile syntax for biomolecular sequence motifs and its...
coinfinder 1.2.1 doc dev GPL-3.0-only XX 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 XX Collects MGF files and dd_results from an XMass setup_QDD.tcl...
collectl 4.3.20.1 doc dev Artistic XXX Collectl is a light-weight performance monitoring tool capable of...
colombo 4.0 Creative XXX A software framework equipped with a GUI for the prediction of genomic...
colorbrewer 0.3 dev Apache-2.0 XXX An easy way to get access to ColorBrewer schemes from within a Python program.
colord 1.1.0 GPL-3 XX A versatile compressor of third generation sequencing reads.
colorid_bv 0.1.0 MIT XX Experiments with using BIGSI data structure for metagenomic and QC applications
colormap 0.9.8 GNU XX Utilities to ease manipulation of matplotlib colormaps and color codecs...
combined-pvalues 0.50.6 MIT XXX 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 XX Comet is a command line tool that does MS/MS database search.
commec 1.0.2 doc dev MIT X commec: a free, open-source, globally available tool for DNA sequence screening
commet 24.7.14 doc dev AGPL-3.0-or-later XX Comparing and combining multiple metagenomic datasets.
compalignp 1.0 GPL X Compute fractional "identity" between trusted alignment and...
comparative-annotation-toolkit 0.1 Apache XXX A straightforward end-to-end pipeline that takes as input a HAL-format...
compare-reads 0.0.1 MIT XX cythonized function to compare reads by name.
comparem 0.1.2 GPL-3 X A toolbox for comparative genomics.
comparem2 2.16.2 doc dev GPL-3.0-or-later X CompareM2 genomes-to-report pipeline
comparems2 1 GPL3 XX 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 doc dev BSD-2-Clause XX Clustering cONtigs with COverage and ComposiTion.
concoord 2.1.2 Apache XX 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 XX Long- and short-read hybrid de novo transcriptome assembly
confindr 0.8.2 doc dev MIT XXX Detect intra- and inter-species bacterial contamination in NGS reads.
conifer 1.0.3 dev BSD-2-Clause XX 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 XXX A command-line tool to deduplicate bam files based on custom, inline barcoding.
consan 1.2 doc dev GPL-2.0-or-later XX Pairwise RNA structural alignment, both unconstrained and constrained...
consel 0.20 doc dev GPL-2.0-or-later XX CONSEL calculates the probability value (i.e., p-value) to assess the...
consensify 2.4.0 doc dev GPL-3.0-or-later XX A method for generating a consensus pseudohaploid genome sequence
consensusfixer 0.4 GPL-3.0 XXX Computes a consensus sequence with wobbles, ambiguous bases, and...
consent 2.2.2 doc dev AGPL-3.0-or-later XX Scalable long read self-correction and assembly polishing with multiple...
conservation 1.0.1 MIT X Evolutionary Conservation of Amino Acids and Codons
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 XX estimation of mtDNA contamination from a set of potential contaminant genomes.
contatester 1.0.0 CeCILL XX 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 XX Copy number and genotype annotation from whole genome and whole exome...
conus 1.0 file XX 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 0.4.0 dev GPL-3.0-or-later X Jupyter notebook based genomic data visulization toolkit.
cooler 0.10.4 doc dev BSD-3-Clause XXX 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 XX Analysis tools for genomic interaction data stored in .cool format
coot-headless 1.1.20 doc dev GPL-3.0-or-later XX Coot Headless API - Software for macromolecular model building.
coprarna 2.1.4 MIT XX 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 XX Coral is an efficient tool to bridge paire-end RNA-seq reads.
core-snp-filter 0.2.0 GPLv3 XX 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...
coreprofiler 2.0.0 doc dev GPL-3.0-only X CoreProfiler, a robust and integrable cgMLST software.
coreutils 8.25 GPL XX The GNU Core Utilities are the basic file, shell and text manipulation...
corgi 0.4.3 doc dev Apache-2.0 X Classifier for ORganelle Genomes Inter alia
corneto 1.0.0b2 dev GPL-3.0-or-later X CORNETO: A Unified Framework for Omics-Driven Network Inference.
corona_lineage_dynamics 0.1.7 dev ASL XX 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 doc dev GPL-3.0-or-later XX Software for clustering de novo assembled transcripts and counting...
corsid 0.1.3 dev MIT X Core Sequence Identifier
cortex_con 0.04c GPL3 XX cortex_con (primary contact Mario Caccamo) is for consensus genome assembly
cortexpy 0.46.5 doc dev Apache-2.0 XX 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 XX cosi2 is an efficient coalescent simulator with support for selection,...
cosigt 0.1.7 dev GNU XX 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 XX 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
covar 0.2.0 dev MIT XX Linked-read variant calling tool for wastewater sequencing data.
coverageanomalyscanner 0.2.3 GPL-3.0 X Application to find local anomalies in read coverage and to predict...
coverm 0.7.0 doc dev GPL-3.0-or-later XX 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 1.4.0 doc dev MIT XX covtobed - generate a BED file of covered regions from a BAM file.
cpat 3.0.5 doc dev GPL-2.0-or-later XXX 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 XXX CPINSim is a package for the simulation of protein complex assembly...
cpstools 3.0 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 1.14.0 dev MIT X Crabs (Creating Reference databases for Amplicon-Based Sequencing) is a...
cram-archiver 1.1.0 doc dev agpl-3.0-or-later X A samtools wrapper for CRAM conversion automation.
cramino 1.3.0 dev MIT XX A tool for very fast quality assessment of long read cram/bam files.
cramtools 3.0.b127 Apache XXX A set of Java tools and APIs for efficient compression of sequence read data
craq 1.10 doc dev MIT X Pinpoint assembly errors for genomic assessing and correcting.
crass 1.0.1 dev GPL-3.0-or-later XX Crass (The CRISPR Assembler) is a program that searches through raw...
crazydoc 0.2.2 MIT X Read genetic sequences from stylized docx files
crb-blast 0.6.9 MIT XX Conditional Reciprocal Best BLAST - high confidence ortholog assignment.
cressent 1.0.2 doc dev MIT X A comprehensive toolkit for ssDNA virus analysis
crimson 1.1.1 BSD XXX 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 XXX 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 XX A software pipeline for the analysis of targeted CRISPR-Cas9 sequencing data
crispresso2 2.3.3 doc dev CC0-1.0 XX A software pipeline designed to enable rapid and intuitive...
crispritz 2.7.0 GPL3 XX 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 2.1.8 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 1.0.8 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 XXX 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
crossfilt 0.2.1 dev GPL-3.0-only X Tools to filter reads causing alignment bias in cross-species genomic...
crossmap 0.7.3 doc dev GPL-3.0-or-later XXX CrossMap is a program for convenient conversion of genome coordinates...
crumble 0.9.1 multiple XX Controllable lossy compression of BAM/CRAM files
crunchstat-summary 3.2.0 doc AGPL-3.0-only X Arvados crunchstat-summary reads crunch log files and summarizes resource usage.
crussmap 1.0.1 doc dev MIT XX crussmap is a faster tool to convert genome coordinates between...
crux-toolkit 4.2 dev Apache-2.0 XX A cross-platform suite of analysis tools for interpreting protein mass...
cryfa 20.04 GPL3 XX 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 1.5.0 dev Apache-2.0 X This package crypto_typer: tool to subtype the parasite,...
csb 1.2.5 MIT XXX Computational Structural Biology Toolbox
csblast 2.2.3 GPL3 XX 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
csubst 1.4.20 doc dev BSD-3-Clause XX Tool for analyzing combinatorial codon substitutions in DNA sequences.
csvtk 0.31.0 MIT XX A cross-platform, efficient, practical CSV/TSV toolkit
ctat-lncrna 1.0.1 BSD-3-Clause XXX ctat-lncrna uses slncky
ctat-metagenomics 1.0.1 BSD-3-Clause XXX ctat-metagenomics uses centrifuge
ctat-mutations 2.1.0 BSD-3-Clause XXX Mutation detection in RNA-Seq using GATK-v4.0 in RNA-Seq variant...
ctc-scite 1.0.2 dev GPL-3.0-or-later XX 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 1.0.5 dev USC-RL XX Genotyping sequence-resolved copy-number variation using pangenomes.
cufflinks 2.2.1 Boost XX Transcriptome assembly and differential expression analysis for RNA-Seq.
cuna 0.3.0 dev MIT X CUNA: Cytosine Uracil Neural Algorithm for ancient DNA damage detection...
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 XXX CuReSim (Customized Read Simulator) is a customized tool which...
curlywhirly 1.17.08.31 BSD-2-Clause XXX CurlyWhirly is an application for viewing multi-dimensional data, with...
curve-curator 0.6.0 doc Apache-2.0 X CurveCurator is an open-source analysis platform for any dose-dependent...
curves 3.0.3 Apache XX CURVES+: Conformational analysis of single nucleic acid structures or...
customtkinter 5.2.2 MIT X Create modern looking GUIs with Python
cutadapt 5.2 dev MIT XX Trim adapters from high-throughput sequencing reads
cutefc 1.0.2 MIT X Regenotyping structural variants through an accurate and efficient...
cutehap 1.0.2 MIT XX Haplotype-Aware Structural Variant Detector
cutesv 2.1.3 dev MIT X cuteSV is a long-read based human genomic structural variation detection tool.
cutesv-ol 1.0.2 MIT XX cuteSV-OL: real-time structural variation detection for nanopore sequencing
cutqc 0.07 MIT X generate aggregated fastqc report of both before and after trimming.
cuttlefish 2.2.0 doc dev BSD-3-Clause XX Construction of the compacted de Bruijn graph efficiently.
cvanmf 1.0.0 GPL-2.0-only X Bi-cross validation of NMF and signature generation and analysis
cvbio 3.0.0 doc MIT X Tools for working with genomic and sequencing data, including...
cvlr 1.0 dev MIT XX Clustering and Visualization of Long Reads.
cwl2wdl 0.1dev44 MIT XXX Proof of concept converter from Common Workflow Language (CWL) to the...
cwltest 2.2.20220521103021 Apache-2.0 XXX Common workflow language testing framework
cwltool 1.0.20180225105849 Apache XXX Common Workflow Language reference implementation
cycle_finder 1.0.0 dev GPL-3.0-or-later XX A de novo analysis tool for tandem and interspersed repeats based on...
cyntenator 0.0.r2326 GPL XX progressive gene order alignments
cyordereddict 0.2.2 BSD XX 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 3.10.4 dev LGPL XX 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 XX A Cython wrapper over uShuffle - a useful tool for shuffling biological...
cyvcf 0.8.0 MIT XX A cython wrapper around htslib built for fast parsing of Variant Call...
cyvcf2 0.31.4 doc dev MIT XX 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 doc dev MIT XX The C/C++ binding for the D4 file format.
d4tools 0.3.11 doc dev MIT XX 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 XX Fit population genetic models using diffusion approximations to the...
dagchainer r120920 MIT XX DAGchainer identifies syntenic regions.
daisyblast 0.2.0 MIT X A Python tool to find, plot, and export synteny blocks from all-vs-all BLAST.
daisysuite 1.3.0 dev GPL-3.0-or-later XX DaisySuite - mapping-based pipeline for horizontal gene transfer (HGT)...
dajin2 0.7.4 doc dev MIT X One-step genotyping tools for targeted long-read sequencing.
daligner 2.0.20240118 doc dev Custom XX DALIGNER: Find all significant local alignments between reads.
damageprofiler 1.1 GPL-3.0 XXX A Java based tool to determine damage patterns on ancient DNA as a...
damasker 1.0p1 dev Custom XX DAMASKER: Module to determine where repeats are and make soft-masks of said.
damidseq_pipeline 1.6.2 doc dev GPL-2.0-or-later XXX An automated pipeline for processing DamID sequencing datasets.
dammet 1.0.4 MIT XX Software to reconstruct methylomes from HTS data from ancient specimen
dammit 1.2 dev BSD XXX simple de novo transcriptome annotator
dampa 0.2.0 dev MIT X DAMPA designs probes for use in targetted metagenomics. It leverages...
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 1.3.1 doc dev MIT X An sklearn implementation of discriminant analysis of principal...
darkprofiler 0.1.3 MIT X DarkProfiler: Alignment and Classification of Peptides from...
dart 1.4.6 MIT XX Dart: a fast and accurate RNA-seq mapper
dartunifrac 0.2.8 doc dev MIT XX DartUniFrac is an ultra-fast UniFrac algorithm that scales to millions...
dartunifrac-gpu 0.2.8 doc dev MIT X DartUniFrac is an ultra-fast UniFrac algorithm that scales to millions...
das_tool 1.1.7 BSD XX Recovery of genomes from metagenomes via a dereplication, aggregation...
dascrubber 0.0.1a2 Custom XX Alignment-based Scrubbing pipeline
dashing 1.0 GPL-3 XX Fast and accurate genomic distances using HyperLogLog
dashing2 2.1.20 doc dev MIT X A fast toolkit for k-mer and minimizer encoding, sketching, comparison,...
dastk 1.0.1 dev BSD-3 X Differential ATAC-seq toolkit
data_hacks 0.3.1 Apache XX 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 XX None
datma 2.0 GPL-3.0 X DistributedAuTomaticMetagenomicAssembly andAnnotation framework
dawg 2.0.beta1 GPL-2 XX DNA Assembly with Gaps (Dawg) is an application designed to simulate...
dazz_db 1.0 Custom XX DAZZ_DB: The Dazzler Data Base
dbcan 5.2.1 doc dev GPL-3.0-only X Standalone version of dbCAN annotation tool for automated CAZyme annotation.
dbcanlight 1.1.1 doc dev MIT X A lightweight CAZyme annotation tool
dbg2olc 20200723 doc dev Unknown XX Efficient Assembly of Large Genomes Using Long Erroneous Reads of the...
dbghaplo 0.0.2 MIT XX Haplotyping small sequences from heterogeneous long-read sequencing...
dbgraph 1.0.0 dev GPL-3.0-or-later XX 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 XX 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 XXX dDocent is an interactive bash wrapper to QC, assemble, map, and call...
ddprimer 0.1.1 dev MIT X Pipeline for designing primers optimized for droplet digital PCR
ddqc 1.0 BSD-3-Clause X Biology-centered data-driven quality control for scRNA-seq.
ddquint 0.1.0 dev MIT X Droplet Digital PCR Multiplex Analysis for chromosomal copy number detection
ddrage 1.8.1 MIT XXX Simulator for ddRADseq (double digest restriction site associated DNA...
deacon 0.13.2 MIT XX Fast alignment-free sequence filter
deap 1.0.2 GNU XXX 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 XXX Deblur is a greedy deconvolution algorithm based on known read error profiles.
debreak 1.3 MIT XX DeBreak, Deciphering the exact breakpoints of structural variations...
debwt 1.0.1 Unknown XX A efficient method to construct BWT index of a given DNA sequence,...
decenttree 1.0.0 dev GPL-2.0-only X Scalable Neighbour-Joining and related algorithms for phylogenetic inference
dechat 1.0.1 dev MIT XX Repeat and haplotype aware error correction in nanopore sequencing...
decifer 2.1.4 dev BSD-3-Clause XX 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.
deconveil 0.1.4 doc dev MIT X An extension of PyDESeq2/DESeq2 designed to account for genome aneuploidy.
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 XXX 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 XXX A signal-level demultiplexer for Oxford Nanopore reads.
deepblast 1.0.2 dev BSD-3-Clause X Neural Networks for Protein Sequence Alignment.
deepchopper 1.2.9 doc dev Apache-2.0 XX A Genomic Language Model for Chimera Artifact Detection in Nanopore...
deepchopper-cli 1.2.9 doc dev Apache-2.0 XX A CLI for Genomic Language Model for Chimera Artifact Detection in...
deepdetails 0.1.1rc1 dev GPL-3.0 X Deep-learning-based DEconvolution of Tissue profiles with Accurate...
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 3.1.13 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 XX 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 1.2.4 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 XXX A set of user-friendly tools for normalization and visualzation of...
deeptoolsintervals 0.1.9 MIT XX A python module creating/accessing GTF-based interval trees with...
deepvariant 1.9.0 doc dev BSD-3-Clause XX DeepVariant is an analysis pipeline that uses a deep neural network to...
defense-finder 2.0.1 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 XX 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 XX Collapse homopolymer runs in FASTQ files
delegation 1.1 doc dev BSD X Simple implementation of the delegate pattern.
delly 1.7.2 doc dev BSD-3-Clause XX Structural variant discovery by integrated paired-end and split-read analysis.
deltabs 0.1 GPL3 XXX 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 dev AGPL-3.0-only XX DeltaPD is a tool used to determine outliers in a gene tree when...
delve-bio 0.2.0 MIT XX A variant caller for mixed infections
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...
demultiplexer2 1.1.6 doc dev MIT X A python command line interface to demultiplex illumina reads.
demuxem 0.1.8 doc dev BSD-3-Clause X DemuxEM is the demultiplexing module of Pegasus, which works on...
demuxlet 1.0 doc dev GPL-3.0-or-later XX Genetic multiplexing of barcoded single cell RNA-seq.
dendropy 5.0.8 doc dev BSD-3-Clause XXX A Python library for phylogenetics and phylogenetic computing: reading,...
denovogear 1.1.1 GPL3 X None
density-fitness 1.2.0 doc dev BSD-2-Clause XX Application to calculate the density statistics (RSR, SRSR, RSCCS,...
deploid 0.5 GPLv3 XX A software that deconvolutes mixed genomes with unknown proportions.
derip2 0.4.1 MIT X Predict ancestral sequence of fungal repeat elements by correcting for...
derna 1.0.4 doc dev BSD-3-Clause XX RNA sequence design for a target protein sequence.
desalt 1.5.6 doc dev MIT XX De Bruijn graph-based Spliced Aligner for Long Transcriptome reads.
desman 2.1 BSD XX De novo Extraction of Strains from MetAgeNomes
detonate 1.11 GPL XX DETONATE (DE novo TranscriptOme rNa-seq Assembly with or without the...
devider 0.0.1 MIT XX Haplotyping small sequences from heterogeneous long-read sequencing...
dextractor 1.0p2 Custom XX Bax File Decoder and Data Compressor
dfam 3.7 doc Creative XX The Dfam database is a collection of Repetitive DNA element sequence...
dfast 1.3.7 dev GPLv3 XXX DDBJ Fast Annotation and Submission Tool - Prokaryotic genome...
dfast_qc 1.0.7 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 XXX DIA-Umpire is an open source Java program for computational analysis of...
dialign-tx 1.0.2 doc LGPL-2.1-or-later XX 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 2.1.17 doc dev GPL-3.0-or-later XX Accelerated BLAST compatible local sequence aligner.
diamond_add_taxonomy 0.1.2 MIT XXX Utility to work with NCBI taxonomy database including tool to annotate...
diapysef 1.0.10 MIT X Analysis, conversion and visualization of diaPASEF data.
diatracer 1.2.5 Academic X A diaPASEF spectrum-centric analysis tool
dice 1.1.0 GPL-3.0-only X Cell lineage reconstruction from single-cell CNA data
dicey 0.3.4 doc dev GPL-3.0-or-later XX 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 XX dig2 is a simple but flexible in silico digester of protein sequences...
digest 0.3.0 MIT XX 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 XXX Python package for data processing of direct-infusion mass...
dinamo 1.0 dev GPL-3.0-or-later XX 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 doc dev MIT XX 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
dipper 0.1.2 doc dev MIT X DIPPER: An ultrafast tool for phylogenetic tree reconstruction.
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 XX DISCASM aims to extract reads that map to reference genomes in a...
disco 1.3 GPL-3.0-or-later XX Multi-threaded Distributed Memory Overlap-Layout-Consensus (OLC)...
discosnp 2.6.2 doc dev AGPL-3.0-or-later XX 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 XX Estimation of Rates-Across-Sites Distributions in Phylogenetic...
distle 0.3.0 GPL-3.0-only XX Fast distance matrix calculations on fasta and cgmlst files
distree 1.0.0 GPL-3.0-only XX A tool to calculate distances between phylogenetic trees.
disty 0.1.0 MIT XX Disty McMatrixface - compute a distance matrix from a core genome...
ditasic 0.2 MIT XX DiTASiC is designed as a comprehensive approach for abundance...
divvier 1.01 dev GPL-3.0-or-later XX A program for removing MSA uncertainty.
djinn 1.1 doc dev GPL-3.0-or-later X Convert your linked-read data between formats, almost like magic.
dkfz-bias-filter 1.2.3a GPLv3 XXX The DKFZ bias filter flags SNVs that appear to be biased based on the...
dlcpar 1.0 GPLv3 XXX 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
dmox 0.2.1 doc dev GPL-3.0-or-later XX Rust-based demultiplexing of haplotagging linked-read data.
dms 1.1 dev GPL-3.0-or-later XX 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 XX Model and predict short DNA sequence features with neural networks.
dna_features_viewer 3.1.5 doc dev MIT X Plot features from DNA sequences (e.g. Genbank) with Python.
dnaapler 1.3.0 doc dev MIT X Reorients assembled microbial sequences
dnacauldron 2.0.12 MIT X Cloning simulation for DNA assembly (Golden Gate, Gibson...).
dnachisel 3.2.16 doc dev MIT X Optimize DNA sequences under constraints.
dnadotplot 0.1.4 doc dev MIT XX DNA dot plot generator.
dnaio 1.2.3 MIT XX 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 XXX 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 1.5.1 doc dev GPL-3.0-or-later XX dnmtools is a set of tools for analyzing DNA methylation data from...
dnoise 1.4.2 GPL-3.0-only X Denoise sequence data sets from Illumina using distance corrected...
dnp-binstrings 1.0 MIT XX Convert fasta strings into dinucleotide binary indicator string as 00101...
dnp-corrprofile 1.0 MIT XX Profile of correlations between the patterns of dinucleotide frequency...
dnp-diprofile 1.0 MIT XX Dinucleotide frequency of occurrence in a batch of fasta sequences
dnp-fourier 1.0 MIT XX Periodogram of dinucleotide frequency pattern
dnp-mapping 1.0 MIT XX 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 XX 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
domainator 0.8.0 doc MIT X A flexible suite for domain-based gene neighborhood and protein analysis.
domclust 1.2.8 doc GPL-3.0-or-later XX Effective tool for orthologous grouping in multiple genomes.
dominate 2.1.16 GNU XX 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 4.3.0.post1 doc dev MIT X Method to detect and enable removal of doublets from single-cell RNA-sequencing.
downpore 0.3.4 MIT XX Suite of tools for use in genome assembly and consensus.
dpcstruct 0.1.1 dev GPL-3.0-or-later X Unsupervised clustering algorithm for identifying and classifying...
dr-disco 0.18.3 GPL-3.0+ XXX Dr. Disco: fusion gene and genomic breakpoint detection in random...
dragmap 1.3.0 dev GPL-3.0-or-later 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 XXX A pipeline for Detecting Resistome Associated taXa.
dream-stellar 2.1.0 dev BSD-3-Clause X DREAM-Stellar: a fast and accurate pairwise local aligner.
dreamtools 1.3.0 BSD XX Scoring functions for the DREAM / SAGE challenges
drep 3.6.2 doc dev MIT XXX De-replication of microbial genomes assembled from multiple samples.
drevalpy 1.4.0 doc dev MIT X Drug response evaluation of cancer drug response models in a fair setting
drhip 0.1.4 doc dev MIT X DRHIP - Data Reduction for HyPhy with Inference Processing
drive 0.3.9 Apache XX Google Drive client for the commandline
drop 1.5.0 doc dev MIT X Detection of RNA Outlier Pipeline
dropbox 5.2.1 https://raw.git XX 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 XXX 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 3.0 LGPL XXX Tools for BED, FASTA, FASTQ, GAF, GFA1/2, GFF3, PAF, SAM, and VCF files
dsk 2.3.3 dev AGPL-3.0-or-later XX DSK is a k-mer counter for reads or genomes.
dsrc 2015.06.04 dev GPL-2.0-or-later XX High-performance compression of sequencing reads stored in FASTQ format.
dudes 0.10.0 MIT XXX 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.
duphist 1.0.9 dev MIT X DupHIST: A toolkit for duplication history inference via...
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 XX Tool designed to improve precision and recall of long-read alignments...
dupre 0.1 MIT XXX Duplicate rate estimation using linear programming and the...
dupsifter 1.3.0.20241113 dev MIT XX 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 dev GPL-2.0-or-later XX Whole Genome Simulator for Next-Generation Sequencing.
dx-cwl 0.1.0a20180905 Apache XXX Import and run CWL workflows on DNAnexus
dxpy 0.400.1 doc dev Apache-2.0 XXX DNAnexus Platform API bindings for Python
dxua 1.5.31 Apache XX command-line tool for uploading files to the DNAnexus Platform
dysgu 1.8.7 doc dev MIT XX 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 XXX Eagle is a webtool for genome variants and snp analysis
eagle2 2.4.1 GPL-3.0-or-later XX The Eagle software estimates haplotype phase either within a genotyped...
earlgrey 6.3.6 doc dev OSL-2.1 XX Earl Grey: A fully automated TE curation and annotation pipeline.
easel 0.49 dev BSD XX Easel is an ANSI C code library for computational analysis of...
eastr 1.1.2 doc dev MIT XX Tool for emending alignments of spuriously spliced transcript reads.
easypqp 0.1.54 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 XX EBFilter (Empirical Bayesian Mutation Filtering)
ebi-eva-common-pyutils 0.8.0 dev Apache-2.0 X EBI EVA - Common Python Utilities.
ebisearch 0.0.3 MIT XXX A Python library for interacting with EBI Search's API
ebolaseq 0.1.6 doc dev GPL-3.0-or-later X Tool for downloading and analyzing Ebola virus sequences.
echidna 1.0.3 MIT X Mapping genotype to phenotype through joint probabilistic modeling of...
ecmwfapi 1.4.1 Apache XXX ECMWF API is a set of services developed by ECMWF http://www.ecmwf.int...
ecopcr 0.5.0 CeCill XX ecoPCR is an electronic PCR software that helps you estimate Barcode...
ecoprimers 1.0 CeCill XX ecoPrimers is a software that finds primers from a set of sequence.
ecopy 0.1.2.2 MIT XX EcoPy: Ecological Data Analysis in Python
ectyper 2.0.0 Apache XXX ECtyper is a python program for serotyping E. coli genomes
edd 1.1.19 MIT XX Enriched domain detector for ChIP-seq data
eden 2.0 MIT XX The Explicit Decomposition with Neighborhoods (EDeN) is a...
edena 3.131028 GPL-3.0-or-later XX De novo short reads assembler.
edentity 1.5.2 doc Apache-2.0 X eDentity metabarcoding pipeline
edittag 1.1 http://www.open XXX Design and check sets of edit metric sequence tags.
edlib 1.2.3 MIT XX 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 XX 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 3.3.5 doc dev BSD-3-Clause X EGAP pipeline for genome assembly and QC analysis
egglib 3.5.2 doc dev GPL-3.0-or-later XX Evolutionary Genetics and Genomics Library. EggLib is a C++/Python...
eggnog-mapper 2.1.13 doc dev AGPL-3.0-only XXX Fast genome-wide functional annotation through orthology assignment.
eider 0.1 Apache-2.0 X Command line bioinformatics tools for DuckDB.
eigen 3.2 MPL2 XX None
eigensoft 8.0.0 Custom XX 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 1.22.0 doc dev MIT X Perform Legionella pneumophila Sequence Based Typing (SBT) from short...
elastic-blast 1.5.0 dev Public X ElasticBLAST is a cloud-based tool to perform your BLAST searches...
elasticluster 0.1.3bcbio GPL XX 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 dev AGPL-3.0-only XXX elPrep is a high-performance tool for preparing .sam/.bam files for...
ema 0.7.0 doc dev MIT XX Fast & accurate alignment of barcoded short-reads.
embassy-phylip 3.69.650 GPL XX embassy/emboss wrappers for phylip functions
embl-api-validator 1.1.180 Apache-2-0 XXX ENA flat file validator for submission
emblmygff3 2.4 doc dev GPL-3.0-or-later X An efficient way to convert gff3 annotation files into EMBL format...
emboss 6.6.0 doc GPL-2.0-only XX The European Molecular Biology Open Software Suite.
emerald 1.2.1 AGPL-3.0 XX 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 XX 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 XX 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 3.5.5 MIT X Emu is a relative abundance estimator for 16s genomic data.
emu-pca 1.5.0 dev GPL-3.0-only XX EM-PCA for Ultra-low Coverage Sequencing Data.
emvc-2 1.0 dev MIT XX 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 0.9.0 MIT X Command Line Interface to upload data to the European Nucleotide Archive
ena-webin-cli 9.0.1 Apache-2.0 X Data submissions to ENA can be made using the Webin command line...
enabrowsertools 1.7.2 dev Apache-2.0 X enaBrowserTools is a set of scripts that interface with the ENA web...
enano 1.0 MIT XX ENANO is a FASTQ compression tool especially designed for nanopore...
enasearch 0.2.2 MIT XXX A Python library for interacting with ENA's API
encode-blacklist 2.0 GPL3 XX 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 1.4 dev MIT X endorS.py calculates endogenous DNA from samtools flagstat files and...
enhancedsppider 0.2.2 dev MIT X Enhanced sppIDer for species identification from sequencing data
enhjoerning 2.4.0 doc dev MIT XX A tool for computing statistics on short read alignments.
enrichm 0.6.6 dev GPL-3.0-or-later X EnrichM is a toolbox for comparing the functional composition of...
ensembl-genomio 1.6.2 doc dev Apache-2.0 X Ensembl GenomIO - tools to convert basic genomic data into Ensembl...
ensembl-py 3.0.1 doc dev Apache-2.0 X Ensembl Python base library
ensembl-utils 0.8.0 doc dev Apache-2.0 X Ensembl Python general-purpose utils
ensembl-vep 115.2 doc dev Apache-2.0 XX Ensembl Variant Effect Predictor
ensemblcov 0.1.0 dev MIT X Parallel threaded variant linker.
entrez-direct 24.0 doc Public XXX 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 0.1.3 doc GPL-3.0-only X Tool for training model and classifying reads from environmental ONT...
enzbert 1.1 AGPL-3 X Run EnzBert model that predicts the functional annotation of enzymes...
enzymm 0.3.1 doc dev MIT X Detect catalytic enzyme residues in protein structures by matching a...
eoulsan 2.5 dev LGPL XX A pipeline and a framework for NGS analysis (RNA-Seq and Chip-Seq)
epa-ng 0.3.8 GNU XX Massively parallel phylogenetic placement of genetic sequences
ephemeris 0.10.11 doc dev Academic XXX Ephemeris is an opinionated library and set of scripts for managing the...
epic 0.2.12 GNU XXX Chip-Seq broad peak/domain finder.
epic2 0.0.54 MIT X Ultraperformant Chip-Seq broad domain finder based on SICER.
epicore 0.1.7 dev MIT X Compute core epitopes from multiple overlapping peptides.
epicseg 1.0 GPL-3 XX EpiCSeg (Epigenome Count-based Segmentation) is a software for...
epik 0.2.0 MIT XX EPIK is a tool for fast alignement-free phylogenetic placements.
epimetheus-py 0.7.7 dev MIT XX CLI tool for fast lookup in pileup for motif methylation.
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 XX 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 XX Package to detect eQTLs jointly in multiple subgroups (e.g. tissues)...
equirep 1.0.0 BSD-3-Clause XX 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 XX EricScript is a computational framework for the discovery of gene...
erne 2.1.1 GPLv3 XX ERNE - Extended Randomized Numerical alignEr
ervdetective 1.0.9 LGPL-2.1-or-later X An efficient pipeline for identification and annotation of endogenous...
ervmancer 0.0.4 MIT X Quantifies HERV short read RNA sequencing expression data
escher 1.7.3 MIT X Escher: A Web Application for Building, Sharing, and Embedding...
esimsa 1.0 GPL3 XX Simple deconvolution of electrospray ionization peak lists
eskrim 1.0.9 dev 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_mpich_4_3_1 8.8.1 ESMF X ESMF - Earth System Modeling Framework
esme_esmf_mvapich_4_0 8.8.1 ESMF X ESMF - Earth System Modeling Framework
esme_esmf_mvapich_4_0_ofi 8.8.1 ESMF X ESMF - Earth System Modeling Framework
esme_esmf_mvapich_4_0_ucx 8.8.1 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_esmf_psmpi_5_10_0 8.8.0 ESMF X ESMF - Earth System Modeling Framework
esme_esmf_psmpi_5_12_1 8.9.0 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_mpich_4_3_1 1.14.6 BSD-3-Clause X HDF5 - Hierarchical Data Format 5
esme_hdf5_mvapich_4_0 1.14.6 BSD-3-Clause X HDF5 - Hierarchical Data Format 5
esme_hdf5_mvapich_4_0_ofi 1.14.6 BSD-3-Clause X HDF5 - Hierarchical Data Format 5
esme_hdf5_mvapich_4_0_ucx 1.14.6 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_hdf5_psmpi_5_10_0 1.14.5 BSD-3-Clause X HDF5 - Hierarchical Data Format 5
esme_hdf5_psmpi_5_12_1 1.14.6 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_mpich_4_3_1 1.0.2 BSD-3-Clause X Earth System Modelling Environment (ESME) - A bundle for scientific...
esme_mvapich_4_0 1.0.2 BSD-3-Clause X Earth System Modelling Environment (ESME) - A bundle for scientific...
esme_mvapich_4_0_ofi 1.0.2 BSD-3-Clause X Earth System Modelling Environment (ESME) - A bundle for scientific...
esme_mvapich_4_0_ucx 1.0.2 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_mpich_4_3_1 4.9.3 MIT NetCDF-C - netCDF interface for C
esme_netcdf-c_mvapich_4_0 4.9.3 MIT X NetCDF-C - netCDF interface for C
esme_netcdf-c_mvapich_4_0_ofi 4.9.3 MIT X NetCDF-C - netCDF interface for C
esme_netcdf-c_mvapich_4_0_ucx 4.9.3 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-c_psmpi_5_10_0 4.9.2 MIT X NetCDF-C - netCDF interface for C
esme_netcdf-c_psmpi_5_12_1 4.9.3 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_mpich_4_3_1 4.6.2 MIT X NetCDF-Fortran - netCDF interface for Fortran
esme_netcdf-fortran_mvapich_4_0 4.6.2 MIT X NetCDF-Fortran - netCDF interface for Fortran
esme_netcdf-fortran_mvapich_4_0_ofi 4.6.2 MIT X NetCDF-Fortran - netCDF interface for Fortran
esme_netcdf-fortran_mvapich_4_0_ucx 4.6.2 MIT 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_netcdf-fortran_psmpi_5_10_0 4.6.1 MIT X NetCDF-Fortran - netCDF interface for Fortran
esme_netcdf-fortran_psmpi_5_12_1 4.6.2 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_mpich_4_3_1 7.5.1 BSD-3-Clause X OSU Micro Benchmarks
esme_omb_mvapich_4_0 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_omb_psmpi_5_10_0 7.5 BSD-3-Clause X OSU Micro Benchmarks
esme_omb_psmpi_5_12_1 7.5.1 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_mpich_4_3_1 2.6.6 Apache-2.0 X ParallelIO - High-level parallel I/O library
esme_pio_mvapich_4_0 2.6.6 Apache-2.0 X ParallelIO - High-level parallel I/O library
esme_pio_mvapich_4_0_ofi 2.6.6 Apache-2.0 X ParallelIO - High-level parallel I/O library
esme_pio_mvapich_4_0_ucx 2.6.6 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_pio_psmpi_5_10_0 2.6.5 Apache-2.0 X ParallelIO - High-level parallel I/O library
esme_pio_psmpi_5_12_1 2.6.6 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_mpich_4_3_1 1.14.1 PnetCDF X PnetCDF - Parallel netCDF
esme_pnetcdf_mvapich_4_0 1.14.1 PnetCDF X PnetCDF - Parallel netCDF
esme_pnetcdf_mvapich_4_0_ofi 1.14.1 PnetCDF X PnetCDF - Parallel netCDF
esme_pnetcdf_mvapich_4_0_ucx 1.14.1 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
esme_pnetcdf_psmpi_5_10_0 1.14.0 PnetCDF X PnetCDF - Parallel netCDF
esme_pnetcdf_psmpi_5_12_1 1.14.1 PnetCDF X PnetCDF - Parallel netCDF
esme_psmpi_5_10_0 1.0.1 BSD-3-Clause X Earth System Modelling Environment (ESME) - A bundle for scientific...
esme_psmpi_5_12_1 1.0.2 BSD-3-Clause X Earth System Modelling Environment (ESME) - A bundle for scientific...
esmf_mpich 8.8.0 ESMF X ESMF - Earth System Modeling Framework
esmre 0.3.1 GNU XX Regular expression accelerator
espresso 1.6.0 dev Free XX ESPRESSO (Error Statistics PRomoted Evaluator of Splice Site Options)...
est-sfs 2.04 Free XX est-sfs ( Keightley and Jackson, 2018) is a stand-alone implementation...
estmapper 2008 dev GPL-3.0-or-later XX 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 1.1.2 dev MIT X Read mapping pipeline for detection and measurement of human and animal...
eta 0.9.7 BSD XXX ETA Progress bar for command-line utilities
ete2 2.3.10 GPLv3 XXX Phylogenetic tree analyses and exploration
ete3 3.1.1 GPLv3 XXX A Python framework for the analysis and visualization of trees
eternafold 1.3.1 doc dev BSD-3-Clause XX 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 1.2.4 MIT XX 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 2.1.2 doc dev MIT X Easy taxonomic annotation for eukaryotic microbes.
eva-sub-cli 0.5.1 doc dev 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...
eviann 2.0.5 doc dev GPL-3.0-or-later X Evidence-based eukaryotic genome annotation software.
evidencemodeler 2.1.0 dev BSD-3-Clause XXX 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 0.1.27 doc dev AGPL-3.0-or-later X Tools for evolutionary forecasting.
examine 1.0.1 dev GPL-2.0 X A graphical application to visually analyze network modules.
excludonfinder 0.2.0 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 XX Exonerate - A generic tool for pairwise sequence comparison / alignment.
expam 1.4.0.7 doc dev BSD-3-Clause XX Metagenomic profiling using a reference phylogeny
expansionhunter 5.0.0 dev Apache-2.0 XX A tool for estimating repeat sizes.
expansionhunterdenovo 0.9.0 doc dev Apache-2.0 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 XXX Conversion software tool for annotating tree with GraPhlAn
express 1.5.1 Artistic XX 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 XX 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 XX extract_fullseq is part of BMTagger aka Best Match Tagger, for removing...
extract_genome_region 0.0.3 BSD XXX 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 XX PacBio utility to extract HiFi reads from CCS reads
ezaai 1.2.4 doc dev GPL-3.0-or-later X EzAAI is a suite of workflows for improved AAI calculation performance...
ezcharts 0.15.2 doc dev BSD-4-Clause X eCharts plotting API.
ezclermont 0.7.0 dev MIT X easily determine the Clermont 2013 E coli phylotype
ezfastq 0.2 dev BSD X Organize FASTQs by sample for analysis
ezomero 3.2.2 GPL-2.0-only X A module with convenience functions for writing Python code that...
f5c 1.6 MIT XX An optimised re-implementation of the call-methylation and eventalign...
fa-lint 1.2.0 dev MIT XX A Fasta linter/validator
fadapa 0.3.1 uncopyrighted XXX FAstqc DAta PArser - A minimal parser to parse FastQC output data
fade 0.6.0 MIT XX fade is a D program that provides fast identification and removal of...
fairease-source 1.4.6 dev CC-BY-NC-4.0 X SOURCE: Sea Observations Utility for Reprocessing, Calibration and Evaluation.
fairy 0.5.8 doc dev MIT XX fairy calculates all-to-all approximate coverage for multi-sample...
falco 1.2.5 doc dev GPL-3.0-only XX falco is a drop-in C++ implementation of FastQC to assess the quality...
famsa 2.4.1 dev GPL-3.0-or-later XX Algorithm for large-scale multiple sequence alignments.
famseq 1.0.3 doc GPL-3.0-or-later XX FamSeq is a computational tool for calculating probability of variants...
famus 0.1.2 doc dev MIT X Functional Annotation Method Using Siamese neural networks (FAMUS)
fanc 0.9.23b doc dev ACADEMIC XX Framework for the ANalysis of C-data.
fann 2.2.0 LGPL-2.1 XX Fast Artificial Neural Network Library
faqcs 2.12 dev BSD-3-Clause XX Quality Control of Next Generation Sequencing Data.
fargene 0.1 MIT XXX Fragmented Antibiotic Resistance Gene iENntifiEr takes either...
fast-edit-distance 1.2.2 doc dev MIT XX A implementation of edit distance with improved runtime.
fast-fasta-compressor 1.0 dev GPL-3.0-or-later XX A tool for compressing FASTA files
fast2q 2.8.1 dev GPL-3.0-only X A Python3 program that counts sequence occurrences in FASTQ files.
fast5 0.6.5 MIT XXX A C++ header-only library for reading Oxford Nanopore Fast5 files.
fast5-research 1.2.22 Mozilla XXX ONT Research fast5 read/write package
fast5seek 0.1.1 MIT XXX Get paths for fast5 files contained in BAM, SAM, or fastq.
fasta-splitter 0.2.6 zlib/libpng XXX Divides a large FASTA file into a set of smaller, approximately equally...
fasta3 36.3.8 doc dev Apache XX The FASTA package - protein and DNA sequence similarity searching and...
fasta_ushuffle 0.2 dev Custom XX A wrapper for uShuffle.
fasta_windows 0.2.4 MIT XX 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 XX fastahack --- *fast* FASTA file indexing, subsequence and sequence extraction
fastaindex 0.11c GPLv3 XXX FastA indexing and sequence retrival.
fastalite 0.4.1 MIT X Simplest possible fasta parser
fastan 0.5 dev Custom XX Fast Tandem Repeat Finder.
fastani 1.34 doc dev Apache-2.0 XX 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...
fastcov 0.1.3 MIT X This package installs fastcov and all it's dependencies. fastcov is...
fastdtw 0.2.0 MIT XXX Dynamic Time Warping (DTW) algorithm with an O(N) time and memory complexity
fastdup 1.0.0 dev MIT XX A Scalable Duplicate Marking Tool using Speculation-and-Test Mechanism.
fasten 0.9.0 MIT XX Perform random operations on fastq files, using unix streaming. Secure...
fastg2protlib 1.0.2 MIT X FASTG sequences to a protein library.
fastga 1.3.1 dev BSD-like XX FastGA - A Fast Genome Aligner.
fastindep 1.0.0 MIT XX A fast random heuristic algorithm for identifying large sets of...
fastk 1.1.0 dev https://github. XX 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 0.4.2.1 doc dev MIT XX fastlin, ultra-fast MTBC lineage typing.
fastlmm 0.2.32 Apache XX Fast GWAS
fastmd5 1.0.0 doc dev MIT XX Fast command-line tool to compute and verify MD5 checksums
fastme 2.1.6.3 doc dev GPL-3.0-only XX 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 0.0.19 dev 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 0.5.1 dev MPL-2.0 X FastOMA - a package to infer orthology information among proteomes.
fastool 0.1.4 MIT XX 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 1.0.1 doc dev MIT XX A ultra-fast FASTQ preprocessor with full features...
fastphylo 1.0.3 MIT XX Fastphylo is software project containing the implementations of the...
fastplong 0.4.1 doc dev MIT XX Ultra-fast preprocessing and quality control for long-read sequencing data.
fastppm 1.1.1 MIT XX Fast Perfect Phylogeny Mixture Regression using Tree-Structured Dual...
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 XX Fast handling of FASTQ files
fastq-anonymous 1.0.1 MIT XXX Change the sequence of a fastq file to enable sharing of confidential...
fastq-count 0.1.0 MIT XX Simple fastq read and base counter for paired data.
fastq-dl 3.0.1 MIT X A tool to download FASTQs associated with Study, Experiment, or Run accessions.
fastq-filter 0.3.0 MIT XX A fast FASTQ filter program.
fastq-groupmerge 1.0.2 dev GPL-3.0-only X A tool for merging reads based on metadata groups.
fastq-join 1.3.1 MIT XX Similar to audy's stitch program, but in C, more efficient and...
fastq-multx 1.4.2 MIT XX Demultiplexes a fastq. Capable of auto-determining barcode id's...
fastq-pair 1.0 MIT XX fastq-pair: efficient synchronization of paired-end fastq files
fastq-scan 1.0.1 MIT XX FASTQ summary statistics in JSON format
fastq-screen 0.16.0 dev GPL-3.0-or-later XXX FastQ Screen allows you to screen a library of sequences in FastQ...
fastq-tools 0.8.3 dev MIT XX A collection of fastq manipulation scripts written in C for speed.
fastq_utils 0.25.3 doc dev GPL-3.0-only XX Validation and manipulation of FASTQ files, scRNA-seq barcode...
fastqc 0.12.1 GPL XXX A quality control tool for high throughput sequence data.
fastqc-rs 0.3.4 dev MIT XX A fast quality control tool for FASTQ files written in rust.
fastqe 0.5.2 BSD-3-Clause XXX A emoji based bioinformatics command line tool.
fastqmetrics 0.1.0 MIT XXX Extract metrics from a fastq file, streaming
fastqpuri 1.0.7 GPL3.0 XX fastq quality assessment and filtering tool
fastqsplitter 1.2.0 doc MIT XXX Splits FASTQ files evenly.
fastqtk 0.28 MIT XX fastqtk is a fast and lightweight tool for...
fastquast 1.0.2 doc MIT X Fast and simple Quality Assessment Tool for Large Genomes
fastreer 2.1.2 dev GPL-3.0-only X Phylogenetic, distance, and tree-building utilities for VCF and FASTA files.
fastremap-bio 1.0.0 MIT X FastRemap, a C++ tool for quickly remapping reads between genome...
fastsimbac 1.0.1_bd3ad13d8f79 GPL XX Models bacterial recombination
fastsimcoal2 27093 GPL X fast sequential markov coalescent simulation of genomic data under...
fastspar 1.0.0 GPLv3 XX Rapid and scalable correlation estimation for compositional data
faststructure 1.0 dev MIT XX A variational framework for inferring population structure from SNP...
fasttree 2.2.0 doc dev GPL-2.0-or-later XX FastTree infers approximately-maximum-likelihood phylogenetic trees...
fastuniq 1.1 doc Creative XX FastUniq, A Fast De Novo Duplicates Removal Tool for Paired Short Reads.
fastutils 0.3 GPL-3.0 XX A light toolkit for parsing, manipulating and analysis of FASTA and FASTQ files
fastv 0.10.0 MIT XX 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 XX 'The FASTX-Toolkit is a collection of command line tools for...
fatslim_biobb 0.2.2 doc dev GPL-3.0-or-later XX FATSLiM is a software dedicated to the analysis of molecular dynamics...
favites_lite 1.0.3 dev GPL-3.0-or-later XX 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 XX 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 XXX FlExible Extraction of LncRNA
feems 2.0.1 doc dev MIT X Fast Estimation of Effective Migration Surfaces (FEEMS) + admixture (FEEMSmix)
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 XX A WGS de novo assembler based on the FMD-index for large genomes
fermi-lite 0.1 MIT XX Fermi-lite is a standalone C library as well as a command-line tool for...
fermi2 r204 dev Unknown XX Fermi2 focuses on the exploration of FMD-index as a graph.
fermikit 0.14.dev1 dev MIT XX FermiKit is a de novo assembly based variant calling pipeline for deep...
fetchmgs 2.1.2 GPL-3.0-only X FetchMGs extracts the 40 marker genes from genomes and metagenomes in...
ffgc 2.4.2 doc BSD X Family Free Genome Comparison (FFGC) workflow
ffindex 0.98 CC-BY-SA-3.0 XX 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 XXX FGAP: an automated gap closing tool
fgbio 3.1.1 MIT XXX A set of tools for working with genomic and high throughput sequencing...
fgbio-minimal 3.1.1 MIT X A set of tools for working with genomic and high throughput sequencing...
fgmp 1.0.3 MIT XXX FGMP: assessing fungal genome completeness and gene content.
fgpyo 1.4.0 doc dev MIT X Python bioinformatics and genomics library
fgsmk 0.1.2 dev MIT X Supporting functions for running Snakemake workflows.
fgsv 0.2.1 MIT X Tools to find evidence for structural variation.
fgwas 0.3.6 dev GPL2 XX fgwas is a command line tool for integrating functional genomic...
fibertools-rs 0.8.1 doc dev MIT XX Mitchell Vollger's rust tools for fiberseq data.
ficus 0.5 BSD-3-Clause XXX provides a context manager for matplotlib figures.
fido 1.0 doc dev MIT XX 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 XX 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 XX FileChunkIO represents a chunk of an OS-level file containing bytes data
filtlong 0.3.1 doc dev GPL-3.0-or-later XX Filtlong is a tool for filtering long reads. It can take a set of long...
finaletoolkit 0.11.0 dev MIT X Extract cfDNA fragmentation features from sequencing data.
find_circ 1.2 GPL-3 X Detect head-to-tail spliced (back-spliced) sequencing reads, indicative...
find_differential_primers 0.1.4 MIT XXX Scripts to aid the design of differential primers for diagnostic PCR.
finemap 1.4.2 Custom XX 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 XXX fineSTRUCTURE is a fast and powerful algorithm for identifying...
fingerprintscan 3_597 dev GPL XX Search against FingerPRINTScan with a protein query sequence to...
fings 1.7.1 Apache X Filters for Next Generation Sequencing
firecloud 0.16.38 doc dev BSD-3-Clause XXX API and CLI for Broad Institute's Firecloud workspace/workflow...
fisher 0.1.4 BSD XX Fast Fisher's Exact Test
fishplotpy 1.0.0 dev Apache-2.0 X A Python implementation for visualizing clonal evolution dynamics using...
fishtaco 1.0.5 BSD-3-Clause XXX 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 XXX A tool to fit data to many distributions and best one(s)
flagx 0.2.0 GPL-3.0-only X FLAG-X: FLow cytometry Automated Gating toolboX
flaimapper 3.0.0 GNU XXX FlaiMapper: Detecting small ncRNA derived fragments in small RNA-Seq data
flair 3.0.0b1 doc dev BSD-3-Clause X Correction, isoform definition, and alternative splicing analysis of...
flams 1.1.6 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 XXX Flapjack provides interactive visualizations of high-throughput genotyping data.
flash 1.2.11 GPLv3+ XX Merge mates from fragments that are shorter than twice the read length
flash2 2.2.00 dev GPL-3.0-or-later XX Merge paired-end reads from fragments that are shorter than twice the...
flashlfq 2.1.4 doc dev LGPL-3.0-only XXX Ultrafast label-free quantification algorithm for mass-spectrometry proteomics.
flask-admin 1.4.0 BSD XX Simple and extensible admin interface framework for Flask
flask-bootstrap 3.3.5.7 BSD XX An extension that includes Bootstrap in your project, without any...
flask-bower 1.3.0 GNU XX An extension to manage and serve your javascript assets with bower
flask-markdown 0.3 BSD XX Small extension to make using markdown easy
flask-nav 0.5 MIT XX Easily create navigation for Flask applications.
flask-potion 0.12.1 MIT XX Powerful REST API framework for Flask and SQLAlchemy
flexbar 3.5.0 doc dev BSD-3-Clause XX Flexible barcode and adapter removal.
flexi-formatter 1.0.1 MIT X Moving flexiplex barcode and UMI to bam tags
flexidot 2.0.2 doc dev LGPL-2.1-or-later X Flexible dotplotting of genomic sequences.
flexiformatter 1.0.6 MIT X Moving flexiplex barcode and UMI to bam tags
flexiplex 1.02.5 doc dev MIT XX flexiplex: the flexible demultiplexer
flexserv 1.0.2 Apache XX FlexServ protein structure conformational ensemble generation tools
flexsweep 1.3 doc dev 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 1.1.6 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 XX FLOCK - Flow Cytometry Clustering without K.
floco 1.0.1 MIT X Sequence-to-graph alignment based copy number calling using a network...
flopp 0.2.0 MIT XX flopp is a software package for single individual haplotype phasing of...
floria 0.0.2 dev MIT XX Floria is method for recovering strain-level haplotypes and clusters of...
flowcraft 1.4.1 doc dev GPL3 XXX A Nextflow pipeline assembler for genomics. Pick your modules. Assemble...
flumut 0.6.4 dev AGPL-3.0-or-later X A tool to search for molecular markers with potential impact on the...
flumutdb 6.5 dev AGPL-3.0-or-later X Utility module for FluMut database.
flux-simulator 1.2.1 BSD XXX Tool for modeling RNA-Seq experiments in silico
flye 2.9.6 doc dev BSD-3-Clause XX A fast and accurate de novo assembler for single molecule sequencing...
fmlrc 1.0.0 MIT XX A long-read error correction tool using the multi-string Burrows...
fmlrc2 0.1.8 doc dev MIT XX A rust implementation of fmlrc with faster run times.
fmsi 0.4.0 doc dev MIT XX 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 0.1.0 GPL-3.0-or-later XX Foldcomp: a library and format for compressing and indexing large...
folddisco 1.7514114 doc dev GPL-3.0-or-later XX Folddisco: fast indexing and search of discontinuous motifs in protein...
foldmason 4.dd3c235 GPL-3 XX Multiple Protein Structure Alignment at Scale with FoldMason
foldseek 10.941cd33 GPL-3 XX Foldseek: fast and accurate protein structure search
footprint 1.0.1 GPL-2.0-or-later XX 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 XXX RNA Graph Library
forked-path 0.2.3 Public XX An object oriented file path module
formulaic-contrasts 1.0.0 doc dev BSD-3-Clause X Build contrasts for models defined with formulaic
forwardgenomics 1.0 MIT X Forward Genomics is a framework to associate phenotypic differences...
fpa 0.5.1 MIT XX Filter Pairwise Alignment filter long read mapping information to save...
fpocketr 1.3.4 MIT X CLI tool to find, characterize, and visualize RNA-ligand binding pockets.
fq 0.12.0 MIT XX fq is a library to generate and validate FASTQ file pairs.
fqgrep 1.1.1 MIT XX Search a pair of fastq files for reads that match a given ref or alt sequence
fqtk 0.3.1 doc dev MIT XX A toolkit for working with FASTQ files.
fqtools 2.0 dev GPL-3.0-or-later XX An efficient FASTQ manipulation suite.
fqtrim 0.9.7 Artistic XX 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 XX 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 doc BSD XX FragGeneScan is an application for finding (fragmented) genes in short reads.
fragpipe 24.0 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 XX Computes FRC from SAM/BAM file and not from afg files
fred2 2.0.7 BSD XXX Python-based framework for computational immunomics.
freddie 0.4 MIT X Annotation-independent detection of splicing isoforms using RNA long-reads
freebayes 1.3.10 doc dev MIT XX Bayesian haplotype-based polymorphism discovery and genotyping.
freyja 2.0.2 doc dev BSD-2-Clause XXX Freyja recovers relative lineage abundances from mixed SARS-CoV-2...
frogs 5.0.2 GNU XX FROGS is a workflow designed to metabarcoding sequence analysis
fsa 1.15.9 GPL-3 XX FSA is a probabilistic multiple sequence alignment algorithm which uses...
fseq 1.84 GPL XX F-Seq: A feature density estimator for high-throughput sequence tags
fsm-lite 1.0 GPL-3 XX Frequency-based String Mining (lite)
fsnviz 0.3.0 BSD XXX Tool for plotting gene fusion events detected by various tools using Circos.
fstic 1.0.0 GPL-3.0-only XX High-performance Rust tool for computing multiple genetic distance...
ftputil 3.2 BSD XX High-level FTP client library (virtual file system and more)
fuc 0.38.0 doc dev MIT X Frequently used commands in bioinformatics
fufihla 0.2.3 MIT X HLA typing pipeline for long reads (FuFiHLA) with a location-aware CLI.
fuma 4.0.0 GNU XXX FuMa: reporting overlap in RNA-seq detected fusion genes
funannotate 1.8.17 doc dev BSD-2-Clause XXX funannotate: eukaryotic genome annotation pipeline.
funcannot v2.8 GPLv3 XX Annotates cDNA, protein, mutation type, and other funcational changes...
funnel 0.9.0 MIT XX 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 XX Simple ctypes bindings for FUSE
fusion-filter 0.5.0 BSD-3-Clause XXX FusionFilter provides a common fusion-finding, filtering, and...
fusion-inspector 2.10.0 BSD-3-Clause XX FusionInspector is a component of the Trinity Cancer Transcriptome...
fusion-report 4.0.1 dev GPL-3.0-only X Tool for parsing outputs from fusion detection tools. Part of the...
fusioncatcher 1.33 dev GPL-3.0 XXX Finder of Somatic Fusion Genes in RNA-seq data.
fusioncatcher-seqtk 1.2 dev MIT XX This is modified Seqtk version required for FusionCatcher.
fwdpp 0.9.2 doc dev GPL-3.0-or-later XX A C++ template library for forward-time population genetic simulation.
fwdpy 0.0.4pre1 GNU XX Forward-time population genetic simulation in Python.
fwdpy11 0.24.5 doc dev GPL-3.0-or-later XX Forward-time population genetic simulation in Python.
fxtract 2.4 MIT XX Extract sequences from a fastx file given a subsequence or identifier.
ga4ghmongo 0.0.1.2 MIT XXX 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 XX A Genetic Algorithm Guided Formation of Spaced Dyads Coupled with an EM...
gadma 2.0.3 doc dev GNU XXX Genetic Algorithm for Demographic Inference
gafpack 0.1.3 dev MIT XX Convert alignments to pangenome variation graphs to coverage maps
gaftools 1.3.0 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 doc dev GPL-3.0-only XX 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 25.0.4 doc dev AFL-3.0 X The Galaxy models, datatype framework, and datatype implementations.
galaxy-files 25.1.0 doc dev Apache-2.0 X The Galaxy file sources framework and default plugins.
galaxy-files-full 25.0.4 doc dev Apache-2.0 X The Galaxy file sources framework and default plugins.
galaxy-ie-helpers 0.2.7 MIT XXX Helper scripts to work with Galaxy's Interactive Environments
galaxy-job-config-init 0.1.3 dev MIT X Galaxy configuration.
galaxy-job-execution 25.0.4 doc dev AFL-3.0 X Galaxy job execution runtime utilities.
galaxy-lib 19.5.2 doc dev Academic XXX Subset of Galaxy (http://galaxyproject.org/) core code base designed to...
galaxy-ml 0.10.0 MIT XX APIs for Galaxy machine learning tools
galaxy-objectstore 25.0.4 doc dev Apache-2.0 X The Galaxy object store framework and default implementations.
galaxy-ops 1.1.0 Academic XXX Galaxy interval operations
galaxy-parsec 1.16.0 MIT XXX Command-line utilities to assist in interacting with Galaxy servers...
galaxy-schema 25.0.4 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 XXX 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 XXX Sequence Utilities from the Galaxy project
galaxyxml 0.5.5 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 XX Tool for rapid taxonomic identification of microbial pathogens
gambitcore 0.0.2 doc dev LGPL-3.0-or-later XX 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-2.0 X Tool for Gene Allele Mutation Microbial Assessment.
gangstr 2.5.0 dev GPL-3.0-or-later XX GangSTR is a tool for genome-wide profiling tandem repeats from short reads.
ganon 2.1.1 MIT X ganon2 classifies genomic sequences against large sets of references...
gap2seq 3.1.1a doc dev GPL-3.0-or-later XX 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 25.8.12 dev BSD-2-Clause X gapmm2: gapped alignment using minimap2.
gappa 0.9.0 doc dev GPL-3.0-only XX 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 1.1.4 dev GPL-3.0-only XX Tool for simulating ancient DNA datasets.
gargammel-slim 1.1.2 GPL-3.0-only XX Tool for simulating ancient DNA datasets
garnet 0.4.5 MIT XX 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 XX Genomic Association Tester
gatb 1.4.2 AGPL XX The Genome Analysis Toolbox with de-Bruijn graph
gather 1.0.1 MIT X Assembly of heavy and light chain BCRs using De Bruijn graphs.
gatk 3.8 BSD XXX The full Genome Analysis Toolkit (GATK) framework, v3
gatk-framework 3.6.24 MIT XXX The core MIT-licensed Genome Analysis Toolkit (GATK) framework, free...
gatk4 4.6.2.0 dev BSD-3-Clause XXX Genome Analysis Toolkit (GATK4)
gatk4-spark 4.6.2.0 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 0.3.8 doc dev MIT XX A Python interface to gb-io, a fast GenBank parser and serializer...
gb_taxonomy_tools 1.0.1 GPL-2.0-or-later XX These are four simple utilities which perform certain manipulations and...
gbdraw 0.8.0 dev MIT X A genome diagram generator for microbes and organelles.
gbintk 1.0.3 doc dev GPL-3.0-or-later XXX 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 XX Selection of conserved blocks from multiple alignments for their use in...
gbmunge 2018.07.06 MIT XX 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 doc dev GPL-3.0-or-later XX GCEN: an easy-to-use toolkit for Gene Co-Expression Network analysis...
gci 1.0 doc dev MIT X A program for assessing genome contiguity.
gclib 0.0.1 Artistic XX Genomic C libraries by Geo Pertea
gcluster 2.06 doc 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 XX Auth plugin allowing use the use of OAuth 2.0 credentials for Google...
gcta 1.94.1 GPL-3.0-only XX GCTA (Genome-wide Complex Trait Analysis) estimates the proportion of...
gctb 2.0 doc MIT X GCTB (Genome-wide Complex Trait Bayesian ) is a software tool that...
gdal 1.9.2 Several X None
gdc 2.0 GPL2 XX Utility designed for compression of genome collections from the same species.
gdc-client 2.3 doc dev Apache-2.0 XXX GDC Data Transfer Tool
gdk-pixbuf 2.32.2 GNU XX 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 XXX Set of tools and pipelines to analyse GDSC data (cancerrxgene.org)
gecco 0.10.1 GPL-3.0-or-later X Gene Cluster prediction with Conditional Random Fields.
gecko 1.2 dev GPL-3.0-or-later 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 doc dev MIT XX Generic constraint development environment
gefast 2.0.1 AGPL XX 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 XX The GEM read mapper (v3).
gembs 3.5.5_IHEC GPL-3.0 XX gemBS is a bioinformatics pipeline designed for high throughput...
gemf_favites 1.0.3 dev GPL-3.0-or-later XX User-friendly epidemic simulations
gemini 0.30.2 MIT XX a lightweight db framework for disease and population genetics.
gemma 0.98.5 GPLv3 XX 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 1.38.5 doc dev GPL-3.0-only X gempipe is a tool for the reconstruction of strain-specific...
genbank 0.121 GPL-3.0-or-later XX 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 XX None
genblastg 1.39 GNU XX genBlast is a program suite, consisting of two programs: genBlastA and...
genclust 1.0 GNU XX A genetic algorithm for clustering gene expression data.
gencore 0.17.2 doc dev MIT XX Generate consensus reads to reduce sequencing noises and remove duplications.
gencove 4.2.0 doc dev Apache-2.0 X Gencove is a high-throughput, cost-effective platform for genome...
gencube 1.11.0 dev MIT X GenCube enables researchers to search for, download, retrieve metadata,...
gene-fetch 1.0.21 dev MIT X High-throughput NCBI Sequence Retrieval Tool
gene-trajectory-python 1.0.4 doc dev MIT X Compute gene trajectories
genedom 0.2.2 dev MIT X Genetic part standardization.
genefuse 0.8.0 dev MIT XX Gene fusion detection and visualization.
geneimpacts 0.3.7 MIT XXX prioritize effects of variant annotations from VEP, SnpEff, et al.
genenotebook 0.3.2 AGPL-3.0 XX A colleborative notebook for comparative genomics
genepender v2.6 GPLv3 XX Annotates overlapping BED-defined regions to variants in a VCF file....
genepop 4.8.4 doc dev CeCILL-2 XX 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 dev AGPL-3.0-only XX GeneRax: a parallel tool for species tree-aware maximum likelihood...
genericrepeatfinder 1.0.2 dev GPLv3 XX Generic Repeat Finder (GRF).
genesplicer 1.0 doc OSI XX 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 XX Generation of molecular formulas by high-resolution MS and MS/MS data.
genie 0.7.0 MIT XX A toolkit for working with next-generation sequencing data
genin2 2.1.5 dev AGPL-3.0-or-later X Genin2 is a lightining-fast bioinformatic tool to predict genotypes for...
genion 1.2.3 MIT XX Characterizing gene fusions using long transcriptomics reads
genmap 1.3.0 doc dev BSD-3-Clause XX Ultra-fast computation of genome mappability.
genmod 3.10.2 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 0.4.18 AGPL-3.0 XX 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 XXX Python interface to the GenoLogics LIMS (Laboratory Information...
genomad 1.11.2 doc dev BSD-4-Clause X Identification of mobile genetic elements.
genome-uploader 2.5.1 dev Apache-2.0 X Python script to upload bins and MAGs in fasta format to ENA (European...
genome2tree 1.1.0 doc dev Apache-2.0 X A pipeline to build phylogenetic trees from genome comparisons
genome_profiler 0.4.2 doc dev BSD-2-Clause-Patent X Prokaryotic genome and plasmid profiling pipeline.
genome_updater 0.7.0 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 dev BSD XX Fast, accurate and versatile k-mer based classification system.
genomedata 1.7.4 doc dev GPL-2.0-or-later XX Tools for accessing large amounts of genomic data.
genomelake 0.1.4 BSD XX Simple and efficient random access to genomic data for deep learning models.
genomepy 0.16.3 doc MIT XXX Install and use genomes & gene annotations the easy way!
genomescope2 2.1.0 Apache-2.0 X Reference-free profiling of polyploid genomes
genomestrip 2.00.1833 custom XXX Genome STRiP (Genome STRucture In Populations) is a suite of tools for...
genomesyn2 1.0.0 MIT X A Comparative Genomics Framework Integrating Synteny Visualization
genometester4 4.0 GPL3 XX 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 XX None
genometools-genometools 1.6.6 doc dev BSD XX 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 0.3.1 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 XXX A package to test common files in genomics (.vcf.gz, .bam)
genomicconsensus 2.3.3 BSD-3-Clause-Clear XXX 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 XXX 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...
genotypy 0.3.4 CeCiLL X Automatically detect genomic barcodes integrated into loci of interest...
genrich 0.6.1 MIT XX Detecting sites of genomic enrichment.
gentle 1.9.5.alpha1 dev GPL-2.0-or-later XX 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 XXX Download FASTQ files from GEO-NCBI and ENA with ease
geofetch 0.12.9 doc dev 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 XX GERP identifies constrained elements in multiple alignments by...
get_fasta_info 2.5.0 MIT XX get_FAST{A,Q}_info - Get fast info on fasta and fastq files
get_homologues 3.7.5 GPL-3.0-or-later XX A versatile software package for pan-genome analysis, including...
get_mnv 1.0.0 doc dev GPL-3.0-or-later XX 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 20250904 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 XX Coroutine-based network library
gfa1 0.53.alpha GPL3 XX gfa1 toolkit
gfaffix 0.2.1 dev MIT XX GFAffix identifies and collapses walk-preserving shared affixes in...
gfainject 0.2.0 dev MIT XX Inject alignment into pangenome graphs
gfapy 1.2.3 ISC XXX Library for handling data in the GFA1 and GFA2 formats
gfastats 1.3.11 MIT XX The swiss army knife for genome assembly
gfatools 0.5.5 doc dev MIT XX 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 XXX 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 XXX Submitting annotated genomes to EMBL is a very difficult and time...
gffcompare 0.12.10 doc dev Artistic XX 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 XX GFF/GTF utility providing format conversions, region filtering, FASTA...
gfftk 25.6.10 dev BSD-2-Clause X GFFtk: genome annotation GFF3 tool kit
gffutils 0.13 doc dev MIT XXX Work with GFF and GTF files in a flexible database framework
gfinisher 1.4 Unknown XX GFinisher is an application tools for refinement and finalization of...
gfmix 1.0.2 GNU XX 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 1.4.1 MIT XX A de Bruijn graph-based gene-caller and pangenome analysis tool
ggcat 2.0.0 doc dev MIT XX 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 XX 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 XX 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 XX An interpreter for the PostScript language and for PDF.
ghostx 1.3.7 BSD-2-Clause XX GHOSTX is a homology search tool which can detect remote homologues...
ghostz 1.0.2 doc BSD-2-Clause XX GHOSTZ is a highly efficient remote homologue detection tool.
gia 0.2.23 MIT XX Genomic Interval Arithmetic (gia)
giatools 0.7.1 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 0.18.1 doc dev MIT XX Motif prediction pipeline and various motif-related tools.
gimmemotifs-minimal 0.18.1 doc dev MIT XX 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 XX Glimmer is a system for finding genes in microbial DNA
glimmerhmm 3.0.4 doc Artistic XX GlimmerHMM is a gene finder based on a Generalized Hidden Markov Model (GHMM).
glimpse-bio 2.0.1 MIT XX 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 XX 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 XX GNU Linear Programming Kit
gmap 2025.07.31 doc dev Apache-2.0 XX Genomic mapping and alignment program for mRNA and EST sequences.
gmap-fusion 0.4.0 BSD-3-Clause XXX 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...
gmove 1.3 doc dev MIT XX Gmove is a gene prediction tool.
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 XX 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 XX gNALI (gene nonessentiality and loss-of-function identifier) is a tool...
gndiff 0.3.0 dev MIT XX 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 1.12.1 dev MIT XX 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 XX Retrieve files using HTTP, HTTPS and FTP
gnuplot 5.0.4 Gnuplot XX Gnuplot, plotting from command line
gnuplot-py 1.8 LGPL XXX 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 0.4.0 GPL-2.0 XX goalign is a set of command line tools to manipulate multiple alignments
goat 0.2.5 MIT XX Query metadata for any taxon across the tree of life.
goatools 1.2.3 BSD-2-Clause XXX Python scripts to find enrichment of GO terms
goblin 1.0.0 MIT X Generate trusted prOteins to supplement BacteriaL annotatIoN
gocr 0.52 doc GPL-3.0-or-later XX GOCR is an OCR (Optical Character Recognition) program.
godmd 1.7 dev Apache XX 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 XX 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 XX Linear-time de novo long read assembler, from the Bioinformatics Technology Lab
goleft 0.2.6 doc dev MIT XX goleft is a collection of bioinformatics tools distributed under MIT...
google-api-python-client 1.4.2 Apache XX None
google-cloud-sdk 166.0.0 Apache XX Command-line interface for Google Cloud Platform products and services
google-sparsehash 2.0.3 BSD XX None
gopeaks 1.0.0 dev MIT XX 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 2.0 doc GPL-3.0-or-later XX A search tool that finds shorter sequences (usually genes) in large...
gotree 0.5.1 doc dev GPL-2.0-or-later XX gotree is a set of command line tools to manipulate phylogenetic trees.
gottcha 1.0 GNU X Genomic Origin Through Taxonomic CHAllenge (GOTTCHA)
gottcha2 2.1.10 doc dev BSD-3-Clause X Genomic Origin Through Taxonomic CHAllenge (GOTTCHA) v2.
gpatch 0.3.8 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 XXX Functional enrichment analysis and more via the g:Profiler toolkit
gpsw 0.9.1 doc dev MIT X GPSW is a tool for analysing Global Protein Stability Profiling data.
gqlib 2.14.4 dev MIT X A gene quantification library.
gqt 1.1.3 MIT XX GQT is a genotype query interface.
grabix 0.1.8 dev MIT XX 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+ XXX GraftM is a pipeline used for identifying and classifying marker gene...
grampa 1.4.4 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 XXX Compute a 2D embedding of a data matrix given supervised class information.
graphaligner 1.0.20 doc dev MIT XX 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 XX The set of individual perl wrappers extracted from GraphClust pipeline
graphembed 0.1.8 dev MIT XX Efficient and Robust Graph/Network Embedding via High-Order Proximity...
graphicsmagick 1.3.26 MIT XX GraphicsMagick is the swiss army knife of image processing
graphlan 1.1.3 MIT XXX GraPhlAn is a software tool for producing high-quality circular...
graphlite 1.0.5 MIT XXX embedded graph datastore
graphmap 0.6.4 doc dev MIT XX 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 doc dev GPL-3.0-or-later 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 XX Grep searches one or more input files for lines containing a match to a...
grepq 1.5.4 doc dev MIT XX Quickly filter FASTQ files.
gretel 0.0.94 MIT XXX An algorithm for recovering haplotypes from metagenomes
gretl 0.1.1 dev MIT XX gretl is a tool to compute a range of statistics on variation graphs in...
grid 1.3 MIT XX Growth Rate Index (GRiD) measures bacterial growth rate from reference...
gridss 2.13.2 dev GPL-3.0-only XXX 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 XX GROMACS is a versatile package to perform molecular dynamics.
gromacs_mddb 2025.3 doc dev LGPL-2.1-or-later X GROMACS is a versatile package to perform molecular dynamics.
gromacs_mpi 2021.1 LGPL-2.1-or-later XX 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 dev LGPL-3.0-or-later XX Metagenomic binning suite.
groot 1.1.2 doc dev MIT XX A tool for resistome profiling of metagenomic samples.
group_humann2_uniref_abundances_to_go 1.3.0 Apache XX Group abundances of UniRef50 gene families obtained with HUMAnN2 to...
grz-check 0.2.1 doc dev MIT X grz-check is a tool for validating incoming files of Modellvorhaben...
grz-cli 1.5.1 MIT X Tool for validation, encryption and upload of MV submissions to GDCs.
grz-common 1.6.1 dev MIT X Common library for grz applications.
grz-db 1.2.0 MIT X SQL models for grz-cli and grz-watchdog
grz-pydantic-models 2.5.0 MIT X Pydantic models for the GRZ metadata schema
grzctl 1.4.0 doc dev MIT X Control CLI for GRZ administrators.
gs-tama 1.0.3 GPL-3.0 X Gene-Switch Transcriptome Annotation by Modular Algorithms
gsalign 1.0.22 dev MIT XX GSAlign: An ultra-fast sequence alignment tool
gsea 4.3.2 BSD-3-Clause X Gene Set Enrichment Analysis (GSEA)
gseapy 1.1.11 doc dev BSD-3-Clause XXX Gene Set Enrichment Analysis in Python.
gsearch 0.3.3 MIT XX gsearch is an ultra-fast and scalable microbial genome search program...
gsmap 1.73.6 doc dev MIT X gsMap (genetically informed spatial mapping of cells for complex traits).
gsort 0.1.5 doc dev MIT XX Sort genomic files according to a genomefile.
gtdb_to_taxdump 0.1.9 MIT X GTDB database utility scripts
gtdbtk 2.6.1 doc dev GPL-3.0-or-later XX A toolkit for assigning objective taxonomic classifications to...
gtf_to_genes 1.40 MIT XXX Fast GTF parser
gtfparse 2.5.0 dev Apache-2.0 XXX GTF Parsing
gtfsort 0.2.2 MIT XX 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 1.8.16 doc dev GPL-3.0-or-later XXX GToTree is a user-friendly workflow for phylogenomics.
gubbins 3.4.3 doc dev GPL-2.0-or-later XX 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 XX 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 XX GuideScan is a tool for genome-wide CRISPR guide RNA (gRNA) design and...
gum 2.0.2 dev MIT XX 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 1.0.10 doc dev https://github. XX Gustaf is a tool primarily designed for multi-split mapping of sequencing reads.
gvcf-regions 2016.06.23 GPLv3 XXX 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 dev MIT XX Coverage extractor from gVCF files.
gvcfgenotyper 2019.02.26 dev Apache-2.0 XX A utility for merging and genotyping Illumina-style GVCFs.
gvcftools 0.17.0 MIT XX a set of utilities to help create and analyze Genome VCF (gVCF) files.
gw 1.2.6 MIT XX View genomic sequencing data and vcf files
gwama 2.2.2 BSD-3-clause XX Genome-Wide Association Meta Analysis
gxf2bed 0.2.7 MIT XX Fastest GTF/GFF-to-BED converter chilling around
gxf2chrom 0.1.0 MIT XX Everything in .chrom from GTF/GFF
gxformat2 0.21.0 dev MIT XXX Galaxy Workflow Format 2 Descriptions.
gzrt 0.9.1 doc dev GPL-2.0-only XX 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 2025.5 Apache-2.0 XXX 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 XX Hail is Python-based data analysis tool for working with genomic data.
hairsplitter 1.9.10 GPL-3.0-or-later XX Recovers collapsed haplotypes from a draft assembly and long reads
hal2vg 1.1.8 doc dev MIT XX A tool for converting from hal to vg format, as well as other tools...
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 0.8.40 MIT XXX 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 1.1.9 doc dev LGPL-3.0-only 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 XXX 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 doc dev BSD-2-Clause XX Tools for haplotype assembly from sequence data.
hapflk 1.3.0 GPLv3 XX hapflk is a software implementing the hapFLK and FLK tests for the...
haphic 1.0.7 BSD X HapHiC: a fast, reference-independent, allele-aware scaffolding tool...
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 dev GPL-3.0-or-later XX 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 XX 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 XX Haplotype-based computational genetic mapping.
haplotaglr 1.1.13 doc dev 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 XX 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 dev GPL-3.0-or-later XX 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 0.6.2 doc dev MIT X Ancestry and haplotype aware simulation of genotypes and phenotypes for...
hardklor 2.3.2 dev Apache-2.0 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 3.1 doc dev GPL-3.0-or-later XX 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 1.3 dev Custom; XX 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 XX 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 XXX 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 XXX hclust2 is a handy tool for plotting heat-maps
hcluster_sg 0.5.1 dev GPL-2.0-or-later XX A tool for hierarchically clustering on a sparse graph.
hdf5_mpich 1.14.5 BSD-3-Clause X HDF5 - Hierarchical Data Format 5
hdmi 1.0.0 MIT X HDMI: HGT detection from MAGs in individuals
heasoft 6.35.2 doc Clear X NASA High Energy Astrophysics Software (HEAsoft)
hecatomb 1.3.4 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 1.3.1 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 XXX A collection of bioinformatics-related helper functions
hera 1.1 MIT XX hera is a bioinformatics tool that helps analyze RNA-seq data,...
hesslab-gambit 0.5.1 doc AGPL-3.0-or-later XX 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 10.1.0 doc dev MIT XXX Classes for Mercurial and Git repositories.
hgvs 1.5.6 doc dev Apache-2.0 X HGVS Parser, Formatter, Mapper, and Validator.
hhsuite 3.3.0 doc dev GPL-3.0-or-later XX HH-suite3 for fast remote homology detection and deep protein annotation.
hi-corrector 1.2 dev BSD-3-Clause XX Remove biases from chromatin contact matrices generated by genome-wide...
hic-straw 1.3.1 doc dev MIT XX Straw bound with pybind11.
hic2cool 1.0.1 MIT XXX 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 1.0.1 dev MIT X Statistical profiling based tool for contact data (Hi-C, ChIA-PET,...
hicbrowser 1.0 GPL3 XX A simple web browser to visualize Hi-C and other genomic tracks...
hicexplorer 3.7.6 doc dev GPL-3.0-or-later XXX Set of programs to process, analyze and visualize Hi-C and capture Hi-C data
hichipper 0.7.7 BSD XXX 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 2.2.0 doc dev MIT XX Blazing fast toolkit to work with .hic and .cool files
hictkpy 1.4.0 doc dev MIT XX Python bindings for hictk: read and write .cool and .hic files directly...
hicup 0.9.2 GPLv3 XXX A tool for mapping and performing quality control on Hi-C data
hiddendomains 3.1 GNU XXX hiddenDomains is a suite of programs used to identify significant...
hifi_trimmer 2.1.0 MIT X hifi_trimmer is a tool for filtering and trimming extraneous adapter...
hifiadapterfilt 3.0.0 dev GPL-3.0-or-later X Convert .bam to .fastq and remove reads with remnant PacBio HiFi...
hifiasm 0.25.0 doc dev MIT XX Haplotype-resolved assembler for accurate Hifi reads.
hifiasm_meta hamtv0.3.5 dev MIT XX 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 XX Python library for normalizing and analyzing HiC and 5C data
hiline 0.2.4 MIT XX 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 1.5.0 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...
hippunfold-dev 2.0.0 MIT X Meta-package that installs hippunfold with development dependencies.
hisat-3n 0.0.3 doc dev GPL-3.0 XX Graph-based alignment of next generation sequencing reads to a...
hisat2 2.2.1 doc dev GPL-3.0 XX Graph-based alignment of next generation sequencing reads to a...
hisat2-pipeline 1.1.1 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 0.4.5 doc dev GPL-3.0-or-later XX Utilities for processing high-throughput sequencing experiments.
hivtrace 1.5.0 dev MIT XXX 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 XXX HLAProfiler uses k-mer profiles to predict HLA types from paired-end...
hmftools-amber 4.2 GPL-3.0-only X Generates a tumor BAF file for use in PURPLE.
hmftools-bam-tools 1.5 GPL-3.0-only X Rapidly process BAMs for various tasks.
hmftools-bwa-plus 1.0.0 MIT XX bwa-mem with extensions for WiGiTS
hmftools-chord 2.1.2 GPL-3.0-only X Predict HRD using somatic mutations contexts
hmftools-cider 1.1 GPL-3.0-only X Determine a comprehensive list of CDR3 sequences for each of the IG and...
hmftools-cobalt 2.2 GPL-3.0-only X Calculate read-depth counts and GC ratios to use in PURPLE.
hmftools-cuppa 2.4 GPL-3.0-only X Predict tissue of origin for tumor samples from WGTS data.
hmftools-esvee 1.2 GPL-3.0-only X Structural variant caller specialised for breakend-breakpoint calling.
hmftools-gene-utils 1.3 GPL-3.0-only X Routines to generate resources files from Ensembl for use by many of...
hmftools-gripss 2.4 GPL-3.0-only X GRIPSS applies a set of filtering and post processing steps on GRIDSS...
hmftools-isofox 1.7.2 GPL-3.0-only X Isofox is a tool for counting fragment support for identifying and...
hmftools-lilac 1.7.3 GPL-3.0-only X LILAC is a WGS tool to determine HLA Class I types.
hmftools-linx 2.2 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 1.2.1 GPL-3.0-only X Identification of neoepitope and calculation of allele specific...
hmftools-orange 4.1.2 GNU X ORANGE summarizes the key outputs from all algorithms in the Hartwig suite.
hmftools-pave 1.8.2 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 4.3 GPL-3.0-only X PURPLE is a purity ploidy estimator for tumor samples.
hmftools-redux 1.2.2 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 4.2 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-teal 1.3.6 GPL-3.0-only X Characterises telomeres in tumor and normal samples from WGS data.
hmftools-virus-interpreter 3.7_beta GPL-3.0-only X Post-process VIRUSBreakend summary results.
hmftools-wisp 1.2 GPL-3.0-only X WISP performs tumor fraction estimate for longitudinal samples
hmmcopy 0.1.1 GPL-3.0-or-later XX C++ based programs for analyzing BAM files and preparing read counts --...
hmmer 3.4 doc BSD XX Biosequence analysis using profile hidden Markov models.
hmmer2 2.3.2 GPLv2 XX 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 1.5.1 MIT X Fusion analysis 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 XX Software for motif discovery and next generation sequencing analysis
homoeditdistance 0.0.1 MIT X An implementation of the homo-edit distance algorithm.
homopolish 0.4.2 dev GPL-3.0-or-later X High-quality Nanopore-only genome polisher.
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 2.0.2 doc dev MIT X Hostile: accurate host decontamination.
hotspot3d 1.8.2 GPLv3 XXX 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 doc dev MIT XX 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 XX 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 r350 dev MIT XX HTSbox is a fork of early HTSlib. It is a collection of small...
htseq 2.0.9 doc dev GPL-3.0-only XX 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 1.23 doc MIT XX 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 XX "HTStream is a quality control and processing pipeline for High...
httpretty 0.8.10 MIT XX HTTP client mock for Python
hubward 0.2.2 BSD XX None
hubward-all 0.2.1 The XX Meta-package for hubward including bedtools and UCSC tools
hulk 1.0.0 MIT XX Histosketching Using Little Kmers
humanfilt 1.0.0 MIT X WGS human-read filtering with auto-downloaded human references
humann 3.9 doc dev MIT X HUMAnN: The HMP Unified Metabolic Analysis Network, version 3
humann2 2.8.1 MIT XX HUMAnN2: The HMP Unified Metabolic Analysis Network 2
humid 1.0.37 doc MIT XX 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 2.3.3 doc dev GPL-3.0-or-later XXX 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 1.9 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 XX Strain aware assembly of low coverage metagenomes.
hymet 1.2.1 doc dev MIT X HYMET provides hybrid Mash+minimap2 metagenomic classification with...
hymet2 1.0.0 doc dev MIT X HYMET (Hybrid Metagenomic Tool) for taxonomic identification of...
hypercluster 0.1.13 doc dev MIT X A package for automatic clustering hyperparameter optmization
hyperloglog 0.1.5 doc dev LGPL-2.1-or-later X HyperLogLog cardinality counter.
hyphy 2.5.93 doc dev MIT XX An open-source software package for comparative sequence analysis using...
hyplas 1.0.2 dev MIT XX Hybrid long- short- plasmid assembler.
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 XX ibdmix: estimate introgression by IBD
ibdne 04Sep15.e78 Apache XXX The IBDNe program estimates the historical effective population size of...
ibdseq r1206 Apache XXX IBDseq is a software program for detecting segments of...
ibridges 2.0.1 doc dev MIT X Package for accessing data and metadata on iRods servers.
ice-cream 2.0.0 dev MIT X ICEcream: Integrative and Conjugative Elements Classification and...
iced 0.6.0 doc dev BSD-3-Clause XX 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 XXX iCLIPro is a Python package that can be used to control for systematic...
icount 2.0.0 MIT XXX 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 XX A collection of utilities for constructing complex geometries from...
idba 1.1.3 doc dev GPL2 XX 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 XX A Lexogen tool for demultiplexing and index error correcting fastq...
idr 2.0.4.2 GPLv2 XX The IDR (Irreproducible Discovery Rate) framework is a unified approach...
idr-py 0.4.2 doc dev GPL-2.0+ XXX 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 XX quick FCS datatype check
ig-checkflowtypes 1.0.0 BSD XX quick flow-related datatype for galaxy checks
ig-flowtools 2.0.2 BSD XXX set of tools for flow cytometry analysis
igblast 1.22.0 Public XX A tool for analyzing immunoglobulin (IG) and T cell receptor (TR) sequences
igblast-parser 0.0.4 dev MIT XX 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 XXX Analyze antibody repertoires and discover new V genes
igdtools 2.6 doc dev MIT XX Tools for converting VCF to IGD files and processing them.
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 XX IgPhyML is a program designed to build phylogenetic trees and test...
igua 0.1.0 dev GPL-3.0-or-later XX Iterative Gene clUster Analysis, a high-throughput method for gene...
igv 2.19.7 doc dev MIT XXX Integrative Genomics Viewer. Fast, efficient, scalable visualization...
igv-notebook 0.6.2 dev MIT X Package for embedding the igv.js genome visualization in IPython notebooks.
igv-reports 1.16.0 doc dev MIT X Creates self-contained html pages for visual variant review with IGV (igv.js).
igvtools 2.17.3 MIT XXX Command line tools for IGV
illumina-cleanup 1.0.0 MIT XXX Nextflow pipeline for pre-processing Illumina FASTQ files
illumina-interop 1.9.0 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 XX Analytics toolkit for Illumina sequencer metrics.
illumiprocessor 2.10 BSD XXX 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 1.1.1 dev Apache-2.0 X Framework for prediction of collisional cross-section of peptides.
ima3 1.13 GPL XX 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 doc dev MIT XXX IM-Fusion - Tool for identifying transposon insertions and their...
immuneml 3.0.17 doc dev APGL-3.0-only XXX immuneML is a software platform for machine learning analysis of immune...
imods 1.0.4 Copyright XX toolkit to perform Normal Mode Analysis (NMA) in internal coordinates...
impg 0.3.3 doc dev MIT XX impg: implicit pangenome graphs.
impute2 2.3.2 Academic XX 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 XXX A sensitive aligner for 454, Illumina and PacBio data, employing a full...
infernal 1.1.5 doc dev BSD-3-Clause XX Infernal is for searching DNA sequence databases for RNA structure and...
infinity 1.4 BSD XX All-in-one infinity value for Python. Can be compared to any object.
influx-si-data-manager 1.1.1 GPL-3.0-or-later X Data manager for handling influx_si inputs on Workflow4Metabolomics...
influx_si 7.4.1 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 XXX inheritance models for mendelian diseases
inmoose 0.9.0 doc dev GPL-3.0-or-later XX 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 1.2.2 doc dev Apache-2.0 X InstaNovo enables diffusion-powered de novo peptide sequencing in large...
instrain 1.10.0 dev MIT X Calculation of strain-level metrics.
insurveyor 1.1.3 dev GPL-3.0-only XX An insertion caller for Illumina paired-end WGS data.
intarna 3.4.1 doc dev MIT XX Efficient RNA-RNA interaction prediction incorporating seeding and...
integron_finder 2.0.6 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 XXX 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 XX Python tools for handling intervals (ranges of comparable objects).
intervalstats 1.01 unknown XX None
intervaltree_bio 1.0.1 MIT XXX Interval tree convenience classes for genomic data
intervene 0.6.5 MIT XXX A tool for intersection of multiple gene or genomic region sets and...
involucro 1.1.2 Apache-2.0 XX Build and Deliver Software with Containers
iobrpy 0.1.7 doc dev MIT X Immuno-Oncology Biological Research using Python (IOBRpy)
ionquant 1.11.9 Academic X A label free quantification tool
iow 1.0.8 doc dev BSD-3-Clause XX Implementation of Balanced Parentheses.
ipapy2 1.3.0 MIT X Integrated Probabilistic Annotation (IPA) 2.0 - Python implementation
ipcr 4.1.1 doc dev MIT XX In-silico PCR with mismatch thresholds and pretty alignment output.
iphop 1.4.1 dev Modified X Predict host genus from genomes of uncultivated phages.
ipk 0.5.1 dev MIT XX 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 0.9.107 doc dev GPL-3.0-only X Interactive assembly and analysis of RAD-seq data sets.
ipython-cluster-helper 0.6.4 MIT XXX 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 3.0.1 doc dev GPL-2.0-or-later XX Efficient phylogenomic software by maximum likelihood.
ir 2.8.0 GPL-2 XX Program for Calculating the Repetitiveness of DNA Sequences
irep 1.1.7 MIT XXX calculate iRep replication rates from metagenome sequencing
irescue 1.2.0 doc dev MIT X Uncertainty-aware quantification of transposable elements expression in...
irf 3.09 dev AGPL-3.0-or-later XX Inverted Repeats Finder is a program that detects approximate inverted repeats.
irfinder 1.3.1 doc dev MIT XX Intron Retention Finder
irida-linker 1.1.1 Apache-2.0 XXX The NGS Archive Linker is a Perl script used to generate a structure of...
irida-sistr-results 0.6.0 doc dev Apache XXX 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 0.9.5 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,...
is6110 0.3.0 MIT X Tool to find IS6110 insertions in M. tuberculosis NGS data
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 0.14.3 dev MPL-2.0 XXX Metadata tracking tools help to manage an increasingly diverse set of...
iscc-sum 0.1.0 doc dev Apache-2.0 XX High-performance ISCC Data-Code and Instance-Code hashing
iseq 1.9.8 dev MIT X iSeq is a Bash script that allows you to download sequencing data and...
isescan 1.7.3 GNU XX A python pipeline to identify IS (Insertion Sequence) elements in...
islandpath 1.0.6 GNU XXX 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 XX A Isotope Correction for mass spectrometry labeling experiments
isodesign 2.0.3 doc dev GPL-3.0-or-later X Facilitates the choice of the optimal isotopic composition of labeled...
isoformcheck 1.0.0 doc dev MIT X Protein sequence comparison between de novo genome assemblies.
isonclust 0.0.6.1 GPL-3.0 X De novo clustering of long-read transcriptome reads.
isonclust2 2.3 MPL2 XX De novo clustering of long transcriptomic reads
isonclust3 0.3.0 GPL-3.0-or-later XX De novo clustering of long transcript reads into genes
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 3.10.0 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 XX Iso-Seq - Scalable De Novo Isoform Discovery
isospecpy 2.2.2 BSD-3-Clause XX Python interface to IsoSpec++ isotopic envelope calculator library
isotools 2.0.0 doc dev MIT X Framework for the analysis of long read transcriptome sequencing data.
ispcr 33 License XX In silico PCR
itero 1.1.2 BSD XXX A pipeline for iterative, guided contig assembly that integrates...
itk 4.10.1 Apache XX 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 4.1.6 dev 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 XXX ITSx is an open source software utility to extract the highly variable...
itsxpress 2.1.4 dev CC0-1.0 XXX 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 XXX Iterative Virus Assembler
ivar 1.4.4 doc dev GPL-3.0-or-later XX iVar is a computational package that contains functions broadly useful...
jacusa2 2.1.16 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 XXX JAFFA is a multi-step pipeline that takes either raw RNA-Seq reads, or...
jali 1.3 file XX Alignment method for comparing a protein sequence to a protein family,...
jalview 2.11.5.1 GPL-3.0-only XXX Jalview is a free program for multiple sequence alignment editing,...
jamm 1.0.8.0 GPL XXX JAMM is a peak finder for NGS datasets (ChIP-Seq, ATAC-Seq,...
jannovar-cli 0.36 BSD2 XXX 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 XX The Zulu OpenJDK build.
jbrowse 1.16.11 LGPL XX The JBrowse Genome Browser
jbrowse2 3.7.0 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 1.5.11 doc dev BSD-2-Clause XX Python utility libraries on genome assembly, annotation, and...
je-suite 2.0.RC MIT XXX Je is a suite to handle barcoded fastq files with (or without) Unique...
jellyfish 2.2.10 dev GPL-3.0 XX Jellyfish is a tool for fast, memory-efficient counting of k-mers in...
jemalloc 4.5.0 BSD XX 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 XX 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 XXX This tool is able to receive multiple datasets (optionally with their...
juicebox_scripts 0.1.0gita7ae991 GNU X A collection of scripts for working with Hi-C data, Juicebox, and other...
juicertools 2.20.00 MIT X Visualization and analysis software for Hi-C data
julia-divand 2.7.9 GPL2 X Performs an n-dimensional variational analysis/gridding of arbitrarily...
junit-xml 1.8 MIT XXX 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 XXX Simple backoff algorithm in Python
jvarkit 2024.08.25 MIT X Java utilities for Bioinformatics.
jvarkit-bam2svg 201904251722 MIT XXX BAM to Scalar Vector Graphics (SVG)
jvarkit-bam2wig 201904251722 MIT XXX Bam to fixedStep Wiggle converter, or BED GRAPH.
jvarkit-bamstats04 2025.07.28 doc dev 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 XX Lightweight JavaScript shell based on Google's V8 JavaScript engine.
kaiju 1.10.1 doc dev GPL-3.0-or-later XX Fast and sensitive taxonomic classification for metagenomics.
kakscalculator2 2.0.1 GPL-3.0-or-later XX KaKs_Calculator2.0 calculates Ka and Ks.
kalamari 5.8.0 doc dev Creative XXX A curated database of completed assemblies with taxonomy IDs
kalign2 2.04 GPLv2 XX Kalign is a fast and accurate multiple sequence alignment algorithm...
kalign3 3.4.0 GPL-3.0-only XX Kalign is a fast and accurate multiple sequence alignment algorithm.
kallisto 0.51.1 doc dev BSD-2-Clause XX Quantifying abundances of transcripts from RNA-Seq data, or more...
kamino 0.2.1 doc dev MIT XX Tool for building phylogenomic datasets quickly and reproducibly.
kanpig 1.1.0 doc dev MIT XX A fast tool for genotyping structural variants with long-reads.
kaptive 3.1.0 doc dev GPL-3.0-or-later XXX Reports information about surface polysaccharide loci for Klebsiella...
karect 1.0 doc dev GPL-2.0-or-later XX Read error correction tool based on multiple alignment.
kart 2.5.6 MIT XX Kart: a divide-and-conquer algorithm for NGS read alignment
karyopype 0.1.6 MIT X Chromosomal visualization in Python.
kat 2.4.2 doc dev GPL-3.0-or-later XX KAT is a suite of tools that analyse jellyfish hashes or sequence files...
kb-python 0.30.0 doc dev BSD-2-Clause X A wrapper for the kallisto | bustools workflow for single-cell RNA-seq...
kbo-cli 0.2.1 doc dev Dual-licensed XX 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
kcftools 0.4.0 GPL-3.0-only X Rapid method to screen for introgression using k-mer counting
kcounter 0.1.1 GPL-3 XX A simple library for counting DNA k-mers in Python. Written in Rust.
kegalign-full 0.1.2.8 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...
kernel_density_plots 0.1 dev GPL3 X Python tool for generating SNP density and closest neighbor plots from...
kerneltree 0.0.5 dev GPL2 XX 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
kf2vec 1.0.62 dev MIT X K-mer frequency to vector tool.
kfilt 0.1.1 dev MIT XX A fast, multi-threaded tool for filtering FASTA/FASTQ reads based on...
kfoots 1.0 GPL-2 XX 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 2.0.4 dev BSD-3-Clause X Python library for generalized, low-level annotation of MS metabolomics.
khmer 3.0.0a3 doc dev BSD-3-License XX khmer k-mer counting library.
kid 0.9.6 MIT XX 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 XX `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 XX Pipeline for the simulation of RNA--ligand interaction kinetics as...
kipoi 0.8.6 doc dev MIT XXX 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 XX 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 XXX Combining gene-set analysis with network properties
kleborate 3.2.4 doc dev GPL-3.0-or-later X Kleborate: a tool for typing and screening pathogen genome assemblies.
kled 1.2.10 doc dev MIT X An ultra-fast and sensitive structural variant detection tool for...
kma 1.6.8 doc dev Apache-2.0 XX KMA is a mapping method designed to map raw reads directly against...
kmasker 1.1.1 dev GPL3 XX A tool for masking and exploring of sequences from plant species.
kmc 3.2.4 doc dev GPL-3.0-or-later XX Tools for efficient k-mer counting and filtering of reads based on...
kmcp 0.9.4 MIT XX 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-counter 0.1.2 MIT XX kmer-counter is an efficient kmer counter for large sequencing read sets.
kmer-db 2.3.1 dev GPL-3.0-or-later XX Kmer-db is a fast and memory-efficient tool for estimating evolutionary...
kmer-jellyfish 2.3.1 doc dev GPL-3.0-or-later XX Jellyfish is a tool for fast, memory-efficient counting of k-mers in...
kmer2stats 1.0.1 dev GPL-3.0-only X A tool for creating data files for statistic based on kmers.
kmercamel 2.2.0 doc dev MIT XX 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 doc dev Free XX KmerGenie estimates the best k-mer length for genome de novo assembly.
kmerinshort 1.0.1 aGPL XX KmerInShort counts kmers from a fasta/fastq file or list of files, and...
kmerstream 1.1 free XX Streaming algorithm for computing kmer statistics for massive genomics datasets
kmertools 0.2.1 doc dev GPL-3.0-only XX kmertools: DNA Vectorisation Tool
kmetashot 2.0 doc GPL-3.0-only X Fast taxonomic classifier for metagenome bins/MAGs based on k-mer/minimizer
kmindex 0.6.0 doc dev AGPL-3.0-or-later XX A tool for large-scale k-mer indexing
kmtricks 1.5.1 doc dev AGPL-3.0 XX A k-mer matrix framework
kneaddata 0.12.4 doc dev MIT XXX 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 XX Predicts -1 frameshift sites with simple pseudoknots.
kobas 3.0.3 Biopython XXX KEGG Orthology Based Annotation System
kodoja 0.0.10 MIT XXX Kodoja: identifying viruses from plant RNA sequencing data
koeken 0.2.6 MIT XX 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 XX Characterizing metagenomes using K-Core decomposition
kompot 0.6.2 doc dev GPL-3.0-or-later X Differential abundance and gene expression analysis using Mahalanobis...
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 XXX Analysis toolkit and programming library for k-mer profiles
kpop 1.1.1 dev GPL-3.0-only XX An assembly-free and scalable method for the comparative analysis of...
kractor 3.1.0 MIT XX Rapidly extract reads from a FASTQ file based on taxonomic...
kraken 1.1.1 doc dev GPL-3.0-or-later XX 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 XXX Create BIOM-format tables from Kraken output.
kraken-ea 0.10.5ea.3 dev GPL-3.0-or-later XX Kraken is a system for assigning taxonomic labels to short DNA...
kraken2 2.17.1 doc dev GPL-3.0-or-later XX Kraken2 is a system for assigning taxonomic labels to short DNA...
krakenhll 0.4.8 GPLv3 XX KrakenHLL metagenomics classification method with unique k-mer counting...
krakentools 1.2.1 GPL-3.0 X KrakenTools scripts for analysis of Kraken/KrakenUniq/Kraken2/Bracken results
krakenuniq 1.0.4 GPLv3 XX 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 XX This is a c++ extension for python which computes K.R. balanced matrices.
krepp 0.6.0 dev MIT XX A k-mer-based maximum likelihood method for estimating distances of...
krocus 1.0.3 GPL-3.0 XXX krocus performs multi-locus sequence typing from uncorrected long reads.
krona 2.8.1 BSD XXX Krona Tools is a set of scripts to create Krona charts from several...
kronik 2.20 dev Apache-2.0 XX 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 XX C++11 re-implementation of kseq by Heng Li
ksnp 1.0.3 GPL3 XX k-mer based haplotype assembly
kssd 2.21 Apache-2.0 X K-mer substring space decomposition
ksw 0.2.3 MIT XX Ksw: (interactive) smith-waterman in C
kwip 0.2.0 GNU XX kWIP implements a de novo, alignment free measure of sample genetic...
kyber 0.6.0d dev MIT XX 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 XXX 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 XX Lambda is a local aligner optimized for many query sequences and...
lamps 1.0.4 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 0.1.2 doc dev GPL-3.0 X Tool for downloading Lassa virus sequences
lassensus 0.0.5 doc dev GPL-3.0 X Tool for creating Lassa virus consensus sequences
last 1650 doc dev GPL-3.0-or-later XX LAST finds & aligns related regions of sequences.
lastz 1.04.52 doc dev MIT XX LASTZ is a program for aligning DNA sequences, a pairwise aligner.
latch 2.67.21 dev MIT X The Latch python bioinformatics framework.
latentstrainanalysis 0.0.1 MIT XXX Partitioning and analysis methods for large, complex sequence datasets
lca 0.25 dev GPL-3.0-only XX LCA - Lowest Common Ancestor calculation tool.
lcfit 0.5 GPL-3.0 X Likelihood curve fitting by nonlinear least squares.
ldblockshow 1.41 dev MIT XX A tool for showing linkage disequilibrium heatmaps from variant call...
lddt 2.2 GPL3 XX A superposition-free score that evaluates local distance differences in...
ldhelmet 1.10 GPL3 XX 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 2.0.16 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 XXX 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 5.0 dev GPL-3.0-or-later X The Snakemake pipeline to use Lep-Map3 to create linkage maps and...
leviathan 1.0.2 AGPL-3.0-or-later XX Linked-reads based structural variant caller with barcode indexing
leviosam 5.2.1 MIT XX lift-over of alignments for variant-aware references
leviosam2 0.5.0 doc dev MIT XX Fast and accurate coordinate conversion between assemblies.
lexicmap 0.8.1 MIT XX efficient sequence alignment against millions of prokaryotic genomes
lexmapr 0.7.1 GPL-3.0 XXX A Lexicon and Rule-Based Tool for Translating Short Biomedical Specimen...
liana 1.6.1 doc dev GPL-3.0-or-later X LIANA+: a one-stop-shop framework for cell-cell communication.
lib-pod5 0.3.33 doc dev MPL-2.0 XXX Python bindings for the POD5 file format.
libarbdb 6.0.6 doc dev ARB XX ARB 6 Sequence Analysis Suite
libbambamc 0.0.50 GPLv3 XX lightweight C implementation of name collating BAM file input and BAM...
libbigwig 0.4.8 MIT XX A C library for handling bigWig files
libcarna 3.4.0 doc dev MIT X Real-time 3D visualization of biomedical data and beyond
libcarna-python 0.2.0 doc dev MIT X Real-time 3D visualization of biomedical data and beyond in Python
libccp4 8.0.0 doc GPL-3.0-or-later XX Protein X-ray crystallography toolkit.
libcifpp 9.0.5 doc dev BSD-2-Clause XX Library containing code to manipulate mmCIF and PDB files.
libdb 6.1.26 AGPLv3 XX The Berkeley DB embedded database system.
libdeflate 1.2 MIT XX libdeflate is a library for fast, whole-buffer DEFLATE-based...
libdivsufsort 2.0.2 MIT XX 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 doc GPL-2.0-or-later XX A C++ development library designed to make common operations on DNA and...
libgff 2.0.0 doc dev MIT XX A simple "libraryfication" of the GFF/GTF parsing code that is...
libgtextutils 0.7 AGPL XX Gordon Text utils Library
libidn 7.45.0 LGPLv3 XX 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-or-later X libMems is a freely available software development library to support...
libmuscle 3.7 GPL-2.0-or-later XX libMuscle header files.
libopenms 3.5.0 doc dev BSD-3-Clause XX Libraries and headers for developing with OpenMS. They are also a...
libpdb-redo 3.3.1 dev BSD-2-Clause XX Library containing shared code for various PDB-REDO programs.
libsbml 5.20.4 LGPL XX LibSBML is a free, open-source programming library to help you read,...
libsequence 1.9.8 doc dev LGPL-3.0-or-later XX A C++ class library for evolutionary genetics.
libshorah 1.99.4 GPLv3 XX libshorah - Short Reads Assembly into Haplotypes
libssw 1.2.5 doc dev MIT XX An SIMD Smith-Waterman C/C++/Python/Java Library for Use in Genomic...
libstatgen 1.0.15 dev GPL-3.0-or-later XX 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 1.3.3 dev MIT XX A Python package for converting point coordinates between genome...
ligand-validation 0.0.1 doc dev Apache-2.0 X Extract ligand and binding site information from PDB X-ray validation reports
lightassembler 1.0 dev GPL XX Lightweight assembly algorithm designed to be executed on a desktop...
lighter 1.1.3 doc dev GPL-3.0-or-later XX Lighter is a kmer-based error correction method for whole genome...
lightning 0.2.dev0 Unknown XX 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 XX None
linearfold 1.0.1.dev20220829 dev Custom XX 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 XXX Converts between the output linkage formats of Merlin, Simwalk,...
linkedsv 0.1.0 dev MIT XX A novel structural variant caller for 10X Genomics (linked-read) sequencing data
links 2.0.1 dev GPL-3.0-or-later XX Long Interval Nucleotide K-mer Scaffolder.
linkstats 0.1.3 MIT XX 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...
lirtmats 1.0.0 dev GPL-3.0-only X LiRTMaTS - Liverpool retention time matching software
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 XX 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 XX An ultrafast horizontal gene transfer detection method from large...
locarna 2.0.1 doc dev GPL-3.0-or-later XX Multiple alignment of RNAs.
locidex 0.4.0 dev Apache-2.0 X Locidex: Common search engine for similarity based typing applications.
locityper 1.2.1 dev MIT XX 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 1.1.1 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 XX A fast and sensitive variant-caller for inferring SNVs and indels from...
log4cpp 1.1 Lesser XX Log4cpp is library of C++ classes for flexible logging to files,...
logbook 1.4.3 BSD XX 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 XXX A computational tool to evaluate HLA loss using next-generation sequencing data.
lollipop 0.5.3 GNU X A tool for Deconvolution for Wastewater Genomics
longbow 2.3.1 GPL-3.0-or-later X A Python program for nanopore sequencing basecalling configuration prediction
longcalld 0.0.8 dev MIT XX longcallD: local-haplotagging-based small and structural variant calling
longcallr 1.12.0 MIT XX A Rust tool for SNP calling and haplotype phasing with long RNA-seq reads.
longcallr_nn 0.0.2 dev MIT X longcallR_nn is a variant caller specifically designed for long-read...
longdust 1.4 dev Unknown XX Longdust identifies long highly repetitive STRs, VNTRs, satellite DNA...
longestrunsubsequence 1.0.1 MIT X Implementation of a solver for the Longest Run Subsequence Problem....
longgf 0.1.2 dev GPL-3.0-or-later XX A fast tool to detect gene fusion from long-read RNA-seq data.
longphase 2.0 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 XX Long read sequencing data quality control tool
longshot 1.0.0 doc dev MIT XX 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.
longtr 1.2 doc dev BSD-2-Clause XX Tandem repeat genotyping with long reads.
longtrack 1.0.0 dev MIT X Track FMT strains using long-read metagenomic assemblies.
loompy 2.0.16 BSD-2-Clause XXX Work with .loom files for single-cell RNA-seq data
loomxpy 0.4.2 MIT X Python package (compatible with SCope) to create .loom files and extend...
lorax 0.5.1 BSD-3-Clause XX A long-read analysis toolbox for cancer genomics
lordec 0.9 CeCILL XX A hybrid error correction program for long, PacBio reads
lordfast 0.0.10 GPL-3.0 XX Sensitive and Fast Alignment Search Tool for Long Read sequencing Data
lorikeet 20 GPL-3 XXX 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
lotus3 3.03 dev GPL-2.0-only X LotuS3 is a lightweight amplicon sequencing pipeline supporting 16S/18S/ITS
lovis4u 0.1.6 BSD-3-Clause X Loci Visualisation Tool.
lr_gapcloser 1.0 doc dev GPL-3.0-or-later X Use long sequenced reads to close gaps in assemblies.
lra 1.3.7.2 USC-RL X Long read aligner for sequences and contigs
lrez 2.2.4 AGPL-3.0-or-later XX Standalone tool and library allowing to work with barcoded linked-reads
lrge 0.2.1 MIT XX 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 XX Long Range ZIP or Lzma RZIP. This is a compression program optimised...
ls-gkm 0.1.1 doc dev GPL-3.0-or-later XX gkm-SVM, a sequence-based method for predicting regulatory DNA elements.
lsabgc 1.1.10 doc dev BSD-3-Clause X lsaBGC-Pan - refined workflow for pan-BGC-omic evolutionary investigations.
lsc 2.0 Apache XXX LSC is a long read error correction tool that offers fast correction...
lsd 2.2.3 Apache XXX The LAPPS Grid Services DSL (LSD). Used to invoke LAPPS web services...
ltr_finder 1.07 dev MIT XX LTR_Finder is an efficient program for finding full-length LTR...
ltr_finder_parallel 1.3 doc dev MIT X Perl wrapper to parallelize ltr_finder
ltr_harvest_parallel 1.2 doc dev MIT X Perl wrapper for parallel execution of LTR_harvest
ltr_retriever 3.0.4 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 XXX a general probabilistic framework for structural variant discovery
lumpy-sv-minimal 0.3.1 doc dev MIT XX A general probabilistic framework for structural variant discovery....
lusstr 0.11 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 XX Fast and accurate tool for calculating Average Nucleotide Identity...
lz4-bin 131 BSD XX 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 XXX MaAsLin is a multivariate statistical framework that finds associations...
maaslin2 1.16.0 Custom X MaAsLin2 is comprehensive R package for efficiently determining...
maaslin3 0.99.16 Custom X "Refining and extending generalized multivariate linear models for...
maast 1.0.8 MIT XX Microbial agile accurate SNP Typer
macaron 1.0 LGPL-3 X Multi-bAse Codon-Associated variant Re-annotatiON
mace 1.2 GPL3 XX Model Based Analysis for ChIP-exo data
mach2 1.0.2 BSD-3-Clause X Migration Analysis of Clonal Histories 2
machina 1.2 BSD-3 XX Metastatic And Clonal History INtegrative Analysis
macrel 1.6.0 dev MIT XXX 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 XX Model Based Analysis for ChIP-Seq data.
macs3 3.0.3 doc dev BSD-3-Clause XX Model Based Analysis for ChIP-Seq data.
macse 2.07 CeCILL X MACSE: Multiple Alignment of Coding SEquences Accounting for...
macsyfinder 2.1.6 doc GPL-3.0-or-later X MacSyFinder: Detection of macromolecular systems in protein datasets...
macsylib 1.0.4 doc GPL-3.0-or-later X MacSyLib: Python library that help to detect of macromolecular, systems...
madre 0.0.5 doc dev MIT X Strain-level metagenomic classification with Metagenome Assembly driven...
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 XX A tool that postprocesses whole genome alignment (for two or more...
mafft 7.525 BSD XX 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 doc BSD-3-Clause XX MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout), an...
mageck-vispr 0.5.6 MIT XXX 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 XX NCBI BLAST next generation read mapper
magmax 1.1.0 GPL-3.0 XX MAGmax is a robust tool for dereplicating MAGs through bin merging and...
magneto 1.5 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 dev GPL-3.0-or-later XXX 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 3.01.04 doc GPL-3.0-or-later XXX MAKER is a portable and easily configurable genome annotation pipeline.
malder 1.0.1e83d4e Custom XX 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
mameshiba 0.8.1 doc dev MIT X mameshiba installs only the dependencies needed to run MameShiba.
mammal 1.1.1 GNU XX Accelerated Estimation of Frequency Classes in Site-heterogeneous...
mamotif 1.1.0 BSD XXX 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 XXX A robust model for quantitative comparison of ChIP-Seq data sets.
manormfast 0.1.2 GNU XX MAnorm version, Fast but more memory
manta 1.6.0 GPL-3.0-only XX Structural variant and indel caller for mapped sequencing data
mantis 0.2 dev BSD-3-Clause X Mantis: A Fast, Small, and Exact Large-Scale Sequence-Search Index.
mantis-msi 1.0.5 GPL-3 XXX MANTIS is a program developed for detecting microsatellite instability...
mantis-msi2 2.0.0 dev GPL-3.0-or-later XX MANTIS2 is a program developed for detecting microsatellite instability...
mantis_pfa 1.5.5 dev MIT XX Consensus-driven protein function annotation tool
mapad 0.45.0 MIT XX An aDNA aware short-read mapper
mapcaller 0.9.9.41 MIT XX MapCaller: combined short-read mapper and variant caller
mapdamage2 2.2.3 doc dev MIT XXX mapDamage: tracking and quantifying damage patterns in ancient DNA...
mapdia 3.1.0 dev file XX 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 dev Artistic-2.0 XX Consensus calling or `reference assisted assembly`, chiefly of ancient...
mappy 2.30 MIT XX Minimap2 Python binding
mapsembler2 2.2.4 GNU XX Targeted assembly software
mapseq 2.1.1 dual-licensed XX Open source metagenomic 16S/18S read classifier enabling comparative...
mapsplice 2.2.1 doc dev 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
marbel 0.2.4 Apache-2.0 X Marbel generates realistic in silico metatranscriptomic dataset based...
marge 1.0 MIT XXX 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.
markov_genome 1.0.0 BSD-3-Clause XX A Rust package for Markov chain sequence simulation.
mars 1.2.4 MIT X Multiple Alignment-based Refinement of SVs (MARS)
marti 0.9.29 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. XX Fast sequence distance estimator that uses MinHash.
mashmap 3.1.3 doc dev Custom XX 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 XX 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 2.0.12 BSD XX 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 0.1.1 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 4.1.4 doc dev GPL-3.0-only X MaSuRCA (Maryland Super-Read Celera Assembler) genome assembly software.
matam 1.6.2 dev AGPL-3.0-or-later X MATAM is a software dedicated to the fast and accurate targeted...
matchms 0.31.0 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 XXX "Different algorithms for computing small and minimum plain text...
mathstats 0.2.6.5 GPLv3 XXX Statistical functions, goodness-of-fit tests and special and special...
matlock 20181227 GNU XX Simple tools for working with Hi-C data
mauve 2.4.0.snapshot dev GPL-2.0 XX 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 1.1.3 doc dev MIT X MAVE-NN: genotype-phenotype maps from multiplex assays of variant effect.
maverick 1.0.5 doc dev MIT XX Bayesian clustering for genetic data.
mavis 3.1.2 doc dev GPL-3.0-or-later 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 XX mawk is an interpreter for the AWK Programming Language.
maxbin2 2.2.7 dev BSD-3-Clause XX MaxBin is software for binning assembled metagenomic sequences based on...
maxentpy 0.02 dev MIT XX maxentpy is a python wrapper for MaxEntScan to calculate splice site strength.
maxentscan 0_2004.04.21 unknown XX MaxEntScan is based on the approach for modeling the sequences of short...
maxit 11.400 doc RCSB XX MAXIT assists in the processing and curation of macromolecular structure data.
maxquant 2.0.3.0 http://www.coxd XX MaxQuant is a quantitative proteomics software package designed for...
mbg 1.0.17 MIT XX Minimizer based sparse de Bruijn graph constructor
mbgc 2.1 dev GPL-3.0-or-later XX 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 doc dev MIT XX De novo genome assembly and multisample variant calling.
mcl 22.282 doc dev GPL-3.0-only XX 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 XX 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 dev GPL-3.0-or-later X This is MDAsim 2+, a tool to simulate whole genome amplification.
mdmcleaner 0.8.7 GPL-3.0 X A pipeline for the assessment, classification and refinement of...
mdust 2006.10.17 The XX mdust from DFCI Gene Indices Software Tools.
me-pcr 1.0.6 Public XX 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 parameters.
medaka 2.1.1 doc dev Oxford XX A tool to create consensus sequences and variant calls from nanopore...
medicc2 1.1.2 dev GPL-3.0-or-later XX Whole-genome doubling-aware copy number phylogenies for cancer evolution
medpy 0.4.0 GNU XXX 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 XXX Medusa is an approach to detect size-k modules of objects that, taken...
megadepth 1.2.0 MIT XX 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 doc dev GPL-3.0-or-later XX MEGAHIT: An ultra-fast single-node solution for large and complex...
megalodon 2.5.0 doc dev Oxford XX 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 XX MegaPath-Nano: Accurate Compositional Analysis and Drug-level...
megatron 0.1a dev BSD-3 X MEGATRON - MEGA TRajectories of clONes
mehari 0.38.1 doc dev MIT X VEP-like tool for sequence ontology and HGVS annotation of VCF files...
melon 0.3.0 MIT X Melon: metagenomic long-read-based taxonomic identification and...
melt 1.0.3 GNU XXX A nucleotide melt temp calculator
meme 5.5.9 doc Custom XX Motif-based sequence analysis tools.
memopair 0.1.6 MIT XX 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 XXX Analyze exome data for Mendelian disorders.
meneco 1.5.2 GPLv3+ XX Metabolic Network Completion. Compute minimal completions to your draft...
menetools 2.0.6 GPLv3+ XXX 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 XXX 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 XX 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 XXX Python package and routines for merging VCF files
merlin 1.1.2 OpenSource XX 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 1.1.3 doc dev https://github. XX MerquryFK replaces meryl with the FastK k-mer counter suite to...
meryl 2013 doc dev GPL XX meryl is a multi-threaded, multi-process, out-of-core k-mer counter
mess 0.12.0 doc dev MIT X Snakemake pipeline for simulating shotgun metagenomic samples
met4j 2.2.0 CeCILL-2.1 X Met4J is an open-source Java library dedicated to the structural...
meta-apo 1.1 GPL3 XX Meta-Apo improves accuracy of 16S-amplicon-based prediction of...
meta-neuro 2.0.1 doc dev BSD-3-Clause XX Medial Tractography Analysis (MeTA)
meta-sparse 0.1.12 GNU XX 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 2.18 doc dev BSD-3-Clause-LBNL XX 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 0.9.85 doc dev GPL-3.0-or-later X Python package to process 1D and 2D NMR spectroscopic data for...
metabolights-utils 1.4.15 doc dev Apache-2.0 X MetaboLights open metabolomics data repository command line interface...
metabolishmm 2.22 doc dev GPL-3.0-or-later X Constructing phylogenies and performing functional annotations with HMM markers.
metabuli 1.1.0 GPLv3 XX Metabuli: specific and sensitive metagenomic classification via joint...
metacache 2.5.1 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 XXX 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 XXX MetaCoAG: Binning Metagenomic Contigs via Composition, Coverage and...
metacompass 1.12 doc dev Artistic-License-2.0 XX MetaCompass: Reference-guided Assembly of Metagenomes.
metacortex 0.5.1 GPL-3.0-or-later X MetaCortex is an assembler for metagenomic, or environmental sequence data.
metadmg 0.4.2 doc dev GPL-3.0-or-later, XX metaDMG-cpp: fast and efficient method for estimating mutation and...
metaeuk 7.bba0d80 GPL-3 XX MetaEuk - sensitive, high-throughput gene discovery and annotation for...
metafun 1.0.0 doc dev MIT X Scalable and agile analysis pipeline for metagenomic and comparative...
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 XX MetaGeneAnnotator is a gene-finding program for prokaryote and phage
metagenome-atlas 19.0.1 doc dev BSD-3-Clause XX ATLAS - Three commands to start analysing your metagenome data
metagraph 0.4.5 doc dev MIT XX 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 XX MetaMaps is a tool for long-read metagenomic analysis
metamate 0.5.2 GPL-3.0 X metaMATE: your metabarcoding friend!
metamdbg 1.2 doc dev MIT XX MetaMDBG: a lightweight assembler for long and accurate metagenomics reads.
metameta 1.2.0 The XX MetaMeta - pipeline for integrating metagenome analysis tools to...
metametamerge 1.1 The XXX 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 dev MIT XX Produce targeted databases for mass spectrometry analysis.
metaomestats 0.4 MIT X Scripts for calculating statistics from FASTA sequences
metaphlan 4.2.4 doc dev MIT X Metagenomic Phylogenetic Analysis.
metaphlan2 2.96.1 MIT XXX 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 XX 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 XXX Quantitative microbiome analysis
metaquantome 2.0.2 dev Apache X Quantitative metaproteomics analysis of taxonomy and function.
metasbt 0.1.5 dev MIT X Microbial genomes characterization with Sequence Bloom Trees.
metaseq 0.5.6 MIT XX Framework for integrated analysis and plotting of ChIP/RIP/RNA/*-seq data.
metaseq-all 0.5.6 The XXX 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 XX SNV calling software
metaspace2020 2.0.9 doc dev Apache-2.0 X Python library for connecting to the METASPACE platform.
metasv 0.5.4 MIT XX An accurate and integrative structural-variant caller for next...
metator 1.3.10 doc dev GPL-3.0-or-later XX Metagenomic binning based on Hi-C data.
metatree 0.0.1 GNU X Visualisation of polyphyletic groups between phylogenetic trees to a...
metav 2.0.0 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 XX 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 XX 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 XX MetaWatt is a metagenomic binning tool
metawrap 1.2 MIT XX MetaWRAP is a pipeline for genome-resolved metagenomic data analysis
metawrap-annotate-bins 1.3.0 MIT X MetaWRAP requirements for annotate_bins step
metawrap-assembly 1.3.0 MIT X MetaWRAP requirements for assembly step
metawrap-binning 1.3.0 MIT X MetaWRAP requirements for binning step
metawrap-blobology 1.3.0 MIT X MetaWRAP requirements for read_qc step
metawrap-classify-bins 1.3.0 MIT X MetaWRAP requirements for classify_bins step
metawrap-kraken 1.3.0 MIT X MetaWRAP requirements for kraken step
metawrap-mg 1.3.0 dev MIT X MetaWRAP is a pipeline for genome-resolved metagenomic data analysis
metawrap-quant-bins 1.3.0 MIT X MetaWRAP requirements for quant_bins step
metawrap-read-qc 1.3.0 MIT X MetaWRAP requirements for read_qc step
metawrap-reassemble-bins 1.3.0 MIT X MetaWRAP requirements for reassemble_bins step
metawrap-refinement 1.3.0 MIT X MetaWRAP requirements for bin_refinement step
metaxa 2.2.3 GPL-3.0 XXX Improved Identification and Taxonomic Classification of Small and Large...
metaxaqr 3.0rc2 GPL-3.0-or-later X Improved Identification and Taxonomic Classification of Small and Large...
metdatamodel 0.6.0 BSD-3-Clause X Data models for metabolomics
meteor 2.0.22 dev GPL-3.0-or-later X Meteor is a plateform for quantitative metagenomics profiling of...
metfrag 2.4.5 GNU XXX MetFrag is a freely available software for the annotation of high...
methbat 0.17.0 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 dev GPL-3.0-or-later XX A pipeline for analyzing DNA methylation data from bisulfite sequencing.
methplotlib 0.21.2 MIT X Plot methylation data obtained from nanopolish
methurator 0.1.7 MIT X Python package designed to estimate sequencing saturation for...
methylartist 1.5.3 dev MIT X Tools for parsing and plotting nanopore methylation data.
methyldackel 0.6.1 MIT XX A (mostly) universal methylation extractor for BS-seq experiments....
methylextract 1.9.1 GNU XXX 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 XX Bisulfite sequencing data processing and differential methylation analysis
metilene 0.2.9 doc GPL-2.0-or-later XX Fast and sensitive detection of differential DNA methylation.
mfold 3.6 Custom XX 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 XX mGEMS - sequencing data binning based on probabilistic classification
mgf-formatter 1.0.0 Eclipse XXX Tools for convert peak lists into MGF files formatted for particular...
mgikit 2.1.1 dev AFL-3.0 XX mgikit is a collection of tools used to demultiplex fastq files and...
mgkit 0.5.8 GPL-2.0-or-later XX Metagenomics Framework
mglex 0.2.1 GPL-3.0 XXX MGLEX - MetaGenome Likelihood EXtractor
mgltools 1.5.7 OTHER XX MGLTools is an program for visualization and analisys of molecular structures.
mgnify-pipelines-toolkit 1.4.10 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 XXX 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 2.1.5 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 XXX 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...
mi-pimento 1.0.2 dev Apache-2.0 X A PrIMEr infereNce TOolkit to facilitate large-scale calling of...
micall-lite 0.1rc5 GNU XX A bioinformatic pipeline for mapping of FASTQ data to a set of...
mice 0.1.2 MIT XX Markers Inferred by Compacting Elements (mice). Synteny blocks from pangenomes.
micom 0.37.1 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 XXX A command-line tool for estimating average genome size from shotgun...
microhapdb 0.12 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 XXX microPITA is a computational tool enabling sample selection in...
microview 0.11.0 BSD-3-Clause XX Generate reports from taxonomic classification data
midas 1.3.2 GPL-3.0 XX An integrated pipeline for estimating strain-level genomic variation...
midsv 0.13.0 MIT X Python module to convert SAM to MIDSV format.
miga 1.0.0 dev LGPL-3.0 XX Python package to optimize mutual information between two multiple...
migmap 1.0.3 Apache-2.0 XXX A wrapper for IgBlast V-(D)-J mapping tool designed to facilitate...
migraine 0.6.0 CeCILL XX 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 XX 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 1.2.1 doc dev MIT XXX Scan genomes for internally repeated sequences, elements which are...
mimi 1.0.4 doc dev Academic X Molecular Isotope Mass Identifier.
mimick 3.0.1 doc dev GPL-3.0-or-later X Simulate linked-read data
mimodd 0.1.9 GPL3 XX Tools for Mutation Identification in Model Organism Genomes
mimseq 1.3.9 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 XXX 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 dev AGPL-3.0-or-later XX MindTheGap performs detection and assembly of DNA insertion variants in...
minepy 1.2.3 GNU XX 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 doc dev AGPL-3.0-or-later XX Minia is a short-read assembler based on a de Bruijn graph, capable of...
minialign 0.6.0 doc dev MIT XX Fast and accurate alignment tool for PacBio and Nanopore long reads.
miniasm 0.3 doc dev MIT XX 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 XX Proof-of-concept seq-to-graph mapper and graph generator.
minimac4 4.1.6 GPL-3.0-or-later XX Computationally efficient genotype imputation
minimap 0.2 MIT XX Experimental tool to find approximate mapping positions between long sequences
minimap2 2.30 doc dev MIT XX 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 XX The simplest possible mock library
minimod 0.4.0 MIT XX A bioinformatics tool for viewing and calculating base modification...
minipileup 1.4b MIT XX Minipileup is a simple pileup-based variant caller
minipolish 0.2.0 doc dev GPL-3.0-or-later X A tool for Racon polishing miniasm assemblies.
miniprot 0.18 doc dev MIT XX Miniprot aligns a protein sequence against a genome with affine gap...
miniprot-boundary-scorer 1.0.1 dev Artistic-1.0 XX Miniprot boundary scorer parses introns, starts, stops and exons from...
minirmd 1.1 GPL-3.0-only XX Remove duplicate and near-duplicate reads
minisplice 0.4 doc dev MIT XX minisplice is a command-line tool to estimate the odds-ratio score of...
minkemap 0.1.0 MIT X A Python-based Circular Genome Visualization Tool
minnow 1.2 GPLv3 XX 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 XXX Generate tRF profiles from short RNA-Seq datasets
minute 0.12.1 doc dev MIT X MINUTE-ChIP data analysis workflow
minvar 2.2.2 Custom XXX A tool to detect minority variants in HIV-1 and HCV populations
minys 1.1 file XX MinYS allows targeted assembly of bacterial genomes using a...
mir-prefer 0.24 GPL XXX microRNA PREdiction From small RNA-seq data
mira 5.0.0rc2 doc dev GPL-2.0-or-later X MIRA is a whole genome shotgun and EST sequence assembler for Sanger,...
mira-moods 1.9.4.2 MIT XX MOODS: Motif Occurrence Detection Suite
mira-multiome 2.1.1 BSD-3-Clause-LBNL X Single-cell multiomics data analysis
miranda 3.3a dev GPLv2 XX 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 XXX 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 XXX 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 0.3.0.2 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 0.3.4 MIT X miRScore: A rapid and precise microRNA validation tool
mirtop 0.4.30 doc dev MIT XXX 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 XX Mixture of Isoforms model (MISO) for isoform quantitation using RNA-Seq
mist_typing 1.0.0 dev GPL-3.0-or-later X MiST is a rapid, accurate and flexible (core-genome) multi-locus...
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 XX Mitofinder is a pipeline to assemble mitochondrial genomes and annotate...
mitorsaw 0.2.7 Pacific X A tool for mitochondrial analysis for HiFi sequencing data
mitos 2.1.10 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 2.0.1 doc dev 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 0.5.2 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 XX Takes as input a file with assembled reads from a single diploid...
mlst 2.32.2 GPL-2.0 XXX 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 0.1.7 dev MIT X A Python package to update and manage the MLST database for the MLST tool.
mm2plus 1.2 MIT X Fast long-read mapper and whole-genome aligner (accelerated version of minimap2)
mmannot 1.1 GPL3/LGPL3 XX mmannot annotates reads, or quantifies the features. mmmannot takes...
mmcif 1.1.0 doc dev BSD-3-Clause XX mmCIF Core Access Library
mmdb2 2.0.22 GPL-3.0-or-later XX C++ toolkit for working with macromolecular coordinate files.
mmft 0.3.2 MIT XX Max's minimal fasta toolkit
mmlong2 1.2.1 GPL-3.0-only X An all-in-one genome-centric metagenomics workflow using long reads
mmlong2-lite 1.2.1 GPL-3.0-only X Lightweight workflow for microbial genome recovery using either...
mmpdb 3.1.3 doc dev BSD-4-Clause X A package to identify matched molecular pairs and use them to predict...
mmquant 1.0.9 GPL3/LGPL3 XX RNA-Seq quantification tool, with special handling on multi-mapping reads.
mmseqs2 18.8cc5c MIT XX MMseqs2: ultra fast and sensitive sequence search and clustering suite
mmseqs2-server 8.c4b9644 GPLv3 XX Server for MMseqs2, Foldseek and ColabFold
mmtf-python 1.0.2 MIT XX A decoding libary for the PDB mmtf format
mmult 0.0.0.2 MIT XX 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 XX Mutual nearest neighbors correction in python.
moabs 1.3.9.6 doc dev MIT XX Methylation analysis on Bisulfite-Sequencing reads.
mob_suite 3.1.9 doc dev Apache-2.0 XXX 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 XXX NGS tool for detecting MEI and gene retrotransposition events in WGS...
moca 0.4.3 ISC XXX Tool for motif conservation analysis
mockinbird 1.0.0a1 doc dev GPL-3.0-or-later XX A fully automatic and reproducible PAR-CLIP analysis pipeline
modeltest-ng 0.1.7 doc dev GPL-3.0 XX ModelTest-NG is a tool for selecting the best-fit model of evolution...
modlamp 4.3.2 doc BSD X python package for in silico peptide design and QSAR studies
modle 1.1.0 doc dev MIT XX 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 XXX moFF is an OS independent tool designed to extract apex MS1 intensity...
mogaaap 1.1.0 GPL-3.0-only X MoGAAAP: Modular Genome Assembly, Annotation and quality Assessment Pipeline
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 XX Deprecated and no longer maintained programs for the (pre-NGS-era)...
moments 1.5.0 doc dev MIT XX 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 XXX 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 XXX 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 XX 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 XX mosaicatcher: counts Strand-seq reads and classifies strand states of...
mosaik 2.2.26 GPL XX 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 0.3.12 doc dev MIT XXX Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing.
moss 0.1.1 MIT X A multi-sample somatic SNV caller
mothur 1.48.3 doc dev GPL-3.0-or-later XX This project seeks to develop a single piece of open-source, expandable...
motifraptor 0.3.0 Partners XX Motif-centric analysis on GWAS data
motifscan 1.3.0 BSD XX 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 XXX Marker gene-based OTU (mOTU) profiling
mp-est 3.1.0 doc dev GPL-3.0-or-later XX 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 XX 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
mpboot 1.2 doc dev GPL-2.0-only XX Fast phylogenetic maximum parsimony tree inference and bootstrap approximation.
mpra-data-access-portal 0.1.10 MIT X Saturation mutagenesis MPRA data access portal.
mpralib 0.9.0 MIT X Library to analyze count data of MPRA experiments.
mqc 1.10 GNU XX 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 XX Bayesian Inference of Phylogeny
mrbayes_volpiano 3.2.7a doc dev GPL-3.0-or-later XX Bayesian Inference of Phylogeny (Volpiano edition)
mreps 2.6.01 GPL-2.0-or-later XX mreps is a flexible and efficient software for identifying serial...
mrpast 0.2 doc dev GPL-3.0-only XX Demographic inference from Ancestral Recombination Graphs.
mrsfast 3.4.2 BSD XX mrsFAST - micro-read substitution-only Fast Alignment Search Tool.
mrtrix3 3.0.8 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 XX This package provides a Python implementation of calculating spectral...
ms2deepscore 2.6.0 dev Apache-2.0 X Deep learning similarity measure for comparing MS/MS spectra with...
ms2pip 4.1.0 doc dev Apache-2.0 XX MS²PIP: MS² Peak Intensity Prediction
ms2query 1.5.4 doc dev Apache-2.0 X Reliable and fast MS/MS spectral based analogue search.
ms2rescore 3.2.0.post1 doc dev Apache-2.0 X Modular and user-friendly platform for AI-assisted rescoring of peptide...
ms2rescore-rs 0.4.3 Apache-2.0 XX 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 XXX 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 XX microbiome-related extension to samtools
msaprobs 0.9.7 doc GPL-3.0-or-later XX MSAProbs is a well-established state-of-the-art multiple sequence...
mseqtools 0.9.1 MIT XX fastq/fasta file manipulation toolkit
msfragger 4.2 Academic X Ultrafast, comprehensive peptide identification for mass...
msgf_plus 2024.03.26 https://github. XXX MS-GF+ is a MS/MS database search tool
msi 0.3.8 doc dev GPL-3.0-or-later 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 XX 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 doc dev GPL-3.0-or-later 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 0.4.1 doc dev MIT X MSMetaEnhancer is a Python tool that adds more annotations (e.g....
msms 2.6.1 Free XX MSMS is a program written in the C programming language to compute...
msoma 0.1.2 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 XX A fast and accurate coalescent simulator.
msproteomicstools 0.11.0 BSD XX msproteomicstools is a Python library that can be used in LC-MS/MS...
msstitch 3.17 dev MIT XXX MS proteomics post processing utilities.
mstmap 1 GPL3 XX Accurate construction of genetic maps (Wu et al., PLoS Genetics,...
msweep 2.2.1 MIT XX 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 XX 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 dev 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 0.1.12 Apache-2.0 X A package for Mutation Attention Tool
mudskipper 0.1.0 BSD XX mudskipper is a tool for converting genomic BAM/SAM files to...
mugsy 1.2.3 Artistic XX Mugsy is a multiple whole genome aligner.
multigps 0.74 MIT X MultiGPS is a framework for analyzing collections of multi-condition...
multiqc 1.33 doc dev GPL-3.0-or-later XXX Aggregate results from bioinformatics analyses across many samples into...
multiqc-bcbio 0.2.9 GPL3 XXX MultiQC plugin for bcbio report visualization.
multiqc-xenium-extra 1.0.2 doc dev MIT X MultiQC plugin for extra Xenium spatial transcriptomics analysis
multiqc_sav 0.2.0 GPL3 X MultiQC plugin to visualize Illumina SAV plots
multirnafold 2.1 GPL-2.0-or-later XX 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 1.3.2 dev 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 XX DNA multiple sequence aligner from Penn State's Miller lab.
mumemto 1.3.4 doc dev GPL-3.0-only XX Finding maximal unique matches across pangenomes.
mummer 3.23 The XX 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 XX MUMmer is a system for rapidly aligning entire genomes.
munkres 1.0.7 Apache XXX munkres algorithm for the Assignment Problem
mupbwt 0.1.2 doc dev GPL-3.0-or-later XX A light pbwt-based index.
muscle 5.3 doc dev GPL-3.0-only XX Multiple sequence and structure alignment with top benchmark scores...
muse 2.1.2 doc dev GPL-2.0-or-later XX 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 XX MUltiScale enrIchment Calling for ChIP-Seq Datasets
music-deconvolution 0.1.1 GPL X Multi-subject single cell deconvolution
musicc 1.0.4 BSD XXX MUSICC: A marker genes based framework for metagenomic normalization...
mustang 3.2.4 doc file XX Mustang is a program that implements an algorithm for structural...
mutalyzer_hgvs_parser 0.3.9 doc dev MIT X Mutalyzer HGVS variant description parser
mutamr 0.0.2 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 1.14.1 doc dev MIT XX Detect and visualize target mutations by scanning FastQ files directly.
mutserve 2.0.3 MIT X Mutserve2 is a variant caller for the mitochondrial genome to detect...
mutyper 1.0.2 doc MIT XX A Python package and command line utility for annotating the local...
mvicuna 1.0 https://www.bro XX 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+ XXX detect creation/destruction of sequence motifs as a result of mutations
mwga-utils 0.1.6 GPL3 XX Collection of utilities for processing Multispecies Whole Genome Alignments
mycotools 1.0.0 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 XXX Python Client for MyGene.Info services.
mykatlas 0.6.1 MIT X Assists in discoveries of antibiotic-resistance with mykrobe
mykrobe 0.13.0 doc dev MIT XX Antibiotic resistance prediction in minutes.
myloasm 0.3.0 doc dev MIT X myloasm - high-resolution metagenome assembly for (noisy) long reads
mylotools 2.0.0 MIT X Utilities for manipulation and quality control of the myloasm long-read...
mypmfs_py 0.1.8 dev MIT X Python package for mypmfs training (includes batch download from PDB).
myriad 0.1.4 MIT XX Simple distributed computing.
mysql-connector-c 6.1.6 LGPL XX MySQL Connector/C, the C interface for communicating with MySQL servers.
mysqlclient 1.3.10 GNU XX Python interface to MySQL
mysterymaster 0.0.8 dev GPL X Graphical Oxford Nanopore read demultiplexer
mzmine 4.7.29 doc dev MIT X Integrative analysis of multimodal mass spectrometry data.
mzml2isa 1.1.1 GNU XXX 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 1.0.7 doc dev Apache-2.0 X HUPO-PSI Spectral library format
mztosqlite 2.1.1 GPL, XXX Convert proteomics data files into a SQLite database.
n50 1.9.3 doc dev MIT XXX A command-line tool to calculate the N50 value of a set of sequences...
naf 1.3.0 zlib XX Compressed binary file format for DNA/RNA/protein sequence data
nafcodec 0.3.1 doc dev MIT XX 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...
nail 0.4.0 dev BSD-3-Clause XX Profile Hidden Markov Model (pHMM) biological sequence alignment tool.
naltorfs 0.1.2 MIT X Nested Alternate Open Reading Frames (nAlt-ORFs)
namfinder 0.1.3 MIT XX Finds Non-overlapping Approximate Matches (NAMs) between query and...
nanoblaster 0.16 dev MIT XX Basic Local Alignment and Search Tool for Oxford Nanopore Long Sequences.
nanocall v0.7.4 MIT X An Oxford Nanopore Basecaller
nanocaller 3.6.2 MIT X NanoCaller for accurate detection of SNPs and indels in...
nanocomp 1.25.6 MIT XXX 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 XXX Filtering and trimming of Oxford Nanopore Sequencing data
nanoget 1.19.4 GPL-3.0-only XXX 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 XXX Removing lambda DNA control reads from fastq dataset
nanomath 1.4.0 dev GPL-3.0-or-later XXX 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 0.8.0 dev GPL-3.0-or-later X Python tools for detecting structural variation from nanopore sequence data.
nanomotif 1.0.2 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 1.46.2 dev MIT XXX Plotting suite for long read sequencing data and alignments.
nanoplotter 1.10.0 GPL-3.0 XXX Plotting functions of Oxford Nanopore sequencing data for NanoPack
nanopolish 0.14.0 dev MIT XX 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 XXX Nanopore SimulatION is a tool for simulating an Oxfornd Nanopore...
nanoq 0.10.0 MIT XX Ultra-fast quality control and summary reports for nanopore reads
nanoqc 0.10.0 dev GPL-3.0-or-later XXX Create fastQC-like plots for Oxford Nanopore sequencing data.
nanoraw 0.5 Other XXX Analysis of nanopore sequencing data.
nanosim 3.2.3 dev GPL-3.0-only XXX NanoSim is a fast and scalable read simulator for Nanopore sequencing data.
nanosim-h 1.1.0.4 GPLv3 XXX NanoSim-H is a simulator of Oxford Nanopore reads that captures the...
nanosimh v1.0.1.8 GPL XX NanoSimH is a fork of NanoSim (https://github.com/bcgsc/NanoSim), a...
nanosplit 0.1.4 MIT XX 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 XXX Calculate statistics for Oxford Nanopore sequencing data and alignments
nanosv 1.2.4 MIT XXX Structural variation detection tool for Oxford Nanopore data.
nanovar 1.8.3 GPL-3.0-or-later XX 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 XX NASP: an accurate, rapid method for the identification of SNPs in WGS...
nbitk 0.7.3 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 XX AMRFinder find acquired antimicrobial resistance genes in protein or...
ncbi-amrfinderplus 4.2.5 doc dev Public XX AMRFinderPlus finds antimicrobial resistance and other genes in protein...
ncbi-datasets-pyclient 18.13.0 doc dev BSD-3-Clause X NCBI Datasets API
ncbi-datasets-pylib 16.6.1 doc dev Unlicense X Easily gather data from across NCBI databases
ncbi-fcs-gx 0.5.5 NCBI-PD X The NCBI Foreign Contamination Screen. Genomic cross-species aligner,...
ncbi-genome-download 0.3.3 Apache XXX Download genome files from the NCBI FTP server.
ncbi-ngs-sdk 3.0.1 Public XX NGS is a new, domain-specific API for accessing reads, alignments and...
ncbi-stxtyper 1.0.45 doc Public XX StxTyper identifies and types Stx operons from assembled genomic sequence.
ncbi-util-legacy 6.1 Public X NCBI software development toolkit
ncbi-vdb 3.3.0 doc dev Public XX SRA tools database engine.
ncbi-vdb-py 3.2.1 dev Public X SRA tools database engine (Python bindings).
ncbimeta 0.8.3 MIT X Efficient and comprehensive metadata acquisition from the NCBI...
ncbitax2lin 3.0.0 dev MIT X NCBItax2lin
ncbitk 1.0a17 MIT X A tool kit for accessing NCBI's GenBank
ncfp 0.2.0 doc dev MIT XXX A program/module to find nt sequences that code for aa sequences
ncls 0.0.70 dev BSD-3-Clause XX A fast interval tree-like implementation in C, wrapped for the Python...
ncrf 1.01.02 MIT XX Noise-Cancelling Repeat Finder, Uncovering tandem repeats in...
nda-tools 0.5.0 dev MIT X Python package for interacting with NDA web services.
ndex-python 3.0.11.23 BSD XXX NDEx Python includes a client and a data model.
ndex2 3.11.0 doc dev BSD-3-Clause X Nice CX Python includes a client and a data model.
neat 4.3.5 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 XX NECAT is an error correction and de-novo assembly tool for Nanopore...
nedbit-features-calculator 1.2 MIT XX 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 0.7.1 dev MIT XX Fast FASTX parsing in Python
neffy 0.1.1 doc GPL-3.0-only XX A Python interface of NEFFy C++ tool: NEFF Calculator and MSA File Converter
neffy-cli 0.1.1 doc dev GPL-3.0-only XX NEFF calculator and MSA file converter
negative_training_sampler 0.3.1 MIT X Generates negative samples with the same GC distribution as the...
negspy 0.2.24 doc dev MIT X Python NGS tools
nemo 2.3.51 GPLv2 XX Individual-based forward-time genetics simulation software
nemo-age 0.30.0 GPL-3 XX In Nemo-age, it is possible to model genetic and phenotypic evolution...
neodisambiguate 1.1.1 doc MIT X Disambiguate reads that were mapped to multiple references.
neofox 1.2.3 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 XXX 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 XX 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 XX Metadata information from netcdf file for Galaxy use.
netifaces 0.10.4 MIT XX None
netmd 1.0.3 doc dev MIT X NetMD is a computational method for identifying consensus behavior...
netreg 1.8.0 doc GPL3 XX netReg fits linear regression models using network-penalization.
netsyn 1.0.0 CeCiLL X NetSyn is a tool to detect conserved genomic contexts (i.e. synteny...
networkxgmml 0.1.6 UNKNOWN XXX XGMML parser for networkx
neurodocker 0.5.0 Apache-2.0 XXX Neurodocker is a command-line program that generates custom Dockerfiles...
newick_utils 1.6 BSD XX The Newick Utilities are a suite of Unix shell tools for processing...
newmap 0.2 doc dev GPL-3.0-or-later X Tool for creating mappability data for reference sequences.
newt 0.52.18 GPL X None
nextalign 2.14.0 doc dev MIT XX Viral genome alignment
nextclade 3.18.1 doc dev MIT XX Viral genome alignment, mutation calling, clade assignment, quality...
nextclade2 2.14.0 doc dev MIT XX Viral genome alignment, mutation calling, clade assignment, quality...
nextclade_js 0.14.4 MIT XX SARS-CoV-2 genome clade assignment, mutation calling, and sequence...
nextdenovo 2.5.2 doc dev GPL-3.0-or-later XX String graph-based de novo assembler for long reads (CLR, HiFi and ONT)
nextflow 25.10.2 Apache-2.0 XXX A DSL for data-driven computational pipelines http://nextflow.io
nextgenmap 0.5.5 MIT XX NextGenMap is a flexible highly sensitive short read mapping tool that...
nextpolish 1.4.1 doc dev GPL-3.0-or-later XX Fast and accurately polish the genome generated by noisy long reads
nextpolish2 0.2.2 doc dev GBPL XX Repeat-aware polishing genomes assembled using HiFi long reads.
nextstrain 20200304 doc dev The X Nextstrain toolchain (meta-package)
nextstrain-cli 10.4.1 doc dev MIT X The Nextstrain command-line interface (CLI).
nf-core 3.5.1 doc dev MIT X Python package with helper tools for the nf-core community.
nf-test 0.9.3 MIT X nf-test is a simple test framework for Nextflow pipelines.
ngless 1.5.0 MIT XX A tool for short-read processing with a focus on metagenomics
nglview 1.1.7 doc dev MIT XXX An IPython widget to interactively view molecular structures and...
ngmaster 1.1.1 doc dev GPL-3.0-only X In silico multi-antigen sequence typing for Neisseria gonorrhoeae...
ngmerge 0.5 doc dev MIT XX Merging paired-end reads and removing sequencing adapters.
ngmlr 0.2.7 doc dev MIT XX ngmlr is a long-read mapper designed to align PacBio or Oxford Nanopore...
ngs-bits 2025_09 dev MIT XX 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 dev MIT XX 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 XXX 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 20.0 GPL-3.0-or-later XX Basic ChIP/DNaseI/ATAC analysis - from FASTQ to visualisation of...
ngsfetch 0.1.1 doc dev MIT X Fast retrieval of metadata and fastq files with ffq and aria2c
ngshmmalign 0.1.1 GNU XX 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, XX ngsLCA: fast and flexible taxonomic classification of DNA reads aligned...
ngsngs 0.9.2 GPLv3, XX NGSNGS: Next Generation Simulator for Next Generation Sequencing data
ngsplotdb-ngsplotdb-hg19 3.00 GPL-2.0 XX HG19 genome database for NGSplot
ngsrelate 2.0 dev GPL-2.0-only X Software tool for estimating pairwise relatedness from next-generation...
ngsutils 0.5.9 BSD XX 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 XX Niema's C++ implementations of graph generators
nifflr 2.0.0 doc dev GPL-3.0-or-later X NIFFLR: Novel IsoForm Finder using Long RNASeq reads.
nii2dcm 0.1.2 dev BSD-3 X nii2dcm: NIfTI to DICOM creation with Python
nim-abif 0.2.0 doc dev MIT XX Parse ABIF files from the command line
nim-falcon 3.0.2 MIT XX 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 XX Nearly Infinite Neighbor Joining Application
nlstradamus 1.8 GNU XX NLStradamus: a simple Hidden Markov Model for nuclear localization...
nmrglue 0.9 BSD-3-Clause XX A module for working with NMR data in Python
nmrml2isa 0.3.3 GPL-3.0-or-later XXX nmrml2isa - nmrML to ISA-Tab parsing tool
nmrpro 20161019 MIT XXX NMRPro reads and processes different types of NMR spectra.
nmslib-metabrainz 2.1.3 dev Apache-2.0 XX Non-Metric Space Library (NMSLIB).
noah-cli 0.2.0 dev MIT X a project management tool for reproducible, portable, and streamlined...
nohuman 0.5.0 doc dev MIT XX Remove human reads from a sequencing run.
noise2read 0.3.0 MIT X Turn noise to read
nolb 1.9 All XX NOn-Linear rigid Block NMA approach (NOLB) is a conceptually simple and...
nomadic 0.7.1 doc dev MIT X Mobile sequencing and analysis in real-time
nonpareil 3.5.5 doc dev Artistic XX Estimate average coverage and create curves for metagenomic datasets.
nopilesum 1.1.2 MIT XX nopilesum is a D program that functions as an alternative to...
nordic 2.7.1 doc dev MIT XX 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 XXX Simple yaml-based config module
nose-capturestderr 1.2 GPL XX Nose plugin for capturing stderr.
notramp 1.1.9 doc BSD-2 X Super-fast Normalization and Trimming for Amplicon Sequencing Data...
novae 1.0.1 doc dev 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 XX Powerful tool designed for mapping of short reads onto a reference...
novobreak 1.1.3rc MIT XX local assembly for breakpoint detection in cancer genomes
novoloci 0.5 dev Other X Haplotype-aware assembler for complex regions and small genomes (ONT/HiFi).
novoplasty 4.3.5 Other XXX The organelle assembler and heteroplasmy caller
np-likeness-scorer 2.1 XX 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 XXX Writing user interfaces without all that ugly mucking about in hyperspace
nrpys 0.1.1 AGPL-3.0-or-later XXX Python language bindings for nrps-rs substrate specificity predictor.
nseg 1.0.1 dev Public XX 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 doc dev MIT XX Estimating k-mer coverage histogram of genomics data.
ntedit 2.1.1 doc dev GPL-3.0-or-later XX Ultrafast, lightweight, scalable genome assembly polishing, and SNV...
nthits 1.0.3 MIT XX ntHits is a tool for efficiently counting and filtering k-mers based on...
ntjoin 1.1.5 GPL-3.0 XXX Genome assembly scaffolder using minimizer graphs
ntlink 1.3.11 GPL-3.0 XXX Genome assembly scaffolder using long reads and minimizers
ntm-profiler 0.8.0 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 XXX Ancestry inference from genomic data
ntsm 1.2.1 doc dev MIT XX ntsm - Nucleotide Sequence/Sample Matcher
ntstat 1.0.1 GPL-3.0-or-later XX a toolkit for statistical analysis of k-mer frequency and depth
ntsynt 1.0.4 dev GPL-3.0-or-later XX Detecting multi-genome synteny blocks using minimizer graph mapping.
nucamino 0.1.3 MIT XX A nucleotide to amino acid alignment program optimized for virus gene sequences
nucdiff 2.0.3 MPL-2.0 XXX NucDiff locates and categorizes differences between two closely related...
nucflag 0.3.8 MIT X NucFlag misassembly identifier.
nucleoatac 0.3.4 doc MIT XXX 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 XXX Marks/removes duplicate molecules based on the molecular tagging...
nullarbor 2.0.20191013 GPL2 XX 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 XXX The Naive Variant Caller
nwalign3 0.1.6 dev BSD-4-Clause-UC XX Updated version of nwalign (Needleman-Wunsch global sequence alignment)...
nwkit 0.18.2 BSD-3-Clause X Tools for processing newick trees
nxtrim 0.4.3 doc dev BSD-2-Clause XX Software to remove Nextera Mate Pair adapters and categorise reads...
oakvar 2.12.22 doc dev AGPL-3.0-or-later X OakVar - Genomic Variant Analysis Platform
oarfish 0.9.0 BSD-3-Clause XX oarfish is a tool for fast, accurate and versatile transcript...
oases 0.2.09 GPL-3.0-or-later XX De novo transcriptome assembler for short reads
oatk 1.0 MIT XX Oatk: an organelle genome assembly toolkit
oauth2client 1.5.2 Apache XX client library for OAuth 2.0
obitools 1.2.13 CeCILL-V2 XX The OBITools package is a set of programs specifically designed for...
obitools4 4.4.0 CECILL-2.1 XX A software package for DNA metabarcoding
obonet 1.1.1 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 XX Ococo, the first online consensus caller.
ocrad 0.21 GPL XX Ocrad is an optical character recognition program.
octopus 0.7.4 MIT XX Octopus is a mapping-based variant caller that implements several...
octopusv 0.2.3 dev MIT X OctopusV: Advanced Structural Variant Analysis Toolkit.
odamnet 1.1.0 dev MIT X Study molecular relationships between chemicals and rare diseases
odgi 0.9.3 doc dev MIT XX An optimized dynamic genome/graph implementation.
odose 1.0 MIT XX Ortholog Direction of Selection Engine.
ogdf 201207 GPLv3 XX The Open Graph Drawing Framework is a self-contained C++ class library...
ogmapper 1.0.0 GPLv3 XX A fast and light genomic mapper for short reads
ogtfinder 0.0.2 dev MIT X OGTFinder is an optimal growth temperature prediction tool for...
olga 1.3.0 dev GPL-3.0-only X OLGA (Optimized Likelihood estimate of immunoGlobulin Amino-acid...
oligoarrayaux 3.8.1 ACADEMIC XX OligoArrayAux is a subset of the UNAFold package for use with OligoArray.
oligomap 1.0.1 dev AGPL-3.0-or-later XX Oligomap is a program for fast identification of nearly-perfect matches...
oligon-design 1.0.0 GPL-3.0 X Simple and versatile approach to design specific oligonucleotides from...
oligotyping 2.1 GNU XX The oligotyping and minimum entropy decomposition (MED) pipeline for...
olivar 1.3.3 dev GPL-3.0-or-later X Olivar PCR tiling design
omamer 2.1.2 LGPL-3.0 X OMAmer - tree-driven and alignment-free protein assignment to sub-families
omark 0.4.1 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 XX 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 XXX 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 XX 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 XXX Oxford Nanopore Technologies fast5 API software
ont-modkit 0.6.0 doc dev Oxford XX A bioinformatics tool for working with modified bases in Oxford...
ont-tombo 1.5.1 mpl-2.0 XX Detection of modified bases from raw nanopore sequencing data.
ont_vbz_hdf_plugin 1.0.12 MPL-2 XX VBZ compression plugin for nanopore signal data
ontime 0.3.1 dev MIT XX Extract subsets of ONT (Nanopore) reads based on time.
onto2nx 0.1.1 doc GPL XXX 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 2.16.0 doc dev MIT X OpenCRAVAT - variant analysis toolkit
openbabel 2.3.90dev7d621d9 GPLv2 XX A chemical toolbox designed to speak the many languages of chemical data
opencontactcli 1.1 https://github. XX 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 XXX Exhaustive generation of chemical structures
openms 3.5.0 doc dev BSD-3-Clause XX The OpenMS TOPP tools (without GUI components and adapted thirdparty tools).
openms-thirdparty 3.5.0 doc dev BSD-3-Clause XX A helper package to install OpenMS TOPP tools with all their compatible...
openms-tools 2.4.0 BSD XX OpenMS is an open-source software C++ library for LC-MS data management...
openpyxl 2.4.0 MIT XX A Python library to read/write Excel 2010 xlsx/xlsm files
openslide 3.4.1 GNU XX OpenSlide is a C library that provides a simple interface to read...
openslide-python 1.1.1 GNU XX Python interface to OpenSlide
openstructure 2.11.1 doc dev LGPL-3.0-or-later XX Open-Source Computational Structural Biology Framework.
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 XXX OPSIN is a Java(1.6+) library for IUPAC name-to-structure conversion...
optbuild 0.2.1 GNU XXX build command lines for external programs
opticlust 0.5.0 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 XX Precision HLA typing from next-generation sequencing data
optplus 0.2 UNKNOWN XXX additional options for optparse
orfanage 1.2.0 GPL-3.0-or-later XX Ultra-efficient and sensitive method to search for ORFs in spliced...
orfipy 0.0.4 MIT XX orfipy: fast and flexible search for open reading frames in fasta sequences
orfm 1.4.0 LGPL-3.0 XX 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 XX 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 XX In silico read normalization
orsum 1.8.0 MIT X A tool to filter long lists of enriched terms resulting from one or...
orthanq 1.21.0 doc dev MIT XX Uncertainty aware HLA typing and general haplotype quantification.
orthodb 0.9.1 doc dev GPL3 X Interface to OrthoDB REST API.
orthofinder 3.1.1 doc dev GPL-3.0-only XXX 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 3.8.2 doc dev GPL-3.0-or-later XX Ortholog detection for comparative genomics and fast functional...
orthomcl 2.0.9 EuPathDB XXX 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 0.2.9 doc dev MIT X A comprehensive toolkit for quality control and analysis of single-cell...
outrigger 1.1.1 BSD XXX Outrigger detects *de novo* exons and quantifies their percent spliced-in
ovrlpy 1.0.1 doc dev MIT X A python tool to investigate cell overlaps in imaging-based spatial...
owl 0.4.0 BSD-3-Clause-Clear X Microsatellite analysis for HiFi data
oxbow 0.5.1 dev MIT XX Read genomic file formats into data frames and more.
p7zip 15.09 LGPLv2 X p7zip is a quick port of 7z.exe and 7za.exe (command line version of...
pacbio_falcon 052016 Standard XX A set of tools for fast aligning long reads for consensus and assembly
pacini_typing 2.0.2 dev AGPL-3.0 X YAML-based bacterial genotyping application
pacu_snp 1.0.0 dev GPL-3.0-or-later X PACU is a workflow for whole genome sequencing based phylogeny of...
padloc 2.0.0 MIT X Locate antiviral defence systems in prokaryotic genomes
paf2chain 0.1.1 dev MIT XX convert PAF format to CHAIN format
pafpy 0.2.0 doc Unlicense X A lightweight library for working with PAF (Pairwise mApping Format) files
paidiverpy 0.2.1 dev Apache-2.0 X A library to preprocess image data.
pairix 0.3.9 dev MIT XX 2D indexing on bgzipped text files of paired genomic coordinates
pairsnp 0.3.1 dev MIT XX pairsnp calculates pairwise SNP distance matrices from multiple...
pairtools 1.1.3 doc dev MIT XX 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 XXX Find microsatellite repeat elements from sequencing reads and design...
paladin 1.6.0 doc dev MIT XX Protein Alignment and Detection Interface.
palantir 1.4.2 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 XX pAliKiss predicts RNA secondary structures for fixed RNA multiple...
paml 4.10.9 doc dev GPL-3.0-or-later XX 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 0.4.1 dev MIT XX panacus is a tool for computing counting statistics for GFA files.
panaln 2.09 MIT X Indexing pangenome for read alignment.
panaroo 1.5.2 doc dev MIT X panaroo - an updated pipeline for pangenome investigation
pancake 1.1.2 MIT XXX A Data Structure for Pangenomes -- Identification of Singletons and...
panchip 3.0.14 MIT X Pan-ChIP-seq Analysis of Peak Sets
pandaseq 2.11 GPL3 XX 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 1.7.2 dev Apache-2.0 X Compute gene-cluster specific k-mers over a pangenome
pangbank-api 0.1.2 CeCiLL X API for managing the PanGBank pangenome database, including a CLI to...
pangene r231 dev Unknown XX Pangene is a command-line tool to construct a pangenome gene graph.
pangenie 4.2.1 doc MIT X Genotyping toolkit based on k-mer counting and haplotype panels.
pango-collapse 0.8.2 GPL-3.0-or-later X Collapse Pango sublineages up to user defined parent lineages.
pango-designation 1.36 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 4.3.4 GPL-3.0-only X Phylogenetic Assignment of Named Global Outbreak LINeages
pangolin-data 1.36 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
pangwas 0.1.0 Apache-2.0 X A pipeline for pangenome wide association studies (panGWAS).
pangwes 0.3.0_alpha MIT XX 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...
panman 0.1.4 doc dev MIT XX PanMAN
panoct 3.23 dev GPL-3.0-or-later XXX PanOCT, Pan-genome Ortholog Clustering Tool, is a program for...
panoptes-ui 0.2.3 MIT X panoptes: monitor computational workflows in real time
panorama 0.5.0 doc CeCiLL X A robust pangenome-based method for predicting and comparing biological...
panpasco 1.0.1 MIT X Pipeline for pangenome mapping and pairwise SNP distance
panphlan 3.1 dev MIT XX PanPhlAn is a strain-level metagenomic profiling tool for identifying...
panplexity 0.1.1 dev MIT XX Find low-complexity regions in pangenome graphs
panta 1.0.1 MIT X PanTA - pan-genome pipeline
pantax 2.0.0 GPL-3.0-or-later X Strain-level metagenomic profiling using pangenome graphs with PanTax
pantools 4.3.4 doc dev GPL-3.0-only XXX PanTools is a pangenomic toolkit for comparative analysis of large...
panx 1.6.0 GNU XX 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 XX Paraclu finds clusters in data attached to sequences.
parafly r2013_01_21 The XX Given a file containing a list of unix commands, multithreading is used...
paragone 1.1.3 doc dev GPL-3.0-or-later XXX 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 XX GNU parallel is a shell tool for executing jobs in parallel using one...
parallel-fastq-dump 0.6.7 MIT XXX 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 XXX We developed the PARalyzer algorithm to generate a high resolution map...
paraphase 3.4.0 BSD-3-Clause-Clear X HiFi-based caller for highly homologous genes
parasail 2.6.2 doc dev MIT XX Pairwise Sequence Alignment Library
parasail-python 1.3.4 doc dev BSD-3-Clause XX Python bindings for the parasail C library containing implementations...
parascopy 1.18.0 doc dev MIT XXX 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...
paraviewer 0.1.0 dev Pacific X Automated visualization generator for Paraphase HiFi analysis tool
pardre 2.2.5 GPL-3.0-only XX 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 0.1.44 https://github. X PARM: Promoter Activity Regulatory Model
parnas 0.1.7 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 2.1.5 doc dev custom; XX Parsnp is a command-line-tool for efficient microbial core genome...
pasa 2.5.3 doc dev BSD-3-Clause XX 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 1.9.3 doc dev GPL-3.0-or-later XX 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 1.9.51 doc dev GPL-3.0-or-later X Ancestral character reconstruction and visualisation for rooted...
pastrami 1.0.1 doc dev 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 5.1.0 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 doc dev GPLv3 XXX Species identification and strain attribution with unassembled sequencing data
pathphynder 1.2.4 MIT X A workflow for ancient DNA placement into reference phylogenies.
pathracer 3.16.0.dev GPLv2 XX PathRacer is a tool for alignment of profile HMM against assembly graph.
pathwaymatcher 1.9.1 Apache XXX 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 XXX 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 XX 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 XX 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 XX C utilities for PacBio assembly (pbipa etc.)
pbaa 1.2.0 BSD-3-Clause-Clear XX PacBio tool to cluster HiFi reads and generate high quality consensus sequences
pbalign 0.3.2 BSD-3-Clause-Clear XXX Python wrapper for producing PBBAM valid alignments
pbbam 2.4.0 BSD-3-Clause-Clear XX PacBio BAM C++ library
pbccs 6.4.0 BSD-3-Clause-Clear XX pbccs - Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)
pbcommand 2.1.1 BSD-3-Clause-Clear XXX Library for generating the CLI of various PacBio tools
pbcopper 2.3.0 BSD-3-Clause-Clear XX Core C++ library for data structures, algorithms, and utilities
pbcore 2.1.2 BSD-3-Clause-Clear XXX A Python library for reading and writing PacBio data files
pbcoretools 0.8.1 BSD-3-Clause-Clear XXX 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 XX pbgcpp - GenomicConsensus in C++
pbgzip 2016.08.04 MIT/Expat XX Parallel Block GZIP
pbh5tools 0.8.0 BSD-3-Clause XX A swiss-army knife for interrogating PacBio® HDF5 files (cmp.h5, bas.h5).
pbhoover 1.1.0 GPLv3 XXX Variant caller for legacy and low coverage Pacific Biosciences'...
pbiotools 5.0.0 dev MIT X Miscellaneous bioinformatics and other supporting utilities for Python 3.
pbipa 1.8.0 BSD X Improved Phased Assembly
pbjasmine 2.7.99 BSD-3-Clause-Clear X jasmine
pblaa 2.4.2 BSD-3-Clause-Clear XX PacBio tool to deconvolute mixtures of alleles and loci into phased...
pblat 2.5.1 dev OTHER XX 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 XX A minimap2 frontend for PacBio native data formats
pbpigeon 1.4.0 BSD-3-Clause-Clear XX PacBio transcript toolkit
pbptyper 2.0.0 MIT X In silico Penicillin Binding Protein (PBP) typer for Streptococcus...
pbsim 1.0.3 GPL-2.0-or-later XX PBSIM simulates PacBio reads.
pbsim2 2.0.1 GPL-2.0 XX PBSIM2: a simulator for long read sequencers with a novel generative...
pbsim3 3.0.5 GPL-2.0-only XX 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 2.0.1 dev BSD-3-Clause-Clear X A phase-aware pharmacogenomic diplotyper for PacBio sequencing data
pbsv 2.11.0 BSD-3-Clause-Clear XX 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 XX Positional Burrows-Wheeler Transform - methods for storing and...
pcangsd 1.36.4 doc dev GPL-3.0-or-later XX Framework for analyzing low-depth next-generation sequencing (NGS) data...
pcaone 0.6.0 doc dev GPL-3.0-only XX PCAone - Principal Component Analysis All in One.
pcasuite 1.0.0 Apache XX PCAzip compresses a trajectory, recentering the snapshots using a...
pcdl 3.3.8 doc dev BSD-3-Clause X physicell data loader (pcdl) provides a platform independent, python3...
pcne 2.0.0 dev MIT X Estimates plasmid copy number from assembled genome.
pcst-fast 1.0.10 MIT XX A fast implementation of the Goemans-Williamson scheme for the PCST...
pdb2fasta 1.0 dev GPL-2-only XX Convert PDB structures to FASTA sequences.
pdbx 827b2a2 doc dev UNKNOWN XX A parser module in python for structures of the protein data bank in...
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 XX 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 XXX Peakzilla identifies sites of enrichment and transcription factor...
pear 0.9.6 CC-BY-NC-SA-3.0 XX Paired-End reAd mergeR
pecat 0.0.3 dev BSD-2-Clause X A phased error correction and assembly tool.
ped_parser 1.6.6 BSD XX A ped file parser.
pedagree 0.0.11 MIT X pleasingly pythonic pedigree manipulation
peddy 0.4.8 MIT XXX 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 XX A collection of Bayesian approaches to infer hidden determinants and...
peewee 2.8.0 MIT XX a little orm
pegas 1.0.9 doc dev GPL-2.0-or-later X PeGAS is a Snakemake pipeline for genome analysis
pegasusio 0.10.0 doc dev BSD-3-Clause XX PegasusIO is the IO package for Pegasus.
pegasuspy 1.10.2 doc dev BSD-3-Clause XX 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 XX 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 XXX Peak-calling and Prioritization pipeline for replicated ChIP-Seq data
pepsirf 1.7.1 doc dev GPL-3.0-only XX Peptide-based Serological Immune Response Framework.
peptide-shaker 3.0.11 doc dev Apache-2.0 XXX Independent platform for interpretation of proteomics identification results.
peptides 0.5.0 MIT X Physicochemical properties, indices and descriptors for amino-acid sequences.
perbase 1.2.0 doc dev MIT XXX 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 doc dev CC XX A genome assembler designed for long-reads that have good enough accuracy.
perl-aceperl 1.92 unknown XX Object-Oriented Access to ACEDB Databases
perl-acme-damn 0.08 doc Perl_5 XX 'Unbless' Perl objects.
perl-algorithm-cluster 1.59 unknown XX Perl interface to the C Clustering Library
perl-algorithm-dependency 1.112 perl_5 XXX Base class for implementing various dependency trees
perl-algorithm-diff 1.1903 unknown XXX Compute intelligent differences between two files / lists but use the...
perl-algorithm-munkres 0.08 unknown XXX Munkres.pm
perl-aliased 0.34 perl_5 XXX Use shorter versions of class names.
perl-alien-build 2.84 perl_5 XX Build external dependencies for use in CPAN
perl-alien-build-plugin-download-gitlab 0.01 doc dev Perl_5 X Alien::Build plugin to download from GitLab
perl-alien-libxml2 0.20 doc dev Perl_5 XX Installs the C libxml2 library on your system.
perl-apache-test 1.43 unknown XXX Special Tests Sequence Failure Finder
perl-app-cpanminus 1.7044 perl_5 XX get, unpack, build and install modules from CPAN
perl-appconfig 1.71 perl_5 XXX AppConfig is a bundle of Perl5 modules for reading configuration files...
perl-archive-extract 0.88 perl_5 XXX Generic archive extracting mechanism
perl-archive-tar 3.04 doc Perl_5 XXX Manipulates TAR archives.
perl-archive-tar-wrapper 0.33 gpl_3 XXX API wrapper around the 'tar' utility
perl-archive-zip 1.68 perl_5 XXX Provide an interface to ZIP archive files.
perl-array-compare 3.0.1 perl_5 XXX Perl extension for comparing arrays.
perl-array-set 0.063 perl_5 XXX Perform set operations on arrays
perl-array-utils 0.5 unknown XXX small utils for array manipulation
perl-atlas-modules 0.3.1 Apache XX A package exporting in-house perl functions and classes used in the...
perl-attribute-handlers 0.96 perl_5 XXX Simpler definition of attribute handlers
perl-authen-sasl-saslprep 1.100 perl_5 XXX A Stringprep Profile for User Names and Passwords (RFC 4013)
perl-autodie 2.37 doc Perl_5 XXX Replace functions with ones that succeed or die with lexical scope.
perl-autoloader 5.74 perl_5 XXX load subroutines only on demand
perl-b 1.48 perl_5 XXX The Perl Compiler Backend
perl-b-debug 1.26 perl_5 XXX print debug info about ops
perl-b-hooks-endofscope 0.26 perl_5 XX Execute code after a scope finished compilation
perl-base 2.23 unknown XXX compile-time class fields
perl-bignum 0.67 doc Perl_5 XXX Transparent BigNumber support for Perl.
perl-bio-asn1-entrezgene 1.73 perl_5 XXX Regular expression-based Perl Parser for NCBI Entrez Gene
perl-bio-automatedannotation 2023.03.14.16. doc Open XXX Automated annotation of assemblies.
perl-bio-bigfile 1.07 doc Apache-2.0 XX 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 XXX Parse CIGAR strings and translate coordinates to/from reference/query
perl-bio-coordinate 1.007001 perl_5 XXX 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 doc Apache-2.0 XX 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 0.17 dev BSD-3-Clause XX Perl modules and scripts for interfacing with Sean Eddy's C easel...
perl-bio-eutilities 1.77 perl_5 XXX Webagent which interacts with and retrieves data from NCBI eUtils.
perl-bio-featureio 1.6.905 perl_5 XXX Modules for reading, writing, and manipulating sequence features
perl-bio-gff3 2.0 perl_5 XXX fast, low-level GFF3 manipulation
perl-bio-kmer 0.55 MIT XX A perl module for helping with kmer analysis.
perl-bio-mlst-check 2.1.1706216 gpl_3 XXX Multilocus sequence type checking using blast
perl-bio-monophylizer 1.0.0 doc Perl_5 X A web and command line tool to assess monophyly
perl-bio-phylo 2.0.2 doc Perl_5 XXX 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 doc Perl_5 XXX 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 XX 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 doc Perl_5 XX 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 XXX Parses output from the PAML programs codeml, baseml, basemlg,...
perl-bio-tools-run-alignment-clustalw 1.7.4 perl_5 XXX Object for the calculation of a multiple sequence alignment from a set...
perl-bio-tools-run-alignment-tcoffee 1.7.4 perl_5 XX 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 XXX A Perl distribution for Next-Generation Sequencing (NGS) data analysis
perl-bioperl 1.7.8 perl_5 XXX Bioinformatics Toolkit
perl-bioperl-core 1.007002 perl_5 XXX "Core" packages for the BioPerl toolkit; you really should...
perl-bioperl-run 1.007003 perl_5 XXX BioPerl-Run - wrapper toolkit
perl-biosails 0.02 perl_5 XXX Standard(ized) Analysis Information Layers
perl-biox-seq 0.008009 GPL-3.0-or-later XXX a basic but fast biological sequence object and associated parsers
perl-biox-workflow 1.10 perl_5 XX None
perl-biox-workflow-command 2.4.1 perl_5 XX 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 XXX Efficient bit vector, set of integers and "big int" math library
perl-blib 1.06 perl_5 XXX Use MakeMaker's uninstalled version of a package
perl-bloom-faster 1.7 unknown XX Perl extension for the c library libbloom.
perl-border-style 0.01 perl_5 XXX Border style structure
perl-btlib 0.19 open XX Binary Search Tree library
perl-bundle-bioperl 2.1.9 unknown XXX A bundle to install external CPAN modules used by BioPerl 1.5.2
perl-business-isbn 3.007 artistic_2 XXX work with International Standard Book Numbers
perl-business-isbn-data 20210112.006 perl_5 XXX data pack for Business::ISBN
perl-cache-cache 1.08 unknown XXX extends Cache::SizeAwareMemoryCache
perl-cairo 1.109 lgpl_2_1 XX Perl interface to the cairo 2d vector graphics library
perl-canary-stability 2013 unknown XXX canary to check perl compatibility for schmorp's modules
perl-capture-tiny 0.48 apache_2_0 XXX Capture STDOUT and STDERR from Perl, XS or external programs
perl-carp 1.38 perl_5 XXX alternative warn and die for modules
perl-carp-clan 6.08 perl_5 XXX 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 4.71 doc GPL XX A generic file fetching mechanism.
perl-class-accessor 0.51 perl_5 XXX Automated accessor generation
perl-class-data-inheritable 0.09 perl_5 XXX Inheritable, overridable class data
perl-class-inspector 1.36 perl_5 XXX Get information about a class and its structure
perl-class-load 0.25 perl_5 XXX A working (require "Class::Name") and more
perl-class-load-xs 0.10 artistic_2 XX XS implementation of parts of Class::Load
perl-class-method-modifiers 2.13 perl_5 XXX Provides Moose-like method modifiers
perl-class-methodmaker 2.25 perl_5 XX Create generic methods for OO Perl
perl-class-singleton 1.6 unknown XXX Base class for creating singleton objects
perl-class-std 0.013 perl_5 XXX Support for creating standard "inside-out" classes
perl-class-std-fast 0.0.8 perl_5 XXX 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 XX Generate fast XS accessors without runtime compilation
perl-clone 0.46 perl_5 XX recursively copy Perl datatypes
perl-clone-choose 0.010 perl_5 XXX Choose appropriate clone utility
perl-clone-pp 1.08 perl_5 XXX Recursively copy Perl datatypes
perl-color-theme 0.10.1 perl_5 XXX Color theme structure
perl-common-sense 3.75 perl_5 XXX Sane defaults for Perl programs
perl-compress-bgzf 0.005 gpl_3 XXX Read/write blocked GZIP (BGZF) files
perl-compress-raw-bzip2 2.201 perl_5 XX Low-Level Interface to bzip2 compression library
perl-compress-raw-zlib 2.105 perl_5 XX Basic utilities for writing tests.
perl-config-any 0.33 perl_5 XX Load configuration from different file formats, transparently
perl-config-autoconf 0.320 doc Perl_5 XX A module to implement some of AutoConf macros in pure perl.
perl-config-general 2.67 perl_5 XXX Generic Config Module
perl-config-simple 4.58 unknown XXX simple configuration file class
perl-config-tiny 2.28 perl_5 XXX Read/Write .ini style files with as little code as possible
perl-const-fast 0.014 perl_5 XXX Facility for creating read-only scalars, arrays, and hashes
perl-constant 1.33 perl_5 XXX Perl pragma to declare constants
perl-convert-binary-c 0.86 perl_5 XX Binary Data Conversion using C Types
perl-convert-binhex 1.125 perl_5 XXX extract data from Macintosh BinHex files
perl-cpan-meta 2.150010 perl_5 XXX the distribution metadata for a CPAN dist
perl-cpan-meta-check 0.014 perl_5 XXX Verify requirements in a CPAN::Meta object
perl-cpan-meta-requirements 2.143 perl_5 XXX a set of version requirements for a CPAN dist
perl-cpan-meta-validator 2.140640 perl_5 XXX validate CPAN distribution metadata structures
perl-cpan-meta-yaml 0.018 perl_5 XXX Read and write a subset of YAML for CPAN Meta files
perl-cpan-shell 5.5004 perl_5 XXX None
perl-crypt-openssl-guess 0.15 perl_5 XXX Guess OpenSSL include path
perl-crypt-openssl-random 0.11 perl_5 XX OpenSSL/LibreSSL pseudo-random number generator access
perl-crypt-openssl-rsa 0.37 perl_5 XX RSA encoding and decoding, using the openSSL libraries
perl-crypt-rc4 2.02 unknown XXX Perl implementation of the RC4 encryption algorithm
perl-data-compare 1.25 unknown XXX compare perl data structures
perl-data-dump 1.25 perl_5 XX Pretty printing of data structures
perl-data-dumper 2.183 unknown XX seeds germane, yet not germinated
perl-data-lock 1.03 unknown X makes variables (im)?mutable
perl-data-match 0.06 unknown XXX Complex data structure pattern matching
perl-data-munge 0.111 doc Perl_5 XXX Various utility functions.
perl-data-optlist 0.112 perl_5 XXX 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 XXX Structured Tags
perl-data-utilities 0.04 unknown XXX recursively compare Perl datatypes
perl-data-uuid 1.227 doc BSD XX Globally/Universally Unique Identifiers (GUIDs/UUIDs).
perl-data-visitor 0.30 perl_5 XXX Visitor style traversal of Perl data structures
perl-data-walk 2.01 open_source XXX Traverse Perl data structures.
perl-date-format 2.30 perl_5 XX Date formating subroutines
perl-date-manip 6.98 doc Perl_5 XXX Date manipulation routines.
perl-datetime 1.66 doc Artistic_2 XX A date and time object for Perl.
perl-datetime-format-strptime 1.80 doc Artistic_2 XXX Parse and format strp and strf time patterns.
perl-datetime-locale 1.45 doc Perl_5 XX Localization support for DateTime.pm.
perl-datetime-timezone 2.66 doc Perl_5 XX Time zone object base class and factory.
perl-db-file 1.855 perl_5 XX Perl5 access to Berkeley DB version 1.x.
perl-dbd-mysql 5.013 doc Perl_5 XX A MySQL driver for the Perl5 Database Interface (DBI).
perl-dbd-pg 3.18.0 doc Perl_5 XX DBI PostgreSQL interface.
perl-dbd-sqlite 1.76 doc Perl_5 XX Self Contained RDBMS in a DBI Driver.
perl-dbi 1.643 perl_5 XX Database independent interface for Perl
perl-dbm-deep 2.0019 perl_5 XXX A pure perl multi-level hash/array DBM that supports transactions
perl-devel-assert 1.06 perl_5 XX assertions for Perl >= 5.14
perl-devel-checkbin 0.04 perl_5 XXX check that a command is available
perl-devel-checklib 1.16 doc dev Perl_5 XXX Check that a library is available.
perl-devel-checkos 1.81 unknown XXX check what OS we're running on
perl-devel-cover 1.33 perl_5 XX Code coverage metrics for Perl
perl-devel-cycle 1.12 unknown XXX Find memory cycles in objects
perl-devel-globaldestruction 0.14 perl_5 XXX Provides function returning the equivalent of ${^GLOBAL_PHASE} eq...
perl-devel-overloadinfo 0.007 perl_5 XXX introspect overloaded operators
perl-devel-size 0.85 perl_5 XX Perl extension for finding the memory usage of Perl variables
perl-devel-stacktrace 2.04 artistic_2 XXX An object representing a stack trace
perl-devel-symdump 2.18 perl_5 XXX dump symbol names or the symbol table
perl-digest-crc 0.23 PUBLIC-DOMAIN XX Generic CRC functions
perl-digest-crc32 0.01 perl_5 XXX Cyclic Redundency Check digests implementation
perl-digest-hmac 1.05 doc Perl_5 XXX Keyed-Hashing for Message Authentication.
perl-digest-md5 2.58 perl_5 XX Perl interface to the MD-5 algorithm
perl-digest-md5-file 0.08 unknown XXX Perl extension for getting MD5 sums for files and urls.
perl-digest-perl-md5 1.9 unknown XXX Perl Implementation of Rivest's MD5 algorithm
perl-digest-sha 5.88 perl_5 XXX Perl extension for SHA-1/224/256/384/512
perl-digest-sha1 2.13 perl_5 XX Perl interface to the SHA-1 algorithm
perl-dist-checkconflicts 0.11 perl_5 XXX declare version conflicts for your dist
perl-dumbbench 0.111 perl_5 XXX More reliable benchmarking with the least amount of thinking
perl-dynaloader 1.25 perl_5 XXX Dynamically load C libraries into Perl code
perl-email-date-format 1.005 perl_5 XXX 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 XX allows you to write your script in non-ASCII and non-UTF-8
perl-encode-locale 1.05 perl_5 XXX 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 XXX perl module that imports environment variables as scalars or arrays
perl-env-path 0.19 unknown XXX Advanced operations on path variables
perl-error 0.17030 perl_5 XXX Error/exception handling in an OO-ish way
perl-escape-houdini 0.3.0 perl_5 XX Perl API to Houdini, a zero-dependency C web escaping library
perl-estscan1 1.3 open XX Detects coding regions in DNA sequences even if they are of low...
perl-estscan2 2.1 open XX Detects coding regions in DNA sequences even if they are of low...
perl-eval-closure 0.14 perl_5 XX safely and cleanly create closures via string eval
perl-excel-writer-xlsx 1.15 perl_5 XXX Create a new file in the Excel 2007+ XLSX format.
perl-exception-class 1.45 perl_5 XXX A module that allows you to declare real exception classes in Perl
perl-experimental 0.036 perl_5 XXX Experimental features made easy
perl-exporter 5.72 perl_5 XXX Implements default import method for modules
perl-exporter-tidy 0.08 unknown XXX Another way of exporting symbols
perl-exporter-tiny 1.002002 perl_5 XXX Exporter with the features of Sub::Exporter but only core dependencies
perl-extutils-cbuilder 0.280230 perl_5 XXX Compile and link C code for Perl modules
perl-extutils-config 0.008 perl_5 XXX A wrapper for perl's configuration
perl-extutils-constant 0.25 perl_5 XX generate XS code to import C header constants
perl-extutils-cppguess 0.27 doc Perl_5 XX Guess C++ compiler and flags.
perl-extutils-depends 0.8002 perl_5 XXX Easily build XS extensions that depend on XS extensions.
perl-extutils-helpers 0.026 perl_5 XXX Various portability utilities for module builders
perl-extutils-installpaths 0.012 perl_5 XXX Build.PL install path logic made easy
perl-extutils-makemaker 7.36 perl_5 XX Create a module Makefile
perl-extutils-manifest 1.75 doc Perl_5 XXX Utilities to write and check a MANIFEST file.
perl-extutils-parsexs 3.60 doc Unknown XXX Converts Perl XS code into C code.
perl-extutils-pkgconfig 1.16 unknown XXX 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 0.31 doc Perl_5 X Check that a library is available for FFI.
perl-file-chdir 0.1010 perl_5 XXX a more sensible way to change directories
perl-file-compare 1.1006 perl_5 XXX Compare files or filehandles
perl-file-copy-link 0.200 doc Perl XX Perl extension for replacing a link by a copy of the linked file.
perl-file-copy-recursive 0.45 Perl XX Perl extension for recursively copying files and directories
perl-file-copy-recursive-reduced 0.008 doc Perl_5 XXX Recursive copying of files and directories within Perl 5 toolchain.
perl-file-details 0.003 perl_5 XXX File details in an object, stat, hash, etc..
perl-file-fetch 1.08 doc perl_5 XXX Generic file fetching code.
perl-file-find 1.27 perl_5 XXX Traverse a directory tree.
perl-file-find-rule 0.35 doc perl_5 XXX Alternative interface to File::Find.
perl-file-grep 0.02 unknown XXX Find matches to a pattern in a series of files and related functions
perl-file-homedir 1.004 perl_5 XX Find your home and other directories on any platform
perl-file-listing 6.16 perl_5 XXX parse directory listing
perl-file-next 1.18 artistic_2 XXX File-finding iterator
perl-file-path 2.16 unknown XX Create or remove directory trees
perl-file-pushd 1.016 apache_2_0 XXX change directory temporarily for a limited scope
perl-file-readbackwards 1.06 unknown XXX Read a file backwards by lines.
perl-file-remove 1.57 perl_5 XX Remove files and directories
perl-file-share 0.25 perl_5 XXX Extend File::ShareDir to Local Libraries
perl-file-sharedir 1.118 perl_5 XXX Locate per-dist and per-module shared files
perl-file-sharedir-install 0.14 dev perl_5 XXX Install shared files.
perl-file-slurp 9999.32 perl_5 XXX Simple and Efficient Reading/Writing/Modifying of Complete Files
perl-file-slurp-tiny 0.004 perl_5 XXX A simple, sane and efficient file slurper [DISCOURAGED]
perl-file-slurper 0.014 perl_5 XXX A simple, sane and efficient module to slurp a file
perl-file-sort 1.01 unknown XXX Sort a file or merge sort multiple files
perl-file-spec 3.48_01 perl_5 XXX portably perform operations on file names
perl-file-tee 0.07 unknown XXX replicate data sent to a Perl stream
perl-file-temp 0.2304 perl_5 XX return name and handle of a temporary file safely
perl-file-touch 0.12 perl_5 XXX update file access and modification times, optionally creating files if needed
perl-file-util 4.201720 perl_5 XXX Easy, versatile, portable file handling
perl-file-which 1.23 perl_5 XX Perl implementation of the which utility as an API
perl-filedirutil 0.04 agpl_3 XXX A Moose Role for basic File IO
perl-filesys-df 0.92 unknown XX Perl extension for filesystem disk space information.
perl-filter-simple 0.91 perl_5 XXX Simplified source filtering
perl-findbin 1.54 doc Perl_5 XXX Locate directory of original perl script.
perl-findbin-libs 2.017008 perl_5 XXX locate and a 'use lib' or export directories based on $FindBin::Bin.
perl-findbin-real 1.05 perl_5 XXX Locates the full path to the script bin directory to allow the use of...
perl-font-afm 1.20 perl_5 XXX Interface to Adobe Font Metrics files
perl-font-ttf 1.06 artistic_2 XXX TTF font support for Perl
perl-forks 0.36 doc Perl_5 XX Drop-in replacement for Perl threads using fork().
perl-gd 2.83 perl_5 XX 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 1.56 doc perl_5 XXX Produces charts with GD.
perl-gdgraph-histogram 1.1 unknown XXX Histogram plotting module for Perl5
perl-gdtextutil 0.86 unknown XX Text utilities for use with GD
perl-getopt-argvfile 1.11 artistic_1 XXX interpolates script options from files into @ARGV or another array
perl-getopt-long 2.58 unknown XXX Module to handle parsing command line options
perl-getopt-long-descriptive 0.116 doc dev Perl_5 XXX 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 XXX Wrap git(7) command-line interface
perl-git-wrapper-plus 0.004011 perl_5 XXX A Toolkit for working with Git::Wrapper in an Object Oriented Way.
perl-go-perl 0.15 BSD-3-Clause XXX perl modules for GO and other OBO ontologies
perl-graph 0.9735 perl_5 XXX a Perl extension for keeping data partially sorted
perl-graph-readwrite 2.10 perl_5 XXX modules for reading and writing directed graphs
perl-graphics-colornames 2.11 perl_5 XXX defines RGB values for common color names
perl-graphics-colorobject 0.5.0 unknown XXX convert between color spaces
perl-graphviz 2.26 doc perl_5 XXX 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 XX Perl script and dependent library files required for GTDB-Tk.
perl-hash-merge 0.302 perl_5 XXX Merges arbitrarily deep hashes into a single hash
perl-hash-util-fieldhash-compat 0.11 perl_5 XXX Use Hash::Util::FieldHash or ties, depending on availability
perl-heap 0.80 perl_5 XXX Perl extensions for keeping data partially sorted
perl-heap-simple 0.13 unknown XXX Fast and easy to use classic heaps
perl-heap-simple-perl 0.14 unknown XXX A pure perl implementation of the Heap::Simple interface
perl-heap-simple-xs 0.10 unknown XX An XS implementation of the Heap::Simple interface
perl-hook-lexwrap 0.26 perl_5 XXX Lexically scoped subroutine wrappers
perl-hpc-runner 2.48 perl_5 X None
perl-hpc-runner-command 3.2.13 perl_5 XXX Create composable bioinformatics hpc analyses.
perl-hpc-runner-command-plugin-logger-sqlite 0.0.3 perl_5 XX Log HPC::Runner workflows to a sqlite DB.
perl-hpc-runner-mce 2.41 perl_5 XX None
perl-hpc-runner-pbs 0.12 perl_5 XX None
perl-hpc-runner-scheduler 0.09 perl_5 X None
perl-hpc-runner-slurm 2.58 perl_5 XX None
perl-html-element-extended 1.18 unknown XXX Perl extension for manipulating a table composed of HTML::Element style...
perl-html-entities-numbered 0.04 unknown XXX Conversion of numbered HTML entities
perl-html-form 6.11 doc perl_5 XXX Class that represents an HTML form element.
perl-html-formatter 2.16 perl_5 XXX Base class for HTML formatters
perl-html-parser 3.83 perl_5 XX HTML parser class
perl-html-tableextract 2.15 doc Unknown XXX Perl module for extracting the content contained in tables within an...
perl-html-tagset 3.24 Unknown XXX Data tables useful in parsing HTML.
perl-html-template 2.97 perl_5 XXX Perl module to use HTML-like templating language
perl-html-tidy 1.60 doc dev Artistic_2 XX (X)HTML validation in a Perl object.
perl-html-tree 5.07 perl_5 XXX Work with HTML in a DOM-like tree structure
perl-html-treebuilder-xpath 0.14 perl_5 XXX add XPath support to HTML::TreeBuilder
perl-http-cookiejar-lwp 0.014 doc dev Apache-2.0 X A minimalist HTTP user agent cookie jar.
perl-http-cookies 6.11 dev perl_5 XXX HTTP cookie jars.
perl-http-daemon 6.16 perl_5 XXX a simple http server class
perl-http-date 6.06 perl_5 XXX date conversion routines
perl-http-message 7.01 dev perl_5 XXX HTTP style message (base class).
perl-http-negotiate 6.01 perl_5 XXX choose a variant to serve
perl-http-server-simple 0.52 Perl_5 XXX 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 13.44 doc perl_5 XXX ExifTool is a platform-independent Perl library plus a command-line...
perl-image-info 1.45 doc Perl_5 XXX Extract meta information from image files.
perl-image-size 3.300 perl_5 XXX A library to extract height/width from images
perl-import-into 1.002005 perl_5 XXX Import packages into other packages
perl-importer 0.026 perl_5 XXX Alternative but compatible interface to modules that export symbols.
perl-indirect 0.39 perl_5 XX Lexically warn about using the indirect method call syntax.
perl-inline 0.87 dev Perl_5 XXX Write Perl Subroutines in Other Programming Languages.
perl-inline-c 0.82 doc dev Perl_5 XX C Language Support for Inline.
perl-integer 1.01 perl_5 XXX Perl pragma to use integer arithmetic instead of floating point
perl-io-all 0.87 perl_5 XXX Combines all of the best Perl IO modules into a single nifty object...
perl-io-compress 2.214 doc dev Perl_5 XX IO Interface to compressed data files/buffers.
perl-io-compress-deflate 2.064 perl_5 XXX Write RFC 1950 files/buffers
perl-io-gzip 0.20 perl_5 XX Perl extension to provide a PerlIO layer to gzip/gunzip
perl-io-handle 1.42 perl_5 XXX supply object methods for I/O handles
perl-io-html 1.004 perl_5 XXX Open an HTML file with automatic charset detection
perl-io-interactive 1.027 perl_5 XXX 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 XXX Interactively prompt for user input
perl-io-scalar 2.111 perl_5 XXX IO:: interface for reading/writing a scalar
perl-io-sessiondata 1.03 unknown XXX supporting module for SOAP::Lite
perl-io-socket-inet6 2.73 perl_5 XXX Object interface for AF_INET/AF_INET6 domain sockets
perl-io-socket-ssl 2.074 perl_5 XXX Nearly transparent SSL encapsulation for IO::Socket::INET.
perl-io-string 1.08 unknown XXX Emulate file interface for in-core strings
perl-io-stringy 2.111 unknown XXX write a file which is updated atomically
perl-io-tty 1.16 perl_5 XX Pseudo ttys and constants
perl-io-uncompress-bunzip2 2.064 perl_5 XXX Read bzip2 files/buffers
perl-io-uncompress-gunzip 2.064 perl_5 XXX Read RFC 1952 files/buffers
perl-io-uncompress-rawinflate 2.064 perl_5 XXX Read RFC 1951 files/buffers
perl-io-zlib 1.15 GPL-1.0-or-later XXX IO:: style interface to Compress::Zlib
perl-ipc-cmd 1.04 perl_5 XXX A cross platform way of running (interactive) commandline programs.
perl-ipc-run 20250809.0 doc Perl_5 XXX system() and background procs w/ piping, redirs, ptys (Unix, Win32).
perl-ipc-run3 0.049 doc Open-Source XXX Run a subprocess with input/ouput redirection.
perl-ipc-sharelite 0.17 perl_5 XX Lightweight interface to shared memory
perl-ipc-system-simple 1.30 perl_5 XXX Run commands simply, with detailed diagnostics
perl-jcode 2.07 unknown XXX Japanese Charset Handler
perl-json 4.10 dev GPL-1.0-or-later XXX JSON (JavaScript Object Notation) encoder/decoder
perl-json-create 0.35 perl_5 XX fast, minimal, UTF-8-only serialization of data to JSON
perl-json-maybexs 1.004003 perl_5 XXX Use Cpanel::JSON::XS with a fallback to JSON::XS and JSON::PP
perl-json-parse 0.62 perl_5 XX Read JSON into a Perl variable
perl-json-pp 4.11 perl_5 XXX JSON::XS compatible pure-Perl module.
perl-json-validator 5.15 artistic_2 X Validate data against a JSON schema
perl-json-xs 4.04 GPL-1.0-or-later XX JSON serialising/deserialising, done correctly and fast
perl-lib 0.63 perl_5 XXX manipulate @INC at compile time
perl-libwww-perl 6.81 doc dev Perl_5 XXX The World-Wide Web library for Perl.
perl-libxml-perl 0.08 unknown XXX Perl SAX parser using nsgmls
perl-list-compare 0.53 perl_5 XXX Compare elements of two or more lists
perl-list-moreutils 0.430 apache_2_0 XXX Provide the stuff missing in List::Util
perl-list-moreutils-xs 0.430 apache_2_0 XX Provide the stuff missing in List::Util in XS
perl-list-someutils 0.59 perl_5 XX Provide the stuff missing in List::Util
perl-list-uniq 0.23 perl_5 XXX extract the unique elements of a list
perl-list-util 1.38 perl_5 XX A selection of general-utility list subroutines
perl-local-lib 2.000029 perl_5 XXX create and use a local lib/ for perl modules with PERL5LIB
perl-locale 1.03 perl_5 XXX Perl pragma to use or avoid POSIX locales for built-in operations
perl-locale-maketext-simple 0.21 perl_5 XXX Simple interface to Locale::Maketext::Lexicon
perl-lockfile-simple 0.208 unknown X simple file locking scheme
perl-log-any 1.718 doc dev Perl_5 XXX Bringing loggers and listeners together.
perl-log-log4perl 1.55 unknown XXX Log4j implementation for Perl
perl-logger-simple 2.0 perl_5 XXX Implementation of the Simran-Log-Log and Simran-Error-Error modules
perl-lwp-mediatypes 6.04 perl_5 XXX guess media type for a file or a URL
perl-lwp-protocol-https 6.14 doc Perl_5 XXX Provide https support for LWP::UserAgent.
perl-lwp-simple 6.67 Perl XXX 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 XXX 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 2.22 doc Perl_5 XXX Various e-mail related modules.
perl-math-base-convert 0.13 doc Unknown XXX Very fast base to base conversion.
perl-math-bezier 0.01 unknown XXX solution of Bezier Curves
perl-math-bigint 2.005003 perl_5 XXX Arbitrary size floating point math package
perl-math-bigrat 0.2624 perl_5 XXX Arbitrary big rational numbers
perl-math-cdf 0.1 Public XX Generate probabilities and quantiles from several statistical...
perl-math-combinatorics 0.09 unknown XXX Perform combinations and permutations on lists
perl-math-complex 1.59 perl_5 XXX trigonometric functions
perl-math-derivative 1.01 perl_5 XXX 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 XX Random Number Generators
perl-math-random-mt-auto 6.23 unrestricted XX Auto-seeded Mersenne Twister PRNGs
perl-math-round 0.07 unknown XXX Perl extension for rounding numbers
perl-math-spline 0.02 perl_5 XXX Cubic Spline Interpolation of data
perl-math-utils 1.14 perl_5 XXX Useful mathematical functions not in Perl
perl-math-vecstat 0.08 unknown XXX Some basic numeric stats on vectors
perl-mce 1.902 perl_5 XXX Many-Core Engine for Perl providing parallel processing capabilities
perl-mce-shared 1.893 perl_5 XXX MCE extension for sharing data supporting threads and processes
perl-memoize 1.09 perl_5 XXX 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 XX The RFC 2045 encodings; base64 and quoted-printable
perl-mime-lite 3.030 perl_5 XXX Handy-dandy MIME mailing class
perl-mime-quotedprint 3.13 perl_5 XXX Encoding and decoding of quoted-printable strings
perl-mime-tools 5.515 perl_5 XXX Tools to manipulate MIME messages.
perl-mime-types 2.30 perl_5 XXX Definition of MIME types
perl-minion 11.0 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 XXX write your linewise code for handles; this does the rest
perl-mldbm 2.05 perl_5 XXX store multi-level Perl hash structure in single level tied hash
perl-mldbm-sync 0.30 unknown XXX safe concurrent access to MLDBM databases
perl-module-build 0.4231 perl_5 XXX Build and install Perl modules
perl-module-build-tiny 0.039 perl_5 XXX A tiny replacement for Module::Build
perl-module-corelist 5.20251220 doc Perl_5 XXX What modules shipped with versions of perl.
perl-module-extract-use 1.043 artistic_2 XXX Pull out the modules a module explicitly uses
perl-module-fromperlver 0.008002 perl_5 XXX install modules compatible with the running perl.
perl-module-implementation 0.09 artistic_2 XXX Loads one of several alternate underlying implementations for a module
perl-module-list 0.005 doc Perl_5 XXX Module `directory' listing.
perl-module-load 0.34 perl_5 XXX Load modules in a DWIM style
perl-module-load-conditional 0.68 perl_5 XXX Looking up module information / loading at runtime
perl-module-loaded 0.08 perl_5 XXX Mark modules as loaded/unloaded
perl-module-metadata 1.000038 perl_5 XXX Gather package and POD information from perl module files
perl-module-pluggable 5.2 perl_5 XXX automatically give your module the ability to have plugins
perl-module-runtime 0.016 perl_5 XXX runtime module handling
perl-module-runtime-conflicts 0.003 perl_5 XXX Provide information on conflicts for Module::Runtime
perl-module-scandeps 1.37 doc Perl_5 XXX Recursively scan Perl code for dependencies.
perl-module-util 1.09 perl_5 XXX Module name tools and transformations
perl-mojo-pg 4.28 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 XXX Minimalist Object Orientation (with Moose compatibility)
perl-moose 2.2202 perl_5 XX A postmodern object system for Perl 5
perl-moosex-app 1.3701 perl_5 XXX Write user-friendly command line apps with even less suffering
perl-moosex-app-role-log4perl 0.03 perl_5 XX Add basic Log::Log4perl logging to a MooseX::App application as a role.
perl-moosex-clone 0.06 perl_5 XXX Fine-grained cloning support for Moose objects.
perl-moosex-fileattribute 0.03 perl_5 XXX Sugar for classes that have file or directory attributes
perl-moosex-getopt 0.78 doc dev Perl_5 XXX A Moose role for processing command line options.
perl-moosex-nonmoose 0.27 doc Perl_5 XXX MooseX::NonMoose - easy subclassing of non-Moose classes.
perl-moosex-object-pluggable 0.0014 perl_5 XXX Make your classes pluggable
perl-moosex-role-parameterized 1.11 perl_5 XXX Moose roles with composition parameters
perl-moosex-role-withoverloading 0.17 perl_5 XX (DEPRECATED) Roles which support overloading
perl-moosex-singleton 0.30 perl_5 XXX 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 0.51 dev perl_5 XXX Organise your Moose types in libraries.
perl-moosex-types-path-class 0.09 perl_5 XXX A Path::Class type library for Moose
perl-moosex-types-path-tiny 0.012 perl_5 XXX MooseX::Types::Path::Tiny - Path::Tiny types and coercions for Moose
perl-moosex-types-stringlike 0.003 apache_2_0 XXX Moose type constraints for strings or string-like objects
perl-mozilla-ca 20250602 doc Unknown XXX Mozilla's CA cert bundle in PEM format.
perl-mro-compat 0.15 perl_5 XXX 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 XX Keep imports out of your namespace
perl-namespace-clean 0.27 perl_5 XX Keep imports and functions out of your namespace
perl-net-ftp 2.79 perl_5 XXX FTP Client class
perl-net-ftp-recursive 2.04 Perl XXX Recursive FTP Client class
perl-net-http 6.24 doc dev Perl_5 XXX Low-level HTTP connection (client).
perl-net-netrc 2.14 perl_5 XXX OO interface to users netrc file
perl-net-ssleay 1.92 perl_5 XX Perl extension for using OpenSSL
perl-ntlm 1.09 perl_5 XXX An NTLM authentication module
perl-number-compare 0.03 perl_5 XXX Numeric comparisons
perl-number-format 1.76 perl_5 XXX Perl extension for formatting numbers
perl-number-misc 1.2 perl_5 XXX Number::Misc - handy utilities for numbers
perl-number-range 0.12 perl_5 XXX Perl extension defining ranges of numbers and testing if a number is...
perl-number-witherror 1.01 perl_5 XXX Numbers with error propagation and scientific rounding
perl-object-insideout 4.05 perl_5 XXX 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 0.24 unknown XXX Read and write OLE storage files.
perl-onto-perl 1.45 perl_5 XXX PERL modules for manipulating OBO-formatted ontologies, such as the...
perl-package-deprecationmanager 0.17 artistic_2 XXX Manage deprecation warnings for your distribution
perl-package-stash 0.40 perl_5 XX routines for manipulating stashes
perl-package-stash-xs 0.29 perl_5 XX faster and more correct implementation of the Package::Stash API
perl-padwalker 2.5 unknown XX play with other peoples' lexical variables
perl-par 1.014 perl_5 XXX Perl Archive Tookit
perl-par-dist 0.49 unknown XXX Create and manipulate PAR distributions
perl-par-packer 1.036 perl_5 X PAR Packager
perl-parallel-forkmanager 2.04 perl_5 XXX A simple parallel processing fork manager
perl-parallel-iterator 1.002 doc perl_5 XXX Simple parallel execution.
perl-parallel-loops 0.12 perl_5 XXX Execute loops using parallel forked subprocesses
perl-params-check 0.38 perl_5 XXX Templated based param validation
perl-params-coerce 0.14 perl_5 XXX Allows your classes to do coercion of parameters
perl-params-util 1.102 perl_5 XX Simple, compact and correct param-checking functions
perl-params-validate 1.31 artistic_2 XX Validate method/function parameters
perl-params-validationcompiler 0.31 artistic_2 XXX Build an optimized subroutine parameter validator once, use it forever
perl-parent 0.236 perl_5 XXX Establish an ISA relationship with base classes at compile time
perl-parse-recdescent 1.967015 unknown XXX Generate Recursive-Descent Parsers
perl-parse-yapp 1.21 unknown XXX A perl frontend to the Parse::Yapp module
perl-path-class 0.37 perl_5 XXX Cross-platform path specification manipulation
perl-path-tiny 0.122 apache_2_0 XXX File path utility
perl-pathtools 3.75 perl_5 XX Tools for working with directory and file names
perl-pbkdf2-tiny 0.005 apache_2_0 XX 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 XXX Facilitates the creation and modification of PDF files
perl-pdf-table 1.007 doc Perl_5 X A utility class for building table layouts in a PDF::API2 object.
perl-pegex 0.75 doc Perl_5 XXX Pegex Grammar for the Pegex Grammar Language.
perl-perl-osnames 0.122 perl_5 XXX List possible $^O ($OSNAME) values, with description
perl-perl-ostype 1.010 perl_5 XXX Map Perl operating system names to generic types
perl-perl-unsafe-signals 0.03 perl_5 XX Allow unsafe handling of signals in selected blocks
perl-perl-version 1.018 perl_5 XXX Parse and manipulate Perl version strings
perl-perl4-corelibs 0.004 GPL-3.0 XX libraries historically supplied with Perl 4
perl-perldoc 0.20 perl_5 X Documentation Framework for Perl
perl-perlio 1.09 perl_5 XXX On demand loader for PerlIO layers and root of PerlIO::* name space
perl-perlio-encoding 0.18 perl_5 XXX encoding layer
perl-perlio-gzip 0.20 perl_5 XX PerlIO interface to gzip/gunzip
perl-perlio-utf8_strict 0.010 doc Perl_5 XX Fast and correct UTF-8 IO.
perl-pod-checker 1.60 perl_5 XXX Pod::Checker verifies POD documentation contents for compliance with...
perl-pod-coverage 0.23 unknown XXX Checks if the documentation of a module is comprehensive
perl-pod-coverage-trustpod 0.100006 perl_5 XXX allow a module's pod to contain Pod::Coverage hints
perl-pod-elemental 0.103006 perl_5 XX work with nestable Pod elements
perl-pod-escapes 1.07 perl_5 XXX 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 XXX Modules for parsing/translating POD format documents
perl-pod-plaintext 2.07 perl_5 XXX Convert POD data to formatted ASCII text
perl-pod-simple 3.35 perl_5 XXX framework for parsing Pod
perl-pod-simple-text 3.28 perl_5 XXX format Pod as plaintext
perl-pod-usage 2.05 perl_5 XXX Print a usage message from embedded pod documentation.
perl-posix 1.38_03 perl_5 XXX None
perl-postscript 0.06 unknown XXX helper module for PostScript::TextBlock
perl-postscript-simple 0.09 GNU X Produce PostScript files from Perl.
perl-ppi 1.236 perl_5 XXX Parse, Analyze and Manipulate Perl (without perl)
perl-prefork 1.05 perl_5 XXX Optimized module loading for forking or non-forking processes
perl-probe-perl 0.03 perl_5 XXX Information about the currently running perl
perl-proc-fork 0.806 perl_5 XXX simple, intuitive interface to the fork() system call
perl-readonly 2.05 perl_5 XXX Facility for creating read-only scalars, arrays, hashes
perl-regexp-common 2017060201 mit XXX 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 XXX return across multiple call levels
perl-role-tiny 2.002004 perl_5 XXX Roles. Like a nouvelle cuisine portion size slice of Moose.
perl-role-tiny-with 2.000005 perl_5 XXX Neat interface for consumers of Role::Tiny roles
perl-safe 2.37 unknown XXX 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 XX a set of common perl utilities for generating consistent Vcf headers
perl-scalar-list-utils 1.62 perl_5 XX Common Scalar and List utility subroutines
perl-scalar-util-numeric 0.40 perl_5 XX numeric tests for perl scalars
perl-scope-guard 0.21 perl_5 XXX lexically-scoped resource management
perl-sereal 5.004 doc Perl_5 XXX Fast, compact, powerful binary (de-)serialization.
perl-sereal-decoder 5.004 doc perl_5 XX Fast, compact, powerful binary deserialization.
perl-sereal-encoder 5.004 doc Perl_5 XX Fast, compact, powerful binary serialization.
perl-set-intervaltree 0.12 doc Perl_5 XX An interval tree implementation in PERL.
perl-set-intspan 1.19 unknown XXX Manages sets of integers, newsrc style
perl-set-object 1.43 artistic_2 XX Unordered collections (sets) of Perl Objects
perl-set-scalar 1.29 perl_5 XXX basic set operations
perl-slurp 0.4 unknown XXX Slurp entire files into variables
perl-snap 2.1.1 Custom XXX SNAP calculates pairwise synonymous and nonsynonymous distances...
perl-soap-lite 1.27 perl_5 XXX Perl's Web Services Toolkit
perl-socket 2.027 perl_5 XX networking constants and support functions
perl-socket6 0.29 unknown XX IPv6 related part of the C socket.h defines and structure manipulators
perl-sort-key 1.33 Artistic-1.0-Perl XX 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 XXX sort lexically, but sort numeral parts numerically
perl-sort-versions 1.62 perl_5 XXX a perl 5 module for sorting of revision-like numbers
perl-specio 0.53 artistic_2 XXX Type constraints and coercions for Perl
perl-specio-exporter 0.36 perl_5 XX Base class for type libraries
perl-spiffy 0.46 perl_5 XXX Spiffy Perl Interface Framework For You
perl-spreadsheet-parseexcel 0.66 perl_5 XXX Read information from an Excel file.
perl-spreadsheet-writeexcel 2.40 perl_5 XXX 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 XXX SQL parsing and processing engine
perl-statistics-basic 1.6611 open_source XXX None
perl-statistics-caseresampling 0.15 unknown XX Efficient resampling and calculation of medians with confidence intervals
perl-statistics-descriptive 3.0801 perl_5 XXX Module of basic descriptive statistical functions.
perl-statistics-distributions 1.02 perl_5 XXX Perl module for calculating critical values and upper probabilities of...
perl-statistics-frequency 0.04 perl_5 XXX simple counting of elements
perl-statistics-lite 3.62 perl_5 XXX Small stats stuff.
perl-statistics-r 0.34 Perl5 XXX Statistics::R - Perl interface with the R statistical program
perl-statistics-ttest 1.1 perl_5 XXX Perl module to perform T-test on 2 independent samples...
perl-storable 3.15 perl_5 XX persistence for Perl data structures
perl-string-approx 3.27 doc Unknown XX 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 XXX Backslash escapes, quoted phrase, word elision, etc.
perl-string-random 0.30 perl_5 XXX Perl module to generate random strings based on a pattern
perl-string-rewriteprefix 0.009 perl_5 XXX rewrite strings based on a set of known prefixes
perl-string-truncate 1.100603 perl_5 XXX a module for when strings are too long to be displayed in...
perl-string-util 1.26 perl_5 XXX String::Util -- String processing utilities
perl-sub-attribute 0.07 perl_5 XX Reliable subroutine attribute handlers
perl-sub-exporter 0.988 perl_5 XXX a sophisticated exporter for custom-built routines
perl-sub-exporter-formethods 0.100055 perl_5 XXX helper routines for using Sub::Exporter to build methods
perl-sub-exporter-progressive 0.001013 perl_5 XXX Only use Sub::Exporter if you need it
perl-sub-identify 0.14 perl_5 XX Retrieve names of code references
perl-sub-info 0.002 perl_5 XXX Tool for inspecting subroutines.
perl-sub-install 0.928 perl_5 XXX install subroutines into packages easily
perl-sub-name 0.21 perl_5 XX (Re)name a sub
perl-sub-quote 2.006006 perl_5 XXX Efficient generation of subroutines via string eval
perl-sub-uplevel 0.2800 perl_5 XX apparently run a function in a higher stack frame
perl-super 1.20190531 perl_5 XXX control superclass method dispatch
perl-svg 2.87 perl_5 XXX Perl extension for generating Scalable Vector Graphics (SVG) documents
perl-svg-graph 0.02 unknown XXX Visualize your data in Scalable Vector Graphics (SVG) format.
perl-symbol 1.07 perl_5 XXX manipulate Perl symbols and their names
perl-symbol-util 0.0203 perl_5 XX Additional utils for Perl symbols manipulation
perl-sys-info 0.7811 perl_5 XXX Fetch information from the host system
perl-sys-info-base 0.7807 perl_5 XXX Base class for Sys::Info
perl-sys-info-driver-linux 0.7911 doc Perl_5 XX Linux driver for Sys::Info
perl-sys-info-driver-osx 0.7963 doc Perl_5 X OSX driver for Sys::Info.
perl-sys-sigaction 0.23 perl_5 XXX Perl extension for Consistent Signal Handling
perl-tap-harness-env 3.30 perl_5 XXX Parsing harness related environmental variables where appropriate
perl-task-weaken 1.06 perl_5 XXX Ensure that a platform has weaken support
perl-template-toolkit 3.102 doc perl_5 XX Comprehensive template processing system.
perl-term-app-roles 0.031 perl_5 XXX Collection of roles for terminal-based application
perl-term-detect-software 0.227 doc Perl_5 XXX Detect terminal (emulator) software and its capabilities.
perl-term-encoding 0.03 perl_5 XXX Detect encoding of the current terminal
perl-term-progressbar 2.23 doc Perl_5 XXX Provide a progress meter on a standard terminal.
perl-term-table 0.028 perl_5 XXX Format a header and rows into a table
perl-termreadkey 2.38 perl_5 XX A perl module for simple terminal control
perl-test 1.26 unknown XXX provides a simple framework for writing test scripts
perl-test-base 0.89 perl_5 XXX A Data Driven Testing Framework
perl-test-builder-tester 1.23_002 unknown XXX test testsuites that have been built with Test::Builder
perl-test-class-moose 1.00 doc Perl_5 XXX Serious testing for serious Perl.
perl-test-classapi 1.07 perl_5 XXX Provides basic first-pass API testing for large class trees
perl-test-cleannamespaces 0.24 perl_5 XXX Check for uncleaned imports
perl-test-cpan-meta 0.25 artistic_2 XXX Validate your CPAN META.json files
perl-test-deep 1.130 perl_5 XXX Extremely flexible deep comparison
perl-test-differences 0.69 Perl XXX Test strings and data structures and show differences if not ok
perl-test-eol 2.02 perl_5 XXX Check the correct line endings in your project
perl-test-exception 0.43 perl_5 XXX Test exception-based code
perl-test-exec 0.04 perl_5 XXX Test that some code calls exec without terminating testing
perl-test-fatal 0.016 perl_5 XXX incredibly simple helpers for testing code with exceptions
perl-test-file 1.995 perl_5 XXX test file attributes
perl-test-file-contents 0.23 perl_5 XXX Test routines for examining the contents of files
perl-test-files 0.15 unknown XXX A Test::Builder based module to ease testing with files and dirs
perl-test-fork 0.02 perl_5 XXX test code which forks
perl-test-harness 3.44 perl_5 XXX contributing to TAP::Harness
perl-test-inter 1.12 doc Perl_5 XXX Framework for more readable interactive test scripts.
perl-test-leaktrace 0.17 perl_5 XX Traces memory leaks
perl-test-lectrotest 0.5001 perl_5 XXX Easy, automatic, specification-based tests
perl-test-longstring 0.17 perl_5 XXX tests strings for equality, with more helpful failures
perl-test-memory-cycle 1.06 unknown XXX Verifies code hasn't left circular references
perl-test-mockmodule 0.13 gpl_3 XXX Override subroutines in a module for unit testing
perl-test-more 1.001002 perl_5 XXX yet another framework for writing test scripts
perl-test-most 0.38 unknown XXX Most commonly needed test functions and features
perl-test-needs 0.002009 perl_5 XXX Skip tests when modules not available
perl-test-notabs 2.02 perl_5 XXX Check the presence of tabs in your project
perl-test-nowarnings 1.06 Perl XXX Make sure you didn't emit any warnings while testing
perl-test-object 0.08 perl_5 XXX Thoroughly testing objects via registered handlers
perl-test-output 1.031 perl_5 XXX Utilities to test STDOUT and STDERR messages.
perl-test-pod 1.52 perl_5 XXX check for POD errors in files
perl-test-pod-coverage 1.10 artistic_2 XX Check for pod coverage in your distribution
perl-test-prereq 2.002 artistic_2 XXX check if Makefile.PL has the right pre-requisites
perl-test-requires 0.11 perl_5 XXX Checks to see if the module can be loaded
perl-test-requiresinternet 0.05 perl_5 XXX Easily test network connectivity
perl-test-script 1.31 perl_5 XXX Basic cross-platform tests for scripts
perl-test-simple 1.302190 perl_5 XXX Basic utilities for writing tests.
perl-test-subcalls 1.10 perl_5 XXX Track the number of times subs are called
perl-test-sys-info 0.23 perl_5 XXX Centralized test suite for Sys::Info.
perl-test-taint 1.08 doc Unknown XX Checks for taintedness of variables.
perl-test-toolbox 0.4 perl_5 XXX Test::Toolbox - tools for testing
perl-test-trap 0.3.3 perl_5 XXX Trap exit codes, exceptions, output, etc.
perl-test-unit-lite 0.1202 perl_5 XXX Unit testing without external dependencies
perl-test-utf8 1.03 perl_5 XXX handy utf8 tests
perl-test-warn 0.36 perl_5 XXX Perl extension to test methods for warnings
perl-test-warnings 0.031 perl_5 XXX Test for warnings and the lack of them
perl-test-without-module 0.20 perl_5 XXX Test fallback behaviour in absence of modules
perl-test-xml 0.08 perl_5 XXX Compare XML in perl tests
perl-test-yaml 1.07 perl_5 XXX Testing Module for YAML Implementations
perl-test2 1.302075 perl_5 XXX Framework for writing test tools that all work together.
perl-test2-plugin-nowarnings 0.10 doc Artistic-2.0 X Fail if tests warn.
perl-test2-suite 0.000163 perl_5 XXX Distribution with a rich set of tools built upon the Test2 framework.
perl-text-abbrev 1.02 perl_5 XXX abbrev - create an abbreviation table from a list
perl-text-ansitable 0.48 perl_5 XXX Create nice formatted tables using extended ASCII and ANSI colors
perl-text-asciitable 0.22 perl_5 XXX Create a nice formatted table using ASCII characters.
perl-text-balanced 2.07 doc Perl_5 XXX Extract delimited text sequences from strings.
perl-text-csv 2.01 perl_5 XXX comma-separated values manipulator (using XS or PurePerl)
perl-text-csv_xs 1.48 perl_5 XX Text::CSV_XS - comma-separated values manipulation routines
perl-text-diff 1.45 perl_5 XXX Perform diffs on files and record sets
perl-text-format 0.63 Perl_5 XXX Format text.
perl-text-glob 0.11 perl_5 XXX match globbing patterns against text
perl-text-levenshtein 0.13 perl_5 XXX calculate the Levenshtein edit distance between two strings
perl-text-levenshteinxs 0.03 Perl XX An XS implementation of the Levenshtein edit distance
perl-text-nsp 1.31 open_source XXX Extract collocations and Ngrams from text
perl-text-parsewords 3.31 perl_5 XXX parse text into an array of tokens or array of arrays
perl-text-tabs 2013.0523 perl_5 XXX expand and unexpand tabs like unix expand(1) and unexpand(1)
perl-text-tabs-wrap 2021.0814 unknown XXX Expand tabs and do simple line wrapping
perl-text-template 1.46 unknown XXX Expand template text with embedded Perl
perl-text-template-simple 0.91 perl_5 XXX Simple text template engine
perl-text-wrap 2021.0814 perl_5 XXX line wrapping to form simple paragraphs
perl-threaded 5.32.1 Perl XXX The Perl language.
perl-tie-cache 0.21 unknown XXX LRU Cache in Memory
perl-tie-cacher 0.09 perl_5 XXX Cache a (sub)set of key/value pairs. Tie and OO interface.
perl-tie-hash 1.05 perl_5 XXX None
perl-tie-hash-indexed 0.08 perl_5 XX Ordered hashes for Perl
perl-tie-ixhash 1.23 perl_5 XXX ordered associative arrays for Perl
perl-tie-log4perl 0.1 perl_5 XXX Tie a filehandle to log via Log4perl
perl-tie-refhash 1.39 perl_5 XXX use references as hash keys
perl-tie-refhash-weak 0.09 unknown XXX A Tie::RefHash subclass with weakened references in the keys.
perl-tie-toobject 0.03 perl_5 XXX Tie to an existing object.
perl-time-hires 1.9764 perl_5 XX High resolution alarm, sleep, gettimeofday, interval timers
perl-time-local 1.2300 perl_5 XXX efficiently compute time from local and GMT time
perl-time-piece 1.27 perl_5 XXX Object Oriented time objects
perl-timedate 2.33 perl_5 XXX Date formating subroutines
perl-tree-dag_node 1.35 artistic_2 XXX An N-ary tree.
perl-try-tiny 0.31 mit XXX minimal try/catch with proper preservation of $@
perl-try-tiny-retry 0.004 Apache-2.0 XXX Just like Try::Tiny, but with retry instead of try.
perl-type-tiny 1.016006 perl_5 XXX tiny, yet Moo(se)-compatible type constraint
perl-types-serialiser 1.01 perl_5 XXX Simple data types for common serialisation formats
perl-types-standard 1.002001 perl_5 XX bundled set of built-in types for Type::Tiny
perl-unicode-map 0.112 unknown XX An utility to map texts from and to unicode
perl-unicode-normalize 1.26 perl_5 XX Unicode Normalization Forms
perl-unicode-stringprep 1.105 perl_5 XXX Preparation of Internationalized Strings (RFC 3454)
perl-unicode-utf8 0.62 perl_5 XX Encoding and decoding of UTF-8 encoding form
perl-uri 5.12 perl_5 XXX 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 XX 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 XX Associate user-defined magic to variables from Perl.
perl-vars 1.03 perl_5 XXX Perl pragma to predeclare global variable names
perl-vcftools-vcf 0.1.17 doc dev LGPL-3.0-only XXX cpanm ready distribution of VCFtools Perl libraries.
perl-velvetoptimiser 2.2.6 GPLv2 XXX Automatically optimise three of Velvet's assembly parameters.
perl-version 0.9924 perl_5 XX Structured version objects
perl-version-next 1.000 apache_2_0 XXX increment module version numbers simply and correctly
perl-want 0.29 doc Perl_5 XX This module generalises the mechanism of the wantarray function,...
perl-warnings-register 1.03 perl_5 XXX warnings import function
perl-www-mechanize 2.20 doc Perl_5 XXX Handy web browsing in a Perl object.
perl-www-robotrules 6.02 perl_5 XXX database of robots.txt-derived permissions
perl-xml-dom 1.46 unknown XXX A perl module for building DOM Level 1 compliant document structures
perl-xml-dom-xpath 0.14 unknown XXX Perl extension to add XPath support to XML::DOM, using XML::XPath engine
perl-xml-entities 1.0002 perl_5 XXX Mapping of XML entities to Unicode
perl-xml-filter-buffertext 1.01 unknown XXX Filter to put all characters() in one event
perl-xml-libxml 2.0210 dev Perl_5 XX Interface to Gnome libxml2 xml parsing and DOM library.
perl-xml-libxslt 2.003000 perl_5 XX Interface to GNOME libxslt library
perl-xml-namespacesupport 1.12 perl_5 XXX a simple generic namespace support class
perl-xml-parser 2.44 perl_5 XX A perl module for parsing XML documents
perl-xml-parser-lite 0.722 perl_5 XXX Lightweight pure-perl XML Parser (based on regexps)
perl-xml-regexp 0.04 unknown XXX Regular expressions for XML tokens
perl-xml-sax 1.02 unknown XXX Simple API for XML
perl-xml-sax-base 1.09 perl_5 XXX Base class for SAX Drivers and Filters
perl-xml-sax-expat 0.51 perl_5 XXX SAX Driver for Expat
perl-xml-sax-writer 0.57 perl_5 XXX SAX2 XML Writer
perl-xml-semanticdiff 1.0007 perl_5 XXX Perl extension for comparing XML documents.
perl-xml-simple 2.25 perl_5 XXX An API for simple XML files
perl-xml-twig 3.52 perl_5 XXX XML, The Perl Way
perl-xml-writer 0.900 unrestricted XXX Easily generate well-formed, namespace-aware XML.
perl-xml-xpath 1.47 Artistic-2.0 XXX Parse and evaluate XPath statements.
perl-xml-xpathengine 0.14 unknown XXX a re-usable XPath engine for DOM-like trees
perl-xsloader 0.24 perl_5 XX Dynamically load C libraries into Perl code
perl-xxx 0.38 doc dev Perl X See Your Data in the Nude.
perl-yaml 1.30 perl_5 XXX YAML Ain't Markup Language™
perl-yaml-libyaml 0.66 perl_5 XX Perl YAML Serialization using XS and libyaml
perl-yaml-pp 0.39.0 doc Perl X YAML 1.2 Processor
perl-yaml-tiny 1.73 perl XXX Read/Write YAML files with as little code as possible
pfam_scan 1.6 GPL XXX pfam_scan.pl is a Perl script calling HMMER v3 to search a FASTA file...
pfp 0.3.9 dev MIT XX Prefix Free Parsing.
pftools 3.2.13 doc dev GPL-2.0-or-later XX A generalized profile syntax for biomolecular sequence motifs and its...
pgap2 1.0.6 dev MIT X PGAP2: a comprehensive pan-genome analysis pipeline for prokaryotic genomes.
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 0.93.0 doc dev LGPL-3.0-or-later XX Python wrapper for pgenlib's basic reader and writer.
pggb 0.7.4 MIT XX PanGenome Graph Building pipeline renders
pgma-simple 0.1 GNUv3 XX 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 XX A tool for compressing the DNA stream of FASTQ datasets.
pgsa 1.2 Creative XX Pseudogenome Suffix Array is a compact index for collections of reads...
pgscatalog-utils 2.0.2 doc dev Apache-2.0 X Utilities for working with PGS Catalog API and scoring files.
pgscatalog.calc 0.3.1 dev Apache-2.0 X Libraries and applications for working with calculated polygenic scores.
pgscatalog.core 1.0.2 dev Apache-2.0 X Core tools for working with polygenic scores (PGS) and the PGS Catalog.
pgscatalog.match 0.4.0 doc dev Apache-2.0 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 1.5.0 doc dev MIT XXX Phables: from fragmented assemblies to high-quality bacteriophage genomes.
phabox 2.1.13 doc dev GPL-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 XXX A tool to derive SNP matrices and phylogenetic tree from raw reads,...
phanotate 1.6.7 doc dev GPL-3.0-only XX 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 XXX This package computes informative enrichment and quality measures for...
pharokka 1.8.2 doc dev MIT X Fast Phage Annotation Program
phaser 0.1.1ad5f89 file XX phASEr performs haplotype phasing and provides measures of haplotypic...
phasius 0.6.0 dev MIT XX A rust tool to create phase-block maps from phased cram/bam files.
phast 1.5 BSD XX 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 2.0.0 doc dev GPL-2.0-only 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 XX phcue-ck (pronounced "F-Q-Seek") is a simple tool to get FTP...
pheniqs 2.1.0 doc dev GPL3 XX Pheniqs is a flexible generic barcode classifier for high-throughput...
phenix 1.4.1a GPL3 XX 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.
philosopher 5.1.2 GPL-3.0-only X Philosopher is a versatile toolkit for deep proteomics data analysis...
phip-stat 0.5.1 Apache-2.0 X PhIP-seq analysis tools
phipack 1.1 doc GPL-3.0-or-later XX 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 XX Prophage finder using multiple metrics
phist 1.0.0 dev GPL-3.0-or-later XX Phage-Host Interaction Search Tool.
phizz 0.2.3 MIT XXX Tool to query hpo database and some other sources
phlame 1.1.0 doc dev MIT X Novelty-aware intraspecies profiling of metagenome samples.
phold 1.1.0 doc MIT X Phage annotation using protein structures
phonenumbers 7.2.4 Apache XX None
phu 0.4.4 doc dev MIT X Phage Utilities (phu): modular toolkit for clustering, classifying, and...
phyclone 0.7.1 GPL-3.0-or-later X Accurate Bayesian reconstruction of cancer phylogenies from bulk sequencing.
phykit 2.1.2 doc dev MIT X PhyKIT is a UNIX shell toolkit for processing and analyzing phylogenomic data.
phylics 1.0.7 AGPL3 XXX Single-cell CNV data analysis toolkit
phyling 2.3.1 doc dev MIT X A phylogenetic inference tool based on protein-coding genomic sequences
phylip 3.697 doc BSD XX Package of programs for inferring phylogenies
phyloacc 2.4.3 doc dev GPL-3.0-or-later XX Bayesian estimation of substitution rate shifts in non-coding regions
phyloaln 1.1.0 MIT X PhyloAln: a reference-based multiple sequence alignment tool for phylogeny
phylobayes-mpi 1.9 GPL2 XX A Bayesian software for phylogentic reconstrunction using mixture models
phylocsf 1.0.1 AGPL-3.0 XX Phylogenetic analysis of multi-species genome sequence alignments to...
phylocsfpp 1.2.0_9643238d AGPLv3 XX 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 XXX 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 XXX 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 2.0a0 doc dev MIT X Phylogenize is a tool that allows users to link microbial genes to...
phylommand 1.1.0 GPLv3 XX Command-line phylogenetics tools.
phylopandas 0.8.0 MIT XXX Pandas for phylogenetics
phylophlan 3.1.1 MIT X Precise phylogenetic analysis of microbial isolates and genomes from metagenomes
phylopypruner 1.2.6 doc dev GPL-3.0-or-later X Tree-based orthology inference.
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 XX Tools for phylogenetic data analysis including visualization and...
phylovega 0.3 MIT X Interactive Phylogenetic trees in Vega.
phylowgs 20181105 GPLv3 XX Application for inferring subclonal composition and evolution from...
phyluce 1.6.8 BSD XXX Software for UCE (and general) phylogenomics.
phyml 3.3.20220408 doc dev GPL-3.0-only XX Phylogenetic estimation using (Maximum) Likelihood
phynder 1.0 dev MIT XX Efficient likelihood calculations to place samples into a phylogenetic tree.
phynteny 0.1.13 dev MIT X Phynteny: Synteny-based prediction of bacteriophage genes
phynteny_transformer 0.1.3 doc 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 dev GPL-2.0-or-later XX 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 XX 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 XX Phylogenetics tools for linux (and other mostly posix compliant) computers
pia 1.5.7 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 3.4.0 dev MIT XXX Java tools for working with NGS data in the BAM format
picard-slim 3.4.0 dev MIT X Java tools for working with NGS data in the BAM format.
picopore 1.2.0 GNU XXX A tool for reducing the size of Oxford Nanopore Technologies'...
picrust 1.1.4 GPL-3.0 XXX PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of...
picrust2 2.6.3 dev GNU X PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of...
pictrust 1.0.1 GPL XX 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 0.0.9 doc dev MIT XXX A package to quantify RNA localization using OINC-seq data.
pilea 1.3.3 MIT XXX Pilea: profiling bacterial growth dynamics from metagenomes with sketching
pileometh 0.1.13 MIT XX A (mostly) universal methylation extractor for BS-seq experiments.
piler 0.1 public XX PILER is public domain software for analyzing repetitive DNA found in...
piler-cr 1.06 Public XX 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 XXX Pilon is an automated genome assembly improvement and variant detection tool.
pin_hic 3.0.0 dev MIT XX 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 XXX A pipeline for automated multiple sequence alignment, particularly of...
piper 0.14.5 doc dev BSD-2-Clause X A lightweight python toolkit for gluing together restartable, robust...
pipits 4.0 doc dev GPL-3.0-or-later XXX PIPITS: An automated pipeline for analyses of fungal internal...
pipmir 1.1 PIPmiR XX We developed the PIPmiR algorithm to identify novel plant miRNA.
piranha 1.2.1 GNU X Piranha is a peak-caller for CLIP- and RIP-Seq data.
piranha-polio 1.5.3 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 dev GPL-2.0-or-later XXX A tool for conducting RNA seq analysis.
pirs 2.0.2 GPL-2.0 X pIRS is a program for simulating Illumina PE reads.
pisad 1.2.0 MIT XX pisad - Phsaed Intraspecies Sample Anomalies Detection tool
piscem 0.14.2 BSD XX piscem is a next-generation compacted colored de Bruijn Graph-based...
piscem-infer 0.7.0 BSD-3-Clause XX piscem-infer is a flexible tool to perform target quantification from...
pisces 5.2.10.49 GPLv3 XXX Somatic and germline variant caller for amplicon data. Recommended...
pispino 1.1 GNU XXX PISPINO (PIpits SPIN-Off tools): Bioinformatics toolkits for processing NGS data
pixelator 0.20.1 doc dev MIT X A command-line tool and library to process and analyze sequencing data...
pizzly 0.37.3 BSD-2 XX Fast fusion detection using kallisto
pkiss 2.3.0 doc GPL-3.0-or-later XX RNA secondary structure prediction including K-type and kissing...
planemo 0.75.33 doc dev MIT XXX Command-line utilities to assist in building tools for the Galaxy...
plannotate 1.2.4 doc dev 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 XXX Gene family aligner pipeline
plant_tribes_gene_family_classifier 1.0.4 GNU XXX Gene family classifier pipeline
plant_tribes_gene_family_integrator 1.0.4 GNU XXX Gene family integrator pipeline
plant_tribes_gene_family_phylogeny_builder 1.0.4 GNU XXX Gene family phylogeny builder pipeline
plant_tribes_kaks_analysis 1.0.4 GNU XX KaKs Analysis pipeline
plantcv 3.8.0 doc dev MIT X An image processing package for plant phenotyping.
plasann 1.1.6 dev MIT X A tool for plasmid annotation and visualization.
plasclass 0.1.1 MIT X Classification of plasmid sequences
plascope 1.3.1 GPL XXX PlaScope is a targeted approach to assess the plasmidome of bacteria.
plasflow 1.1.0 GNU X PlasFlow - predicting plasmid sequences in metagenomic data
plasmar 1.5 Apache X Plasmid Like Assembly Sequence Matching Algorithm for Resistance (PLASMAR)
plasmidcommunity 1.0.2 doc GPL-3.0 X Klebsiella pneumoniae Plasmid Classification, Assignment, and...
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 XXX 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 XX Plass (Protein-Level ASSembler) and PenguiN (Protein-guided Nucleotide...
plassembler 1.8.1 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 XX plastid is a Python library for genomic analysis -- in particular,...
plateo 0.3.1 doc dev MIT X Read/write microplate and picklist data for lab automation
platon 1.7 dev GPLv3 X Plasmid contig classification and characterization for short read draft...
platypus-conquistador 0.9.0 BSD-3-Clause XX Platypus Conquistador: Confirming specific taxonomic groups within your...
platypus-variant 0.8.1.2 GPLv3 XX A Haplotype-Based Variant Caller For Next Generation Sequence Data
plek 1.2 dev GPL-3.0-or-later XX Predictor of long non-coding RNAs and mRNAs based on k-mer scheme.
plinder 0.2.25 doc dev MIT X PLINDER: The Protein-Ligand INteraction Dataset and Evaluation Resource.
pling 2.0.1 LICENSE X Pling computes the rearrangement distance between plasmids and clusters...
plink 1.90b7.7 GPL XX Whole genome association analysis toolset, designed to perform a range...
plink2 2.0.0a.6.9 GPL-3 XX Whole genome association analysis toolset
plinkio 0.9.8 BSD-3-Clause XX A library for parsing plink genotype files
plmc 20221105 dev MIT XX Inference of couplings in proteins and RNAs from sequence variation.
plncpro 1.2.2 doc GNU XX 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 1.0.0 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 0.1.2 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...
pmidcite 0.3.1 dev AGPL-3.0-only X Download "Cited by" data from the NIH for any paper with a PubMed ID
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 0.0.39 doc dev MIT X Python package for quality control of proteomics datasets, based on...
pmx_biobb 5.2.2 GNU XX Toolkit for free-energy calculation setup/analysis and biomolecular...
pnetcdf_mpich 1.14.0 PnetCDF X PnetCDF - Parallel netCDF
pneumo-typer 2.0.1 doc GNU X Pneumo-Typer is a high-throughput capsule genotype visualization tool...
pneumocat 1.2.1 GPL-3.0 XXX PneumoCaT (Pneumococcal Capsular Typing) uses a two-step step approach...
poa 2.0 dev GPL-2.0-or-later XX POA is Partial Order Alignment, a fast program for multiple sequence...
pod5 0.3.33 doc dev MPL-2.0 X Oxford Nanopore Technologies Pod5 File Format Python API and Tools.
polap 0.5.3.1 doc dev GPL-3.0-or-later X POLAP: plant organelle long-read assembly pipeline
poly-qtlseq 1.2.6 MIT X PolyploidQtlSeq is a program that extends QTL-seq for polyploid F1 populations.
polyat 0.1.2 doc dev GPL-3.0-only X Command-line tool to quantify poly-A/T homopolymers within FASTQ...
polymutt 0.18 custom X Li B, Chen W, Zhan X, Busonero F, Sanna S, et al. (2012) A...
polypolish 0.6.1 doc dev GPL-3.0-or-later XX 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 XX 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 dev GPL-3.0-or-later XX 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 XX 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 XX 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 2.7.7 doc dev Apache-2.0 XXX PopPUNK (POPulation Partitioning Using Nucleotide Kmers)
popscle 0.1 dev MIT XX A suite of population scale analysis tools for single-cell genomics...
popt 1.16 GPL XX 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 XX Adapter removal and demultiplexing of Oxford Nanopore reads
porechop_abi 0.5.1 doc dev GPL-3.0-or-later XX Adapter inferrence and removal of Oxford Nanopore reads.
poretools 0.6.1a1 MIT XXX poretools: a toolkit for working with nanopore sequencing data from...
porfast 0.8.0 MIT XX Extract ORFs from paired end Illumina reads (FASTQ).
portcullis 1.2.4 doc dev GPL-3.0-or-later XX Splice junction analysis and filtering from BAM files.
portello 0.7.0 Pacific X Transfer HiFi read mappings from their own assembly contigs to a...
poseidon-trident 1.6.7.1 MIT XX A tool (trident) to work with modular genotype databases formatted...
poseidon-xerxes 1.0.1.1 MIT XX A tool (xerxes) to analyse genotype databases formatted using Poseidon.
postmaster 0.1.0 dev BSD-3-Clause XX Postmaster is a tool for annotating transcriptome alignments with...
potrace 1.11 GPL XX A tool for tracing a bitmap, which means, transforming a bitmap into a...
pourrna 1.2.0 GPLv2 XX 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 XXX Parallel and distributed programming for Python
pp-sketchlib 1.1.0 Apache-2.0 XX Library of sketching functions used by PopPUNK
ppanggolin 2.2.6 doc dev CeCiLL-2.1 XX PPanGGOLiN: Depicting microbial species diversity via a Partitioned...
ppanini 0.7.4 MIT XXX PPANINI: Prioritization and Prediction of functional Annotations for...
pplacer 1.1.alpha20 dev GPL-3.0 XX 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 1.5.0 doc dev MIT X A Python interface to proteomics data repositories
pqlseqpy 0.1.2 BSD-3-Clause X Fast PQLseq in Python
prank 170427 doc dev GPL-3.0-or-later XX 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 dev GPL-3.0-or-later XX This software aims at reconstructing haplotypes from next-generation...
predictosaurus 0.7.4 doc dev MIT XX Predictosaurus is a command-line tool designed for uncertainty-aware...
preface 0.1.2 GPLv3 X PREFACE -- PREdict FetAl ComponEnt
prefersim 1.0 GPL3 XX PReFerSim is an ANSI C program that performs forward simulations under...
prequal 1.02 GNU XX a pre-alignment quality filter for comparative sequence analyses
preseq 3.2.0 doc GPL-3.0-or-later XX 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 0.7.6 doc dev AGPL-3.0-or-later XXX A bioinformatics toolkit for processing high-throughput lymphocyte...
prestor 07f9c7caeb60 Creative XX 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 0.0.9 doc dev MIT XX Embeds bedgraph data into Pretext contact maps.
pretextmap 0.1.9 MIT XX Paired REad TEXTure Mapper. Converts SAM formatted read pairs into...
pretextsnapshot 0.0.5 MIT XX Commandline image generator for Pretext Hi-C genome contact maps.
primalbedtools 1.0.0 dev 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 XX Design PCR primers from DNA sequence. From mispriming libraries to...
primer3-py 2.2.0 doc dev GPL-2.0-only XX 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 XX 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 XXX PRINSEQ can be used to filter, reformat, or trim your genomic and...
prinseq-plus-plus 1.2.4 doc dev GPL-2.0-or-later XX PRINSEQ++ - Multi-threaded C++ sequence cleaning.
priorcons 0.1.0 APL-1.0 X Tool for integrating consensus sequences using prior information.
privateer MKV doc dev LGPL-3.0 XX The Swiss Army knife for carbohydrate structure validation, refinement...
probabilistic2020 1.2.3 Apache-2-0 X Simulates somatic mutations, and calls statistically significant...
probamconvert 1.0.2 Apache XX proBAMconvert is a conversion tool to convert common peptide...
probcons 1.12 Public XX PROBCONS is a probabilistic consistency-based multiple sequence alignment
probconsrna 1.10 Public XX PROBCONSRNA is an experimental version of PROBCONS for nucleotide sequences
probe 2.18 dev Apache X Evaluate and visualize protein interatomic packing
probeit 2.2 dev AGPL-3.0-or-later XX Probeit: a probe designer for detecting and genotyping pathogen!
proda 1.0 doc Public XX ProDA - Multiple alignment of protein sequences with repeated and...
prodigal 2.6.3 doc dev GPL-3.0-or-later XX Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a...
prodigal-gv 2.11.0 GPL-3.0-only XX A fork of Prodigal meant to improve gene calling for giant viruses
profile_dists 1.0.10 dev Apache-2.0 X Profile Dists: Rapid calcualtion of allele profile distances and...
progenomes 0.3.0 doc dev MIT X A proGenomes command-line tool for interacting with bacterial 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 0.0.48 doc dev MIT X ProkBERT is a genomic language model specifically designed for...
prokka 1.15.6 dev GPL-3.0-only XXX Rapid annotation of prokaryotic genomes
proksee 1.0.0a6 Apache X Proksee is a suite of command line tools for performing assembly,...
promod3 3.6.0 doc dev Apache-2.0 XX ProMod3 is a tool for protein structure prediction and refinement
promotercalculator 1.2.4 dev GPL-3.0-or-later X Promoter-Calculator (Barrick Lab Fork)
pronto 2.6.0 doc dev MIT XXX Python frontend to ontologies.
proot 5.1.0 GPL-2.0 X chroot, mount --bind, and binfmt_misc without privilege/setup
prooverlap 0.1.2 GPL-3.0-only X Assessing feature proximity/overlap and testing statistical...
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 XX ProPhasm – ProPhyle Assembler. Compressing k-mer sets via assembling contigs.
prophex 0.1.1 MIT XX The ProPhex k-mer index.
prophyle 0.3.3.2 MIT XX 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 dev GPL-3.0-or-later XX An ultra-fast motif finding program in large ChIP-seq datasets.
prosic 2.1.2 GPLv3 XX A highly sensitive and accurate Bayesian caller for somatic insertions...
prosolo 0.6.1 GPLv3 XX A highly sensitive and accurate Bayesian caller for variants in single...
prot-scriber 0.1.6 GPL-3.0-only XX Assigns short human readable descriptions (HRD) to query biological...
protal 0.2.1a dev MIT X Reference-based metagenomic analysis.
proteinortho 6.3.6 doc dev GPL-3.0-only XX 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_25292_c9a6a18 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 XXX piRNA detection
provean 1.1.5 GPL-3 XX 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 XX Comparison of pooled-sequencing data for two populations
psauron 1.1.0 doc MIT X PSAURON: a machine learning model for rapid assessment of protein...
psdm 0.3.0 MIT XX Compute a pairwise SNP distance matrix from one or two alignment(s)
pseqsid 1.0.2 MIT XX 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 doc dev GPL-3.0-only XX 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...
psipred 4.0 doc dev CUSTOM XX Protein Secondary Structure Predictor
psirc 1.0.0 doc dev MIT XX Full-length linear and circular transcript isoform reconstruction and...
psm-utils 1.5.1 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 XX This software package infers population size history from a diploid...
psosp 1.1.2 doc dev MIT X PSOSP (Prophage SOS-dependency Predictor)
pstools 0.2a3 MIT X Toolkit for fully phased sequences
pstrain 1.0.3 MIT XX 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 XX 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 XX A tool for all-atom reconstruction and refinement of reduced protein models
pullseq 1.0.2 MIT XX Utility program for extracting sequences from a fasta/fastq file.
pupmapper 0.1.0 dev MIT X Tool & python package for calculating genome wide pileup mappability.
pureclip 1.3.1 dev GPL-3.0-or-later XX PureCLIP is a tool to detect protein-RNA interaction footprints.
purge-dups-runner 2019.12.20 MIT X High Performance Cluster (HPC) runner.
purge_dups 1.2.6 doc dev MIT XX purge_dups is a package used to purge haplotigs and overlaps in an...
purge_haplotigs 1.1.3 MIT XXX 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 XXX 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 1.2.8 doc dev OTHER XX PxBLAT: An Efficient and Ergonomics Python Binding Library for BLAT.
py-graphviz 0.4.10 MIT XXX Simple Python interface for Graphviz
py2bit 0.3.3 doc dev MIT XX A package for accessing 2bit files using lib2bit.
py_fasta_validator 0.6 doc dev MIT XX Simply and quickly validate a fasta file. Invalid files return non-zero...
py_nucflag 0.1.6 MIT X Library to call misassemblies in genome assemblies from long-read alignments.
pyaavf 0.1.0 Apache X An amino acid variant format parser for Python.
pyabpoa 1.5.5 dev MIT XX pyabpoa: SIMD-based partial order alignment using adaptive band
pyalveo 1.0.3 BSD XX A Python library for interfacing with the Alveo API
pyamilyseq 1.3.2 doc dev GPL-3.0-only X PyamilySeq: A pangenome investigation tool
pyani 0.2.13.1 doc dev MIT XXX pyani provides a package and script for calculation of genome-scale...
pyani-plus 1.0.0 doc dev MIT X Whole-genome classification of microbes using Average Nucleotide...
pyasn1-modules 0.0.5 BSD XX a small but growing collection of ASN.1 data structures expressed in...
pyasp 1.4.3 GPLv3+ XX 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 XXX Tools for parsing BAM data
pybamtools 0.0.4 GNU XXX 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).
pybascule 1.0.1 GPL-3.0-only X Bayesian NMF signatures deconvolution and DP clustering.
pybbi 0.4.2 MIT XX 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-or-later XX Maximum likelihood estimation of Birth-Death Exposed-Infectious (BDEI)...
pybedgraph 0.5.43 MIT XX A package for fast operations on 1-dimensional genomic signal tracks
pybedlite 1.1.0 doc dev MIT XXX Lightweight python classes for interfacing with bed intervals.
pybedtools 0.12.0 doc dev MIT XX Wraps BEDTools for use in Python and adds many additional features.
pybel 0.13.2 doc dev Apache-2.0 XXX PyBEL is a Python package for parsing and handling biological networks...
pybigtools 0.2.4 doc dev MIT XX pybigtools: Python bindings to the Bigtools Rust library for...
pybigwig 0.3.24 doc dev MIT XX A python extension written in C for quick access to bigWig files.
pybiolib 1.2.1675 doc 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 XX A python extension written in C for quick access to DNA methylation BM files.
pybwa 2.2.0 doc dev MIT XX 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.
pycistarget 1.1 OTHER X pycistarget is a python module to perform motif enrichment analysis in...
pycistopic 2.0a OTHER X pycisTopic is a Python module to simultaneously identify cell states...
pycli 2.0.3 MIT XXX 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 XX Clustering module for Python
pycomo 0.2.9 dev MIT X PyCoMo is a software package for generating and analysing...
pycoqc 2.5.2 doc GNU XXX 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 XX Python bindings for CoverM
pycrac 1.5.2 Apache-2.0 X Python NextGen sequencing data processing software
pycsg 0.3.12 MIT XXX 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 XXX Streamed and parallel demultiplexing of fastq files in python
pydeseq2 0.5.3 doc dev MIT X A python implementation of DESeq2.
pydmtools 0.1.1 MIT XX A python extension written in C for quick access to DNA methylation DM files.
pydna 5.2.0 BSD-3-Clause XXX Representing double stranded DNA and functions for simulating cloning...
pydna_repeatfinder 0.2.9 doc dev MIT XX Search for direct and inverted repeats in DNA sequences.
pydnase 0.3.0 doc MIT XX 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 1.0.3 MIT XX 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 XXX EGA python client
pyensembl 2.3.13 Apache-2.0 XXX Python interface to ensembl reference genome metadata
pyexcelerator 0.6.4a BSD XX generating Excel 97+ files; importing Excel 95+ files; Excel files...
pyfaidx 0.9.0.3 doc dev BSD XXX pyfaidx: efficient pythonic random access to fasta subsequences
pyfamsa 0.5.3.post1 doc dev GPL-3.0-or-later XX Cython bindings and Python interface to FAMSA, an algorithm for...
pyfasta 0.5.2 MIT XXX fast, memory-efficient, pythonic (and command-line) access to fasta...
pyfastani 0.6.1 doc dev MIT XX Cython bindings and Python interface to FastANI, a method for fast...
pyfastaq 3.18.0 dev GPL-3.0-or-later XXX 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 doc dev MIT XX pyfastx is a python module for fast random access to sequences from...
pyfba 2.62 doc dev MIT XX 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 XX Python code for translating sequences using different NCBI translation...
pygenometracks 3.9 GPL3 XXX 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 XX Python interface to Graphviz
pygresql 5.0.1 Python XX Python PostgreSQL Interfaces
pygrgl 2.4 doc dev GPL-3.0-only XX Genotype Representation Graph Library for efficient storage/use of huge...
pygtftk 1.6.2 dev MIT XX 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 XX Python wrapper for xxHash algorithm
pyhmmer 0.11.4 doc dev MIT XX Cython bindings and Python interface to HMMER3.
pyhmmsearch 2025.10.23.post1 doc dev MIT X Fast implementation of HMMSEARCH optimized for high-memory systems...
pyimagingmspec 0.1.4 Apache XXX Python library for processing imaging mass spectrometry data
pyimzml 1.5.1 Apache-2.0 XXX Parser for conversion of imzML 1.1.0 files
pyjaspar 4.0.0 doc MIT X pyJASPAR: a serverless interface to Biopython to access different...
pyjess 0.9.1 doc dev MIT XX Cython bindings and Python interface to JESS, a 3D template matching software.
pykofamsearch 2025.9.5 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 GPLv3+ XX A Python interface to libsequence
pyliftover 0.4.1 MIT XXX 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 XXX 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 XX Utility library for rp-bp
pymix 0.8 GPL2 XX Python mixture package
pymlst 2.2.2 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 XXX 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 0.12.0 dev GPL-3.0-only XXX Wrapper for MUMmer.
pymvpa 2.6.5 dev perl_5 XX PyMVPA -- Multivariate Pattern Analysis in Python
pymzml 2.5.11 dev MIT XXX High-throughput mzML parsing.
pynacl 0.3.0 Apache XX Python binding to the Networking and Cryptography (NaCl) library
pynast 1.2.2 BSD XXX The Python Nearest Alignment Space Termination tool
pyngost 1.1.3 GPL-3.0-only X pyngoST: fast, simultaneous and accurate and multiple sequence typing...
pynnotator 2.0 BSD X A Python Annotation Framework for VCFs using multiple tools.
pynteny 1.0.0 doc dev Apache-2.0 XX 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
pyonsite 0.0.2 dev MIT X onsite: mass spectrometry post-translational localization tool
pyopal 0.7.3 doc dev MIT XX Cython bindings and Python interface to Opal, a SIMD-accelerated...
pyopenms 3.4.1 doc dev BSD-3-Clause XX 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 XXX 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 1.2.1 dev GPL-3.0-only X Peak Identifier for Nascent Transcripts Starts (PINTS)
pypiper 0.8 dev BSD-2-Clause XXX 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 0.4.0 MIT X Standalone Python re-implementation of the POLCA polisher from MaSuRCA
pypore 0.0.6.dev20180 Apache XX Pythonic/Cythonic Nanopore Translocation Analysis
pyprophet 3.0.5 doc dev BSD-3-Clause XX PyProphet: Semi-supervised learning and scoring of OpenSWATH results.
pyqi 0.3.2 BSD XX pyqi: expose your interface
pyquant-ms 0.2.4 MIT XX A framework for the analysis of quantitative mass spectrometry data
pyquery 1.2.9 BSD XX A jquery-like library for python
pyrad 3.0.66 GPLv3 XXX Assembly and analysis of RADseq data sets
pyranges 0.1.4 doc dev MIT XXX Performant Pythonic GenomicRanges.
pyrle 0.0.42 dev MIT XX Genomic Rle-objects for Python.
pyrodigal 3.6.3.post1 doc dev GPL-3.0-or-later XX 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...
pyrodigal-rv 0.1.0 GPL-3.0-or-later X A Pyrodigal extension to predict genes in RNA 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 XX Suffix array computation with induced sorting algorithm.
pysam 0.23.3 MIT XX Pysam is a Python module for reading and manipulating SAM/BAM/VCF/BCF...
pysamstats 1.1.2 MIT XX Calculate read mapping stats from SAM/BAM/CRAM
pyscaf 0.12a4 GPLv3 XXX 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...
pysctransform 0.1.1 dev GPL-3.0-or-later X Python package to perform normalization and variance-stabilization of...
pyseer 1.4.0 doc dev Apache-2.0 XXX Sequence Element Enrichment Analysis (SEER), python implementation.
pyseq-align 1.0.2 dev MIT XX Python interface for the seq-align C library
pysftp 0.2.9 BSD XX A friendly face on SFTP
pyskani 0.2.0 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 1.3.1 dev Apache-2.0 XX slow5lib Python binding
pysnptools 0.3.13 Apache XX Python library for reading and manipulating genetic data
pyspoa 0.3.2 doc dev MIT XX Python binding to spoa library.
pysradb 2.5.1 doc dev BSD-3-Clause XXX Python package for retrieving metadata and downloading datasets from SRA/ENA/GEO
pysvg 0.2.2 BSD XX Python SVG Library
pysvmlight 0.4 UNKNOWN XX Interface to Thorsten Joachims' SVM-Light
pytabix 0.1 MIT XX Fast random access to sorted files compressed with bgzip and indexed by tabix.
pytantan 0.1.3 doc dev GPL-3.0-or-later XX Cython bindings and Python interface to Tantan, a fast method for...
pytaxonkit 0.10 dev BSD-3-Clause X Python bindings for the TaxonKit library.
pyteomics 4.7.5 Apache-2.0 XXX A framework for proteomics data analysis.
pytest-marks 0.4 GNU XX 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 XXX A multi-omic python package
python-bioext 0.21.10 dev GPL-3.0-only XX 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 XXX A Python library for interacting with Chado database.
python-cluster 1.4.1.post3 LGPL-2.1 XXX 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 XX PacBio Quiver Consensus library for RSII data
python-consensuscore2 3.4.1 BSD-3-Clause-Clear XX 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 XX Lightweight, super fast C/C++ (& Python) library for sequence...
python-eel 1.0 GPL XX Tool for finding evolutionarily conserved mammalian enhancer elements.
python-fakemp 0.9.1 GPL-3 XXX 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 XXX A Python 3 library that makes inferences on HIV-1 transmission networks.
python-hppy 0.9.9 GPL-3 XXX 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 XX HyPhy package interface library
python-intervaltree 3.2.0 Apache-2.0 X Faster than intervaltree_bio
python-levenshtein 0.12.0 GPL XX Python extension for computing string edit distances and similarities.
python-libsbml 5.18.0 LGPL XX LibSBML Python API.
python-mailund-newick 1.3 GNU XX Another python module to read and write the Newick format
python-monovar 0.1 MIT X single cell joint genotyper, patched version
python-msgpack 1.1.2 doc dev Apache-2.0 XX It's like JSON. But fast and small.
python-newick 1.10.0 dev Apache-2.0 XXX 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 XXX 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 XXX Tripal API library
python-weblogo 3.4 Public XX 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 XX .Net and Mono integration for Python
pythonpy 0.4.11 Unknown XXX the swiss army knife of the command line
pytransaln 0.2.2 MIT X Translation-guided nucleotide alignment for coding sequences
pytrf 1.4.2 MIT XX a fast Python package for finding tandem repeat sequences
pytriangle 1.0.9 MIT XX A python interface to the 2D triangulation program TRIANGLE
pytrimal 0.8.5 doc dev GPL-3.0-or-later XX Cython bindings and Python interface to trimAl, a tool for automated...
pytwobit 0.3.1 dev MIT X A fast reader for local or remote UCSC twobit sequence files.
pytximport 0.12.0 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 XX A Variant Call Format reader for Python
pyvcf3 1.0.4 doc dev BSD-3-Clause XXX A Variant Call Format reader for Python.
pyvolve 1.1.0 doc dev BSD-2-Clause XXX Pyvolve is an open-source Python module for simulating sequences along...
pywdl 1.0.22 Apache XXX A Python implementation of a WDL parser and language bindings.
pywfa 0.5.1 dev MIT XX A python wrapper for wavefront alignment using WFA2-lib.
pywgsim 0.6.0 MIT XX pywgsim
pyx 0.14.1 GNU XX Python package for the generation of PostScript, PDF, and SVG files
qax 0.9.6 GPL-3.0-only XX 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...
qcatch 0.2.8 dev BSD-3-Clause X QCatch: Quality Control downstream of alevin-fry / simpleaf.
qcli 0.1.1 GPL XXX qcli
qcumber 2.0.4 LGPL3 XX Quality control, quality trimming, adapter removal and sequence content...
qfilt 0.0.1 MIT XX Filter sequencing data using some simple heuristics
qglmm 0.1.1 BSD-3-Clause X Fast Generalized Linear Mixed Models in Python
qgrs-cpp 1.0 MIT XX 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 XXX Quantitative Insights Into Microbial Ecology
qiime-default-reference 0.1.3 CC XXX Default reference data files for use with QIIME.
qiimetomaaslin 1.1.0 Unknown XX 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 XXX QoRTs toolkit for analysis, quality control, and data management of...
qsignature 0.1pre GPLv3 XXX qsignature is a simple and highly effective method for detecting...
qtip 1.6.2 MIT XX 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 XX Quake is a package to correct substitution sequencing errors in...
qualifilter 1.0.0 dev MIT X Generate a QC report summarizing key quality metrics and sample...
qualimap 2.3 GPL-2.0-or-later XXX Quality control of alignment sequencing data and its derivatives like...
qualrepair 1.0.0 MIT X Update the FASTQ quality scores from a subsequence FASTQ.
quantiprot 0.2.5 MIT X Quantiprot is a Python package for quantitative analysis of protein sequences
quantms-rescoring 0.0.10 dev Apache X PSM rescoring python package with scripts and helpers for the quantms workflow
quantms-utils 0.0.24 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...
quaqc 1.5 doc dev GPL-3.0-only XX Quick ATAC-seq Quality Control.
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 XXX Quasitools is a collection of tools for analysing Viral Quasispecies
quast 5.3.0 doc dev Custom XXX Quality Assessment Tool for Genome Assemblies.
quatradis 1.4.0 dev GPL-3.0-only XXX A set of tools to analyse the output from TraDIS analyses.
query_phenomizer 1.2.1 MIT XXX Tool for query and parsing the phenomizer tool
querynator 0.6.0 doc dev MIT X Python package to query cancer variant databases
quick-variants 1.2.4 MIT X Fast and accurate genetic variant identification
quickbam 1.0.0 BSD X Parallel BAM file access API for high throughput sequence analysis informatics
quickdeconvolution 1.2 GPL3 XX Deconvolves linked-reads sequencing data
quickmerge 0.3 GPL-3 XX Quickmerge uses a simple concept to improve contiguity of genome...
quickmirseq 1.0.0 GPL-3.0-or-later X A pipeline for fast and accurate quantification of both known miRNAs...
quicksect 0.2.2 MIT XX 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 XX Fast implementation of the neighbour-joining phylogenetic inference method.
quip 1.1.8 Custom XX Aggressive compression of FASTQ and SAM/BAM files.
quorum 1.1.1 GPLv3 XX QuorUM (Quality Optimized Reads from the University of Maryland) is an...
quota_anchor 1.0.2 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 XX Combine multidimensional arrays into a single array. This is a...
r-acidbase 0.7.5 dev AGPL-3.0 X Low-level base functions imported by Acid Genomics packages.
r-acidcli 0.3.2 dev AGPL-3.0 X Interative R command line interface toolkit for Acid Genomics packages.
r-acidexperiment 0.5.5 dev AGPL-3.0 X Toolkit to extend the functionality of SummarizedExperiment.
r-acidgenerics 0.7.10 dev AGPL-3.0 X S4 generic functions for Acid Genomics packages.
r-acidgenomes 0.7.5 dev AGPL-3.0 X Toolkit for downloading and processing genome annotations.
r-acidgsea 0.9.1 dev AGPL-3.0 X Parameterized fast gene set enrichment analysis.
r-acidmarkdown 0.3.1 dev AGPL-3.0 X Toolkit for extending the functionality of R Markdown.
r-acidplots 0.7.4 dev AGPL-3.0 X Functions for plotting genomic data.
r-acidplyr 0.5.5 dev AGPL-3.0 X A grammar of S4 class data manipulation.
r-acidsinglecell 0.4.4 dev AGPL-3.0 X Toolkit for single-cell RNA-seq analysis that extends the functionality...
r-ada 2.0_5 GPL XX Performs discrete, real, and gentle boost under both exponential and ...
r-ade4 1.7_2 GPL XX Multivariate data analysis and graphical display.
r-adegenet 2.1.1 GPL XX Toolset for the exploration of genetic and genomic data. Adegenet...
r-adephylo 1.1_11 GPL XX Multivariate tools to analyze comparative data, i.e. a phylogeny and...
r-agricolae 1.2_4 GPL XX 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 XX Provides methods for high-throughput adaptive immune receptor...
r-algdesign 1.1_7.3 GPL XX Algorithmic experimental designs. Calculates exact and approximate...
r-amap 0.8_14 GPL XX Tools for Clustering and Principal Component Analysis (With robust...
r-amlmapr 0.1.0 CC-BY-NC-SA-4.0 X R package for visualizing and analyzing AML transcriptome data
r-ampliconduo 1.1 GPL XX Increasingly powerful techniques for high-throughput sequencing open...
r-ampvis 1.27.0 AGPL-3 XX A package to visualise amplicon data
r-ampvis2 2.8.11 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 XXX Provides tables for converting and annotating Ensembl Gene IDs.
r-aod 1.3 GPL XX This package provides a set of functions to analyse overdispersed...
r-aptreeshape 1.5_0 GPL XX Simulation and analysis of phylogenetic tree topologies using...
r-archr 1.0.3 doc dev MIT XX This package is designed to streamline scATAC analyses in R.
r-argparse 1.0.1 GPL XX A command line parser to be used with Rscript to write "#!"...
r-argparser 0.4 GPL XX Cross-platform command-line argument parser written purely in R with no...
r-argumentcheck 0.10.2 GPL-3 XX The typical process of checking arguments in functions is iterative. ...
r-aroma.affymetrix 3.2.3 LGPL-2.1-or-later XXX A cross-platform R framework that facilitates processing of any number...
r-aroma.apd 0.6.0 LGPL XX DEPRECATED. Do not start building new projects based on this package....
r-aroma.core 3.3.2 dev LGPL-2.1-or-later XXX Core methods and classes used by higher-level 'aroma.*'...
r-ash 1.0_15 GPL XX David Scott's ASH routines ported from S-PLUS to R.
r-asics 1.0.1 GPL XX 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 doc dev GPL-3.0-only XX Azimuth is a Shiny app demonstrating a query-reference mapping...
r-bascule 1.0.1 doc GPL-3.0-or-later X Bayesian inference and clustering of mutational signatures leveraging...
r-base64 1.1 GPL XX Base 64 encoder/decoder
r-basejump 0.18.1 dev AGPL-3.0 XXX Base functions for bioinformatics and R package development.
r-batch 1.1_4 GPL XX Functions to allow you to easily pass command-line arguments into R,...
r-batchjobs 1.6 BSD_2_clause XX Provides Map, Reduce and Filter variants to generate jobs on batch...
r-bayesprism 0 GPL-3 XX BayesPrism: Bayesian cell type and gene expression deconvolution
r-bbmisc 1.11 BSD_3_clause XX Miscellaneous helper functions for and from B. Bischl and some other...
r-bbmle 1.0.18 GPL-2 XX 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 XXX Base functions and generics for bcbio R packages.
r-bcbiornaseq 0.6.2 dev AGPL-3.0 XXX 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 XX Plots univariate comparison graphs, an alternative to...
r-bedr 1.0.4 GPL-2 XX 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 XX Boost provides free peer-reviewed portable C++ source libraries. A...
r-biasedurn 1.07 GPL-3 XX 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 XX Create, store, access, and manipulate massive matrices. Matrices are...
r-bigmemory.sri 0.1.3 LGPL-3 XX This package provides a shared resource interface for the bigmemory and...
r-bio3d 2.3_3 GPL XX Utilities to process, organize and explore protein structure, sequence...
r-biodb 1.2.2 AGPL-3.0 XX An R package for connecting to chemical and biological databases.
r-biom 0.3.12 GPL-2 XX This is an R package for interfacing with the BIOM format.
r-biomark 0.4.5 GPL XX 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 XXX S4 generic functions for bioinformatics.
r-bipartite 2.11 GPL XX 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 XX bitmapped vectors of booleans (no NAs), coercion from and to logicals,...
r-bit64 0.9_5 GPL-2 XX Package 'bit64' provides serializable S3 atomic 64bit (signed)...
r-blockfest 1.6 GPL-2 XX An R implementation of an extension of the 'BayeScan' software...
r-blockmodeling 0.1.8 GPL XX The package is primarly ment as an implementation of Generalized...
r-bma 3.18.6 GPL XX Package for Bayesian model averaging and variable selection for linear...
r-bmix 1.0.0 doc GPL-3.0-or-later X Binomial and Beta-Binomial mixture models for counts data.
r-bpcells 0.3.1 doc dev Apache-2.0 XX Efficient operations for single cell ATAC-seq fragments and RNA counts...
r-breakaway 4.7.9 GPL-2 XXX Understanding the drivers of microbial diversity is an important...
r-brio 0.3.17 dev MIT XXX 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 XX Package for drawing calibrated scales with tick marks on...
r-canopy 1.3.0 GPL-2 XX A statistical framework and computational procedure for identifying the...
r-car 2.1_4 GPL XX Functions and Datasets to Accompany J. Fox and S. Weisberg, An R...
r-caroline 0.7.6 Artistic-2.0 XX The caroline R library contains dozens of functions useful for:...
r-cate 1.1.1 GPL-2 XXX Provides several methods for factor analysis in high dimension (both...
r-catools 1.17.1 GPL-3 XX Contains several basic utility functions including: moving (rolling,...
r-ccqtl 0.0.1_beta.2 GPL3 XX CCQTL is a wrapper around the R/qtl2 (Broman et al, Genetics 2019...
r-ccube 1.0_beta.1 GPL-3 XX R package for clustering and estimating cancer cell fractions (CCF) of...
r-cdseq 0 GPL-3 XX Estimate cell-type-specific gene expression profiles and...
r-cellassign 0.99.2 Apache-2.0 XXX 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 XX 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 XX Implements various mainstream and specialised changepoint methods for...
r-chbutils 0.1_2017_10_26 MIT XXX Useful utility functions used at the Harvard Chan School Bioinformatics core
r-checkmate 1.8.2 BSD_3_clause XX Tests and assertions to perform frequent argument checks. A substantial...
r-checkpoint 0.4.0 GPL-2 XX 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 dev MIT X Stores several motifs as PWMatrixList objects for use in R with...
r-cimpl 1.1 doc dev GPL-3.0-or-later XXX An analysis package for multi sample insertional mutagenesis data...
r-circlize 0.3.3 GPL XX Circular layout is an efficient way for the visualization of huge ...
r-circrnafull 1.0.0 dev Unknown X An R package for reconstruction of full length circRNA sequence using...
r-classdiscovery 3.4.9 Apache-2.0 XXX 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 XX 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-cnaqc 1.1.3 doc GPL-3.0-or-later X Copy number quality control
r-cnogpro 1.1 GPL-2 XX Methods for assigning copy number states and breakpoints in...
r-cobrar 0.2.2 doc dev GPL-3.0-or-later XX 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 XX Simulate species occurrence and abundances (counts) along gradients.
r-coloc 5.1.0.1 GPL XXX Performs the colocalisation tests described in Plagnol et al (2009)...
r-combinat 0.0_8 GPL-2 XX routines for combinatorics
r-compquadform 1.4.1 GPL XX Computes the distribution function of quadratic forms in normal...
r-compute.es 0.2_4 GPL-2 XX This package contains several functions for calculating the most widely...
r-conos 1.5.2 GPL-3.0-only XX 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 XX Provides a bundle of basic and fundamental bioinformatics tools, such...
r-corncob 0.4.2 GPL-2.0-or-later X Statistical modeling for correlated count data using the beta-binomial...
r-corpcor 1.6.8 GPL XX Efficient Estimation of Covariance and (Partial) Correlation
r-corrplot 0.77 GPL XX 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 XX 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 XX Cell-type specific differential expression of a microarray experiment...
r-ctree 1.1.0 doc GPL-3.0-or-later X Clone trees for Cancer Evolution studies from bulk sequencing data.
r-d3heatmap 0.6.1.1 GPL-3 XX Create interactive heat maps that are usable from the R console, in the...
r-dartr 2.9.9.5 doc GPL-3.0-or-later XX Functions are provided that facilitate the import and analysis of SNP...
r-data.table 1.11.6 MPL-2.0 XX 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 XXX Takes sample information in the form of the fraction of mutations in...
r-delaporte 3.0.0 GPL XX Provides probability mass, distribution, quantile, random-variate...
r-deldir 0.1_12 GPL XX Calculates the Delaunay triangulation and the Dirichlet or Voronoi...
r-dendextend 1.1.2 GPL-2 XX 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 XX Differential Evolution (DE) stochastic algorithms for global...
r-deseqanalysis 0.7.2 dev AGPL-3.0 X Toolkit for performing differential expression with DESeq2.
r-dgeclustering 0.1.0 MIT XX DGEclustering is an R package for multidimensional clustering of...
r-diagram 1.6.3 GPL XX Visualises simple graphs (networks) based on a transition matrix,...
r-diffcorr 0.4.5 GPL3 X A method for identifying pattern changes between 2 experimental...
r-digest 0.6.12 GPL XX Implementation of a function 'digest()' for the creation of...
r-dimsum 1.4 dev MIT X An error model and pipeline for analyzing deep mutational scanning...
r-dinamic.duo 1.0.4 GPL-3.0-only X In tumor tissue, underlying genomic instability can lead to DNA copy...
r-diptest 0.75_7 GPL XX 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 XX 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-dndscv 0.1.0 doc GPL-3.0-or-later X dN/dS methods to quantify selection in cancer and somatic evolution.
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 XX Define a command-line interface by just giving it a description in the...
r-dorng 1.6 GPL XX This package provides functions to perform reproducible parallel...
r-downloader 0.0.4 GPL-2 XX 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 XX This package provides functions for fitting dPeak, a statistical...
r-dplyr 0.5.0 MIT XX A fast, consistent tool for working with data frame like objects, both...
r-drc 3.0_1 GPL-2 XX Analysis of dose-response data is made available through a suite of...
r-dsb 2.0.1 CC0 X Normalizing and denoising protein expression data from droplet-based...
r-dt 0.2 GPL-3 XX Data objects in R can be rendered as HTML tables using the JavaScript...
r-dunn.test 1.3.1 GPL-2 XX 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 XX Contains methods for detection of clusters in hierarchical clustering...
r-e1071 1.6_8 GPL-2 XX 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-easypar 1.0.0 dev GPL-3.0-or-later X The easypar package makes it easy to implement parallel computations in...
r-ebimetagenomics 0.6 LGPL-3 XX Functions for querying the EBI Metagenomics Portal...
r-ecodist 2.0.1 GPL XX Dissimilarity-based analysis functions including ordination and Mantel...
r-efglmh 0.1.0 doc dev MIT X Functions For Working With Microhaps for EFGL
r-eggnog 0.3.1 dev AGPL-3.0 X EggNOG database annotations.
r-ellipse 0.3_8 GPL XX This package contains various routines for drawing ellipses and...
r-emdbook 1.3.9 GPL XX Auxiliary functions and data sets for "Ecological Models and...
r-empiricalfdr.deseq2 1.0.3 GPL-3 XXX 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 XXX 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 2.2.0 GPL-2.0-or-later XX Automated compound deconvolution, alignment across samples, and...
r-exactranktests 0.8_29 GPL-2|GPL-3 XX Computes exact conditional p-values and quantiles using an...
r-exomedepth 1.1.18 GPL-3 XX Calls copy number variants (CNVs) from targeted sequence data,...
r-extrafont 0.17 GPL-2 XX Tools to using fonts other than the standard PostScript fonts. This...
r-extrafontdb 1.0 GPL-2 XX 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 XX Cellular Fraction and Copy Numbers from Tumor Sequencing
r-factominer 1.38 GPL XX Exploratory data analysis methods to summarize, visualize and describe...
r-fail 1.3 BSD_3_clause XX More comfortable interface to work with R data or source files in a...
r-fastbaps 1.0.8 MIT XXX A fast approximation to a Dirichlet Process Mixture model (DPM) for...
r-fastcluster 1.1.20 FreeBSD XX This is a two-in-one package which provides interfaces to both R and...
r-fastica 1.2_0 GPL XX Implementation of FastICA algorithm to perform Independent Component...
r-fastmatch 1.1_0 GPL-2 XX Package providing a fast match() replacement for cases that require...
r-fastqcr 0.1.2 GPL-2 XX 'FASTQC' is the most widely used tool for evaluating the...
r-fateid 0.1.8 GPL-3 XX Application of 'FateID' allows computation and visualization of...
r-fda 2.4.4 GPL XX 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 XX Provides a wrapper for several FFTW functions. This package provides...
r-fgwas 0.3.6 GNU XXX GWAS tools for longitudinal genetic traits based on fGWAS statistical model.
r-fields 8.10 GPL XX For curve, surface and function fitting with an emphasis on splines,...
r-findpython 1.0.1 MIT XX 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 XX Extends the fitdistr function (of the MASS package) with several...
r-flanders 1.0.1 MIT X Fast colocalization using AnnData objects in R
r-flashclust 1.01_2 GPL XX Fast implementation of hierarchical clustering
r-flexclust 1.3_4 GPL-2 XX The main function kcca implements a general framework for k-centroids...
r-flexmix 2.3_14 GPL XX A general framework for finite mixtures of regression models using the...
r-floral 0.6.0 GPL-3.0-or-later X Log-ratio Lasso regression for continuous, binary, and survival...
r-flowr 0.9.10 MIT XX This framework allows you to design and implement complex pipelines,...
r-fmsb 0.6.3 GPL XXX Several utility functions for the book entitled "Practices of...
r-fnn 1.1 GPL XX Cover-tree and kd-tree fast k-nearest neighbor search algorithms and...
r-fpc 2.1_10 GPL XX Various methods for clustering and cluster validation. Fixed point...
r-freerange 0.2.8 dev MIT XXX Generate and manipulate genomic ranges.
r-funr 0.2.0 MIT XX A small utility which wraps Rscript and provides access to all R...
r-funrar 1.2.2 GPL XX Computes functional rarity indices as proposed by Violle et al. (2017)...
r-futile.logger 1.4.1 LGPL-3 XX Provides a simple yet powerful logging utility. Based loosely on log4j,...
r-futile.options 1.0.0 LGPL-3 XX A scoped options management framework
r-future 1.2.0 LGPL XX A Future API for R is provided. In programming, a future is an...
r-gam 1.14_4 GPL-2 XX Functions for fitting and working with generalized additive models, as...
r-gamlss 5.0_0 GPL-2 XX Functions for fitting, displaying and checking GAMLSS Models.
r-gamlss.data 5.0_0 GPL-2 XX Data for GAMLSS models.
r-gamlss.dist 5.0_0 GPL-2 XX The different distributions used for the response variables in GAMLSS modelling.
r-gap 1.2.1 GPL XX 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 XX 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 XX Useful tools for writing vector graphics devices.
r-geiger 2.0.6.2 GPL XX Methods for fitting macroevolutionary models to phylogenetic trees.
r-genabel 1.8_0 GPL XX A package for genome-wide association analysis between quantitative or...
r-genabel.data 1.0.0 GPL XX GenABEL.data package consists of a data set used by GenABEL functions
r-geneexpressionfromgeo 1.3 dev 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 XX Using simple input, this package creates plots of gene models. Users...
r-genenet 1.2.13 GPL XX Analyzes gene expression (time series) data with focus on the inference...
r-genometricorr 1.1.17 Artistic-2.0 XX Genometric Correlation (GenometriCorr) is an R package for spatial...
r-genomictools 0.2.9.7 GPL-2 XX 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 XX Split 'geospatial' objects into pieces. Includes support for...
r-geomap 2.3_8 GPL XX 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 XX This is yet another command-line argument parser which wraps the ...
r-ggally 1.3.0 GPL XX The R package 'ggplot2' is a plotting system based on the...
r-ggalt 0.4.0 AGPL XX 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 XX 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 XX 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 XX A system for 'declaratively' creating graphics, based on...
r-ggrasp 1.0 GPL-2 XX Given a group of genomes and their relationship with each other, the...
r-ggrepel 0.6.5 GPL-2 XX Provides text and label geoms for 'ggplot2' that help to avoid...
r-ggsignif 0.4.0 GPL-3 XX Enrich your 'ggplots' with group-wise comparisons. This package...
r-giant 1.2 Artistic-2.0 XX Toolbox for various enrichment analysis methods and quantification of...
r-gkmsvm 0.83.0 GPL-2.0-or-later XX Imports the 'gkmSVM' v2.0 functionalities into R...
r-globaloptions 0.0.8 GPL XX It provides more controls on the option values such as validation and...
r-globals 0.7.1 LGPL XX Identifies global ("unknown") objects in R expressions by code...
r-gmd 0.3.3 GPL XX GMD is a package for non-parametric distance measurement between two...
r-gmodels 2.16.2 GPL-2 XX Various R programming tools for model fitting.
r-gmwt 1.2 GPL-2.0-only XX Generalized Mann-Whitney type tests based on probabilistic indices and...
r-goalie 0.7.8 dev AGPL-3 XXX Assertive check functions for defensive R programming.
r-goeveg 0.4.2 GPL XX A collection of functions useful in (vegetation) community analyses and...
r-googlevis 0.5.10 GPL XX R interface to Google Charts API, allowing users to create interactive...
r-gpca 1.0 GPL XX 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 XX Functional enrichment analysis, gene identifier conversion and mapping...
r-gpseq 0.5 GPL-2 XX Some functions for modeling sequence read counts as a generalized...
r-grain 1.4.5 GPL-2.0-or-later XX Probability propagation in graphical independence networks, also known...
r-grbase 2.0.3 GPL-2.0-or-later XX The 'gRbase' package provides graphical modelling features used...
r-grimport 0.9_0 GPL XX Functions for converting, importing, and drawing PostScript pictures...
r-gsalib 2.1 MIT XX This package contains utility functions used by the Genome Analysis...
r-gsmoothr 0.1.7 LGPL XX Tools rewritten in C for various smoothing tasks
r-gsubfn 0.6_6 GPL XX gsubfn is like gsub but can take a replacement function or certain...
r-guilds 1.3 GPL-2 XX A collection of sampling formulas for the unified neutral model of...
r-gwasexacthw 1.01 GPL-3 XX This package contains a function to do exact Hardy-Weinburg testing...
r-gwpcr 1.0.4 AGPLv3 XX Implements the necessary distributions and parameter estimation...
r-hahmmr 1.0.0 MIT XX Haplotype-aware Hidden Markov Model for RNA (HaHMMR) is a method for...
r-haplo.stats 1.7.7 GPL XX Routines for the analysis of indirectly measured haplotypes. The...
r-hardyweinberg 1.6.3 GPL XX Contains tools for exploring Hardy-Weinberg equilibrium (Hardy, 1908; ...
r-harmony 0.1 dev GPL-3.0-only XX Fast, sensitive and accurate integration of single-cell data with Harmony
r-hdrcde 3.1 GPL XX Computation of highest density regions in one and two dimensions,...
r-hemdag 2.7.4 doc dev GPL-3.0-or-later XX 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 XX Allows the estimation of hierarchical F-statistics from haploid or...
r-histonehmm 1.8 dev GPL XX histoneHMM is a software to analyse ChIP-seq data of histone...
r-hmm 1.0.2 GPL-3 X Functions for hidden Markov Models (HMM).
r-htmltools 0.3 GPL XX 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 XXX Functions for analyzing high throughput sequencing stable isotope...
r-hwriter 1.3.2 LGPL-2.1 XX Easy-to-use and versatile functions to output R objects in HTML format
r-ic10 2.0.2 GPL-3.0-or-later XXX Genome-driven integrated classification of breast cancer validated in...
r-ic10trainingdata 1.0.1 GPL-3 XX Training datasets for iC10; which implements the classifier described...
r-ichorcna 0.5.1 GPL-3.0-only XXX Estimating tumor fraction in cell-free DNA from ultra-low-pass whole...
r-icluster 2.1.0 GPL XX Integrative clustering of multiple genomic data types using a joint...
r-idpmisc 1.1.17 GPL XX The IDPmisc package contains different high-level graphics functions...
r-idr 1.2 GPL XX 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 XX 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 XX Functionality to dynamically define R functions and S4 methods with...
r-inlinedocs 2013.9.3 GPL-2 XX Generates Rd files from R source code with comments. The main features...
r-intego 2.0 GPL3 XX 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 XX 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 expression.
r-isva 1.9 GPL-2 X Independent Surrogate Variable Analysis is an algorithm for feature...
r-itertools 0.1_3 GPL-2 XX 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 XX None
r-jsonlite 0.9.19 MIT XX A fast JSON parser and generator optimized for statistical data and the...
r-kaos 0.1.0 GPL XX Sequences encoding by using the chaos game representation. Löchel et...
r-kernlab 0.9_25 GPL XX Kernel-based machine learning methods for classification, regression,...
r-kinship2 1.6.4 GPL XXX Routines to handle family data with a pedigree object. The initial...
r-klar 0.6_12 GPL-2 XX Miscellaneous functions for classification and visualization developed...
r-km.ci 0.5_2 GPL-2|GPL-3 XX Computes various confidence intervals for the Kaplan-Meier estimator,...
r-kmsurv 0.1_5 GPL XX Data sets and functions for Klein and Moeschberger (1997),...
r-knitr 1.12.3 GPL-2 XX Provides a general-purpose tool for dynamic report generation in R...
r-knitrbootstrap 1.0.0 MIT XX A framework to create Bootstrap 3 HTML reports from knitr Rmarkdown.
r-kriging 1.1 GPL-2 XX Simple and highly optimized ordinary kriging algorithm to plot geographical data
r-ks 1.10.6 GPL-2 XX Kernel smoothers for univariate and multivariate data, including...
r-lambda.r 1.1.7 LGPL-3 XX A language extension to efficiently write functional programs in R....
r-ldrtools 0.2_1 GPL XX Linear dimension reduction subspaces can be uniquely defined using...
r-ldweaver 1.5.2 GPL-3.0-or-later XX Perform genomewide epistasis analysis by evaluating the LD structure in...
r-leapp 1.3 GPL-2.0-or-later XXX These functions take a gene expression value matrix, a primary...
r-leaps 2.9 GPL-2|GPL-3 XX Regression subset selection including exhaustive search
r-learnbayes 2.15 GPL XX LearnBayes contains a collection of functions helpful in learning the...
r-leidenbase 0.1.31 GPL-2.0-only, XX An R to C interface that runs the Leiden community detection algorithm...
r-liger 2.2.1 doc dev GPL-3.0-or-later XX Uses an extension of nonnegative matrix factorization to identify...
r-linxreport 1.1.0 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 XXX A method to assess how well mixed cells with different labels are in...
r-listenv 0.6.0 LGPL XX List environments are environments that have list-like properties. For...
r-lme4qtl 0.1.10 GPL XXX Linear mixed models (lme4) with flexible covariance structure for qtl...
r-lncpipereporter 0.1.1 GPL-2 XX 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 XX 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 XX logging is a pure R package that implements the ubiquitous log4j package.
r-longitudinal 1.1.12 GPL XX Contains general data structures and functions for longitudinal data...
r-loom 0.2.0.2 GPL-3 XXX 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 XX 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 XX Provides a mechanism for chaining commands with a new forward-pipe...
r-maldiquant 1.18 GPL XX A complete analysis pipeline for matrix-assisted laser...
r-maldiquantforeign 0.12 GPL XXX Functions for reading (tab, csv, Bruker fid, Ciphergen XML, mzXML,...
r-maldirppa 1.0.1 GPL XX 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 XX Emulate MATLAB code using R.
r-matrixeqtl 2.1.1 LGPL-3 XX Matrix eQTL is designed for fast eQTL analysis on large datasets....
r-matrixstats 0.51.0 Artistic-2.0 XX 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 XX Scattered data interpolation with Multilevel B-Splines
r-mclust 5.2 GPL XX Normal Mixture Modelling fitted via EM algorithm for Model-Based...
r-mcpcounter 1.1.0 GPL-3 XXX Estimating tissue-infiltrating immune and other stromal subpopulations...
r-merge-kallisto 0.6 Apache X merge_kallisto
r-mess 0.5.5 GPL-2 XX A mixed collection of useful and semi-useful diverse statistical...
r-metablastr 0.3.2 GPL-2.0-or-later XX 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 XX 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 XXX Identify time intervals of differentially abundant metagenomics...
r-metama 3.1.3 GPL XXX 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 XX Implementation of two p-value combination techniques (inverse normal...
r-metstat 1.0 Apache XX 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 XX A collection of functions for computations and visualizations of...
r-microseq 1.2 GPL-2 XX 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 XX Mine MS-MS spectra using a frequent usbgraph mining approach.
r-minionqc 1.4.2 MIT XXX 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 XX 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 XX Toolkit for analysis of genomic data
r-missforest 1.4 GPL XX The function 'missForest' in this package is used to impute...
r-mitools 2.3 GPL-2 XX Tools to perform analyses and combine results from multiple-imputation datasets.
r-mixedcca 1.5.2 GPL-3.0-only XX Semi-parametric approach for sparse canonical correlation analysis
r-mixkernel 0.9 GPL XXX Kernel-based methods are powerful methods for integrating ...
r-mixomics 6.3.1 GPL XX Multivariate methods are well suited to large omics data sets where the...
r-mixtools 1.1.0 GPL XX 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 XX 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 XX Tools for extracting individual genomes from metagenomes
r-mmod 1.3.3 MIT XX Provides functions for measuring population divergence from genotypic data.
r-mobster 0.1.1 doc GPL-3.0-or-later X Model-based subclonal deconvolution from bulk sequencing.
r-momf 0 GPL-2 XX The package can fit single RNA-seq data set(SOMF) and multiple RNA-seq...
r-momr 1.1 Artistic-2.0 XX 'MetaOMineR' suite is a set of R packages that offers many...
r-monocle3 1.4.26 doc dev MIT XXX An analysis toolkit for single-cell RNA-seq.
r-motifbinner 2.0.0 GPL3 XX MotifBinner processes high-throughput sequencing data of an RNA virus...
r-mqtl 1.0 GPL XX mQTL provides a complete QTL analysis pipeline for metabolomic data. ...
r-msm 1.6.7 GPL XX Functions for fitting continuous-time Markov and hidden Markov...
r-mspbwt 0.1.1 doc dev GPL-3.0-only XX Multi Symbol Positional Burrows Wheeler Transform.
r-msqrob 0.7.7 GPL XX Robust statistical inference for quantitative LC-MS proteomics.
r-multicool 0.1_10 GPL-2 XX A set of tools to permute multisets without loops or hash tables and to...
r-multitaper 1.0.11 GPL-2|GPL-3 XX 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 XX R package for extracting and visualizing mutational patterns in base...
r-mutoss 0.1_12 GPL XXX 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 XX This is a non-parametric method for joint adaptive mean-variance...
r-mytai 2.3.4 dev GPL-2.0-or-later XX Investigate the evolution of biological processes by capturing...
r-nabor 0.5.0 BSD XXX An R wrapper for 'libnabo', an exact or approximate k nearest...
r-nam 1.6.4 GPL-3 XX Designed for association studies in nested association mapping (NAM)...
r-nanopore 0.2.9 dev MPL-2.0 XX R methods, associated with Nanopore tutorials, for analysis and...
r-nanostringnorm 1.2.1.1 GPL-2.0-only XXX A set of tools for normalizing, diagnostics and visualization of...
r-nastiseq 1.0 GPL-2.0 XX Pairs of RNA molecules transcribed from partially or entirely...
r-nbpseq 0.3.1 GPL-2.0-only XX Negative Binomial (NB) models for two-group comparisons and regression...
r-ncbit 2013.03.29 GPL XX 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 XXX Quick mining and visualization of NGS data by integrating genomic databases
r-ngsplotdb-hg19 3.00 GPL-2.0 XX HG19 genome database for NGSplot
r-ngsplotdb-hg38 3.00 GPL-2.0 XXX HG19 genome database for NGSplot
r-ngsplotdb-mm10 3.00 GPL-2.0 XXX 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 XX Solve a system of nonlinear equations using a Broyden or a Newton...
r-nodiv 1.3.0 MIT XX 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 XX Onedimensional Normal Mixture Models Classes, for, e.g., density...
r-nozzle.r1 1.1_1 LGPL-2 XX The Nozzle package provides an API to generate HTML reports with...
r-numbat 1.5.1 MIT XX A computational method that infers copy number variations (CNVs) in...
r-oai 0.2.2 MIT XX A general purpose client to work with any 'OAI-PMH' (Open...
r-oncopharmadb 1.9.7 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 XX Simplifies the creation of Excel .xlsx files by providing a high level...
r-optparse 1.3.2 GPL XX A command line parser inspired by Python's 'optparse'...
r-ore 1.3.0 BSD_3_clause XX Provides an alternative to R's built-in functionality for handling...
r-orqa 0.2.1 GPL XX Assess repeatability, accuracy and corss-platform agreement of...
r-outliers 0.14 GPL XX A collection of some tests commonly used for identifying outliers.
r-pack 0.1_1 GPL-3 XX 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 XX Some functions for sample classification in microarrays
r-panther 0.5.1 dev AGPL-3.0 X PANTHER database annotations.
r-params 0.4 GPL-2 XX An interface to simplify organizing parameters used in a package, using...
r-pathfindr 2.7.0 doc dev MIT X Enrichment analysis enables researchers to uncover mechanisms...
r-pathosurveilr 0.4.1 dev 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 XX Quickly and easily visualize longitudinal microbiome profiles using...
r-pcalg 2.6_12 GPL-2 XX Functions for causal structure learning and causal inference using...
r-pcapp 1.9_60 GPL XX Robust PCA by Projection Pursuit
r-pctgcdata 0.3.0 GPL XXX Provides GC percentage of a 1 kilobase window at a genomic position for...
r-peakpick 0.11 MIT X Peak Picking Methods Inspired by Biological Data
r-peer 1.3 GPL X PEER is a collection of Bayesian approaches to infer hidden...
r-pegas 0.11 GPL XX Functions for reading, writing, plotting, analysing, and manipulating...
r-penalized 0.9.47 GPL-2 XX Fitting possibly high dimensional penalized regression models. The...
r-perfmeas 1.2.5 GPL-2.0-or-later XX Package that implements different performance measures for...
r-permute 0.8_4 GPL-2 XX A set of restricted permutation designs for freely exchangeable, line...
r-phangorn 2.4.0 GPL XX Package contains methods for estimation of phylogenetic trees and...
r-pheatmap 1.0.8 GPL-2 XX Implementation of heatmaps that offers more control over dimensions and...
r-phewas 0.99.6 dev GPL-3.0-or-later XX Phenome Wide Association Studies (PheWAS) - Functions to perform...
r-phonr 1.0_3 GPL-3 XX Tools for phoneticians and phonologists, including functions for...
r-phyext2 0.0.4 GPL-3 XXX Based on (but not identical to) the no-longer-maintained package...
r-phylobase 0.8.6 GPL XX Provides a base S4 class for comparative methods, incorporating one or...
r-phylomeasures 2.1 GPL-3 XX Given a phylogenetic tree T and an assemblage S of species represented...
r-phylosignal 1.2.1 GPL-3 XX A collection of tools to explore the phylogenetic signal in univariate...
r-phytools 0.6_99 GPL XXX Phylogenetic tools for comparative biology
r-pinfsc50 1.1.0 GPL XX Genomic data for the plant pathogen "Phytophthora infestans."...
r-pio 0.1.0 doc dev MIT X Pretty I/O output to the console
r-pipette 0.15.3 dev AGPL-3.0 X Pipette biological data in and out of R.
r-plasmidprofiler 0.1.6 Apache XX Contains functions developed to combine the results of querying a...
r-plotly 4.5.6 MIT XX Easily translate ggplot2 graphs to an interactive web-based version...
r-plotrix 3.6_4 GPL XX 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 XX Performs Penalized Multivariate Analysis: a penalized matrix...
r-pmcmr 4.1 GPL XX The Kruskal and Wallis one-way analysis of variance by ranks or van...
r-png 0.1.7 GPL-2 XX This package provides an easy and simple way to read, write and display...
r-polynom 1.3_8 GPL-2 XX A collection of functions to implement a class for univariate...
r-polysat 1.7_4 GPL XX A collection of tools to handle microsatellite data of any ploidy (and...
r-popgenome 2.7.2 GPL-3 XX Provides efficient tools for population genomics data analysis, able to...
r-popgenreport 3.0.4 GPL XXX Provides beginner friendly framework to analyse population genetic...
r-pophelper 2.3.1 GPL-3 XXX A set of useful functions for processing admixture proportion files...
r-poppr 2.8.5 GPL XX An R package for genetic analysis of populations with mixed...
r-pore 0.24 BSD XX An R package to enable organisation and visualisation of nanopore...
r-prabclus 2.2_6 GPL XX Distance-based parametric bootstrap tests for clustering with spatial...
r-pracma 1.8.8 GPL XX Functions from numerical analysis and linear algebra, numerical...
r-precrec 0.9.1 GPL-3 XX Accurate calculations and visualization of precision-recall and ROC...
r-preseqr 2.0.0 GPL-3 XX Estimating the number of species represented r or more times in a random sample.
r-presto 1.0.0 doc dev GPL-3.0-only XX 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 XX Pretty, human readable formatting of quantities. Time intervals:...
r-probmetab 1.1 GPL XX Provides probability ranking to candidate compounds assigned to masses,...
r-progress 1.0.2 MIT XX Terminal progress bars. They are configurable, may include percentage,...
r-proj4 1.0_8 GPL-2 XX A simple interface to lat/long projection and datum transformation of...
r-propcis 0.3_0 GPL XX 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 XX Provides an extensible framework for the efficient calculation of auto-...
r-prroc 1.1 GPL-3 XX Computes the areas under the precision-recall (PR) and ROC curve for...
r-pscbs 0.68.0 GPL-2.0-or-later XXX Segmentation of allele-specific DNA copy number data and detection of...
r-pscl 1.4.9 GPL-2 XX 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 XX A general purpose toolbox for personality, psychometrics and...
r-ptw 1.9_11 GPL XX Parametric Time Warping aligns patterns, i.e. it aims to put...
r-purbayes 1.3 GPL-2 XX 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 XX Open QIIME output files in R, compute statistics, and create plots from...
r-qlcmatrix 0.9.5 GPL-3 XX Extension of the functionality of the Matrix package for using sparse...
r-qorts 1.3.6 Public XXX 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 XX Create Q-Q and manhattan plots for GWAS data from PLINK results.
r-qtl 1.41_6 GPL-3 XX Analysis of experimental crosses to identify genes (called quantitative...
r-qtl2 0.22 GPL-3 XX R/qtl2 provides a set of tools to perform quantitative trait locus...
r-qtlseqr 0.7.5.2 GPL XX QTLseqr is an R package for QTL mapping using NGS Bulk Segregant Analysis.
r-quilt 2.0.4 doc dev GPL-3.0-only XX Rapid and accurate genotype imputation from low coverage short read,...
r-quorts 1.3.0 Public XX The QoRTs software package is a fast, efficient, and portable...
r-r.cache 0.12.0 LGPL XX Memoization can be used to speed up repetitive and computational...
r-r.devices 2.15.1 LGPL XX Functions for creating plots and image files in a unified way...
r-r.filesets 2.10.0 LGPL XX A file set refers to a set of files located in one or more directories...
r-r.huge 0.9.0 LGPL XX DEPRECATED. Do not start building new projects based on this package....
r-r.methodss3 1.7.1 LGPL XX Methods that simplify the setup of S3 generic functions and S3 methods....
r-r.oo 1.21.0 LGPL XX Methods and classes for object-oriented programming in R with or...
r-r.rsp 0.30.0 LGPL XX The RSP markup language makes any text-based document come alive. RSP...
r-r.utils 2.5.0 LGPL XX 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 XX 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 XX Application of 'RaceID' allows inference of cell types and...
r-rainbow 3.3 GPL XX 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 XX Finds the k nearest neighbours for every point in a given dataset in...
r-rapidr 0.1.1 GPL-3 XXX Package to perform non-invasive fetal testing for aneuploidies using...
r-rappdirs 0.3 MIT XX An easy way to determine which directories on the users computer you...
r-rbamtools 2.16.11 Artistic-2.0 XX Provides an R interface to functions of the 'SAMtools'...
r-rbison 0.6.0 MIT XX Interface to the 'USGS' 'BISON'...
r-rblast 1.3.1 doc dev GPL-3.0-or-later XXX Seamlessly interfaces the Basic Local Alignment Search Tool (BLAST) to...
r-rcircos 1.2.0 GPL XX 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 XX High level functions for parallel programming with 'Rcpp'. For...
r-rcpptoml 0.1.3 GPL XX The configuration format defined by 'TOML' (which expands to...
r-readbrukerflexdata 1.8.5 GPL XX Reads data files acquired by Bruker Daltonics' matrix-assisted...
r-readmzxmldata 2.8.1 GPL XX Functions for reading mass spectrometry data in mzXML format.
r-readr 0.2.2 GPL XX Read flat/tabular text files from disk (or a connection).
r-rebird 1.0.0 MIT XX A programmatic client for the eBird database, including functions for...
r-recetox-aplcms 0.14.2 doc dev GPL-2.0-or-later X apLCMS is a software which generates a feature table from a batch of...
r-recetox-waveica 0.2.1 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 XX R package for Regulatory multi-omics with Deep Mitochondrial mutation profiling.
r-relaimpo 2.2_2 GPL-2 XX relaimpo provides several metrics for assessing relative importance in...
r-relations 0.6_6 GPL-2 XX 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 XX Wrappers on 'regexpr' and 'gregexpr' to return the...
r-rentrez 1.1.0 MIT XX Provides an R interface to the NCBI's EUtils API allowing users to...
r-reshape 0.8.6 MIT XX Flexibly restructure and aggregate data using just melt() and cast().
r-restfulr 0.0.16 Artistic-2.0 XX Models a RESTful service as if it were a nested R list.
r-rfoc 3.3_3 GPL XX Graphics for statistics on a sphere, as applied to geological fault...
r-rgbif 1.3.0 MIT XX A programmatic interface to the Web Service methods provided by the...
r-rgraphics 2.0_14 GPL XX Data and Functions from the book R Graphics, Second Edition. There is a...
r-riborex 2.4.0 GPL-3.0 XXX Riborex is a R package for identification of differential translation...
r-ridigbio 0.3.5 MIT XX 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-rldne 1.0.0 doc dev GPL-2.0-only X A Convenient R Interface For NeEstimator V2.1
r-rlist 0.4.6.1 MIT XX Provides a set of functions for data manipulation with list objects,...
r-rmarkdown 0.9.5 GPL-3 XX Convert R Markdown documents into a variety of formats.
r-rmysql 0.10.11 GPL-2 XX A 'DBI' interface to 'MySQL' / 'MariaDB'
r-rnexml 2.4.0 BSD_3_clause XXX Provides access to phyloinformatic data in 'NeXML' format. The...
r-rniftyreg 2.2.0 GPL-2 XX Provides an R interface to the NiftyReg image registration tools...
r-robustrankaggreg 1.1 GPL-2 XX Methods for aggregating ranked lists, especially lists of genes. It...
r-rocr 1.0_7 GPL XX ROC graphs, sensitivity/specificity curves, lift charts, and...
r-rphast 1.6.11 doc dev BSD_3_clause XX Provides an R interface to the...
r-rphylip 0.1_23 GPL XX Rphylip provides an R interface for the PHYLIP package. All users of...
r-rpmg 2.2_1 GPL XX Really Poor Man's Graphical User Interface, used to create...
r-rrbgen 0.0.6 doc dev GPL3 XX A lightweight limited functionality R bgen read/write library
r-rrcov 1.3_11 GPL XX Robust Location and Scatter Estimation and Robust Multivariate Analysis...
r-rseis 3.5_2 GPL XX Multiple interactive codes to view and analyze seismic data, via...
r-rsm 2.7_4 GPL-2 XX 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 XX General Non-linear Optimization Using Augmented Lagrange Multiplier Method.
r-rspectral 1.0.0.14 GPL-2 XX 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 XX Identifies and scores possible Transcription Factor Binding Sites and...
r-rtsne 0.13 BSD XX An R wrapper around the fast T-distributed Stochastic Neighbor...
r-rttf2pt1 1.3.4 file XX Contains the program 'ttf2pt1', for use with the...
r-rubic 1.0.3 Apache-2.0 XXX Pinpoint driver genes in focal recurrent aberrations (across tumor...
r-runit 0.4.31 GPL-2 XX R functions implementing a standard Unit Testing framework, with...
r-rvertnet 0.7.0 MIT XXX Retrieve, map and summarize data from the 'VertNet.org' ...
r-rwave 2.4 GPL XX 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 XX Maximum likelihood tools to fit and compare models of species abundance...
r-saige 1.3.1 dev GPL-3.0-only XX SAIGE is an R package with Scalable and Accurate Implementation of...
r-samr 3.0 LGPL XX Significance Analysis of Microarrays
r-sartools 1.8.2 dev GPL-2.0-or-later XXX Statistical Analysis of RNA-Seq data.
r-sbpiper 1.9.0 MIT XXX Provides an API for analysing repetitive parameter estimations and...
r-scales 0.4.1 MIT XX Graphical scales map data to aesthetics, and provide methods for...
r-scatterplot3d 0.3_36 GPL-2 XX 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 XX 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 XXX scImpute is accurate and robust imputation of single-cell RNA sequencing data.
r-scistreer 1.2.0 GPL-3.0-only XX Fast maximum-likelihood phylogeny inference from noisy single-cell data...
r-scoper 1.2.1 AGPL-3.0-only XX Provides a computational framework for identification of B cell clones...
r-scopfunctions 0 AGPL-3 XX 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 XX 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 XX Given a regression model, segmented `updates' the model by adding...
r-sendmailr 1.2_1 GPL-2 XX Package contains a simple SMTP client which provides a portable...
r-seqinr 3.4_5 GPL XX 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 XX Integrate sequencing data (Variant call format, e.g. VCF or BCF) or...
r-sequenza 3.0.0 GPL-3 XXX Tools to analyze genomic sequencing data from paired normal-tumor...
r-sets 1.0_16 GPL-2 XX Data structures and basic operations for ordinary sets, generalizations...
r-seurat 3.0.2 dev GPL-3 XX A toolkit for quality control, analysis, and exploration of single cell...
r-seurat-data 0.2.2.9002 doc dev GPL-3.0-only XXX Single cell RNA sequencing datasets can be large, consisting of...
r-seurat-disk 0.0.0.9021 dev GPL-3.0-only XXX The h5Seurat file format is specifically designed for the storage and...
r-seurat-scripts 0.0.4 dev GPL-3 XXX A set of wrappers for individual components of the Seurat package....
r-sew 1.0.1 doc dev BSD3 XX SEW
r-sgtr 1.1.4 GPL3 XX Visualize population genomics analyses results in R.
r-shaman 2.0 GPL XX The shaman package - sampling HiC contact matrices for a-parametric...
r-shape 1.4.2 GPL XX Functions for plotting graphical shapes such as ellipses, circles,...
r-shazam 1.1.2 AGPL-3 XXX Provides a computational framework for analyzing mutations in...
r-shinyace 0.2.1 MIT XX Ace editor bindings to enable a rich text editing environment within Shiny.
r-shinyngs 2.3.0 AGPL-3.0 X Provides Shiny applications for various array and NGS applications....
r-sigminer 2.3.1 MIT XXX Genomic alterations including single nucleotide substitution, copy...
r-signac 1.16.0 doc dev MIT XX A framework for the analysis and exploration of single-cell chromatin...
r-signal 0.7_6 GPL-2 XX A set of signal processing functions originally written for...
r-sigqc 0.1.24 GPL-3.0-or-later XXX Provides gene signature quality control metrics in publication ready...
r-sigtree 1.10.6 GPL-3 XX 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 XX Densities and Sampling for the Skellam Distribution
r-sleuth 0.30.2 doc dev GPL-3.0-or-later XXX Tools for investigating RNA-Seq.
r-smartsva 0.1.3 GPL-3 XX Introduces a fast and efficient Surrogate Variable Analysis algorithm...
r-smvar 1.3.3 GPL XX Implements the structural model for variances in order to detect...
r-snow 0.4_1 GPL XX Support for simple parallel computing in R.
r-snowfall 1.84_6.1 GPL XX Usability wrapper around snow for easier development of parallel R...
r-snpassoc 1.9_2 GPL XX This package carries out most common analysis when performing whole...
r-soap-nmr 0.1.0.20170207 GPL2 XX R package for 1H-NMR data pre-treatment
r-solarius 0.3.0.2 GPL XX SOLAR is the standard software program to perform linkage and...
r-som 0.3_5.1 GPL XX 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 XX Set of functions for sparse matrix algebra. Differences with...
r-sparql 1.16 GPL-3 XX Use SPARQL to pose SELECT or UPDATE queries to an end-point.
r-spdep 0.6_8 GPL XX A collection of functions to create spatial weights matrix objects from...
r-speaq 2.7.0 Apache-2.0 XXX Makes Nuclear Magnetic Resonance spectroscopy (NMR spectroscopy) data...
r-speedglm 0.3_1 GPL XX Fitting linear models and generalized linear models to large data sets...
r-spieceasi 1.1.1 GPL-2.0-or-later XXX Estimate networks from the precision matrix of compositional microbial...
r-splancs 2.01_38 GPL XX The Splancs package was written as an enhancement to S-Plus for display...
r-splitstackshape 1.4.2 GPL-3 XX Online data collection tools like Google Forms often export...
r-spocc 0.9.0 MIT XX A programmatic interface to many species occurrence data sources,...
r-spp 1.16.0 doc GPL-2.0-only XX 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 XX Description: Manipulate R data frames using SQL.
r-stampp 1.5.1 GPL-3 XXX Allows users to calculate pairwise Nei's Genetic Distances (Nei...
r-statmod 1.4.29 GPL-2 XX 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 1.8.4 doc dev GPL-3.0-only XX STITCH - Sequencing To Imputation Through Constructing Haplotypes.
r-stringr 1.1.0 GPL-2 XX A consistent, simple and easy to use set of wrappers around the...
r-structssi 1.2.1 doc GPL-2.0-or-later XXX Performs multiple testing corrections that take specific structure of...
r-survey 3.31_5 GPL-2 XX Summary statistics, two-sample tests, rank tests, generalised linear...
r-svdialogs 0.9_57 GPL-2 XX Rapidly construct dialog boxes for your GUI, including an automatic...
r-svgui 0.9_55 GPL-2 XX Functions to manage GUIs from R
r-swamp 1.5.1 GPL XXX Collection of functions to connect the structure of the data with the...
r-syntactic 0.7.2 dev AGPL-3 XXX Make syntactically valid names out of character vectors.
r-tailfindr 1.4 AGPL-3.0 XX An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA...
r-taxa 0.3.2 MIT XX Provides taxonomic classes for groupings of taxonomic names without...
r-taxonomizr 0.7.1 GPL XX Functions for assigning taxonomy to NCBI accession numbers and taxon...
r-tcga2stat 1.2 GPL-2 XXX Automatically downloads and processes TCGA genomics and clinical data...
r-tcr 2.3.2 Apache XX Platform for the advanced analysis of T cell receptor and...
r-testthat 1.0.2 MIT XX A unit testing system designed to be fun, flexible and easy to set up.
r-tfmpvalue 0.0.6 GPL-2 XX In putative Transcription Factor Binding Sites (TFBSs) identification...
r-tftargets 1.3 CC0 X Human transcription factor target genes.
r-tibble 1.2 MIT XX Provides a 'tbl_df' class that offers better checking and...
r-tidygenomics 0.1.2 GPL-3 XX Handle genomic data within data frames just as you would with...
r-tidyheatmap 1.13.1 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-tinc 0.1.0 GPL-3 X TINC is a package that implements algorithms to determine the...
r-tinyarray 2.4.3 MIT X Gene Expression Omnibus(GEO) and The Cancer Genome Atlas(TCGA) are...
r-tmae 1.0.5 MIT XXX Tests and visualizations for mono-allelicly expressed variants.
r-traminer 2.0_9 GPL XX Toolbox for the manipulation, description and rendering of sequences,...
r-transformer 0.2.12 dev MIT XXX Additional S3 and S4 coercion methods for easy interconversion between...
r-transphylo 1.4.0 GPL2 XX Reconstruction of transmission trees using genomic data
r-treesim 2.4 GPL-2 XX Simulation methods for phylogenetic trees where (i) all tips are...
r-trimcluster 0.1_2 GPL XX Trimmed k-means clustering.
r-truncnorm 1.0_7 GPL-2 XX r/d/p/q functions for the truncated normal distribution
r-tsne 0.1_3 GPL XX A "pure R" implementation of the t-SNE algorithm.
r-tximport 0.0.15 GPL XX None
r-txrevise 2.0 Apache X Construct custom transcript annotations for Salmon and kallisto
r-ukbrapr 0.3.8 dev GPL-3.0-only X R functions to use in the UK Biobank Research Analysis Platform (RAP)
r-umi4c 0.0.1 GPL XX 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 XX Creates visualizations of intersecting sets using a novel matrix...
r-vcfr 1.8.0 GPL XX Facilitates easy manipulation of variant call format (VCF) data....
r-vegan 2.3_4 GPL-2 XX Ordination methods, diversity analysis and other functions for...
r-velocyto.r 0.6 GPL-3 XX RNA velocity estimation in R
r-venn 1.2 GPL XX Draws and displays Venn diagrams up to 7 sets, and any Boolean union of...
r-venndiagram 1.6.16 GPL-2 XX A set of functions to generate high-resolution Venn and Euler plots....
r-viber 1.0.0 doc GPL-3.0-or-later X Variational Binomial Mixtures.
r-virfinder 1.1 USC-RL XX VirFinder: a novel k-mer based tool for identifying viral sequences...
r-viridis 0.3.1 MIT XX 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 XX A high-throughput and unbiased module for interpreting scRNA-seq data.
r-wasabi 1.0.1 BSD-3-clause XXX Prepare Sailfish and Salmon output for downstream analysis
r-waveslim 1.7.5 BSD_3_clause XX Basic wavelet routines for time series (1D), image (2D) and array (3D)...
r-wgcna 1.73 GPL-3.0-or-later XX Functions necessary to perform Weighted Correlation Network Analysis on...
r-whopgenome 0.9.7 GPL XX Provides very fast access to whole genome, population scale variation...
r-wicket 0.4.0 MIT XX 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 XX A wrapper around Michel Scheffers's libassp (Advanced Speech Signal...
r-writexls 4.0.0 GPL XX Cross-platform Perl based R function to create Excel 2003 (XLS) and...
r-xcell 1.3 GPL-3 XX 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 XX A simple implementation of XML-RPC for R.
r-xnomial 1.0.4 GPL-2|GPL-3 XX Tests whether a set of counts fit a given expected ratio. For example,...
r-yaml 2.1.13 BSD_3_clause XX This package implements the libyaml YAML 1.1 parser and emitter...
r-zerone 1.0 dev GPL-3 XX Zerone discretizes several ChIP-seq replicates simultaneously and...
r2r 1.0.6 GPL-2 XX software to speed depiction of aesthetic consensus RNA secondary structures
ra 0.9 dev GPL-3.0-or-later XX 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 0.5.5 dev GPL-2.0-or-later X RABIES: Rodent Automated Bold Improvement of EPI Sequences.
rabix-bunny 1.0.4 Apache XXX Open-source development kit for the Common Workflow Language from Seven...
racon 1.5.0 doc dev MIT XX Ultrafast consensus module for raw de novo genome assembly of long...
rad 0.6.0 doc dev MIT XX Read-structure Agnostic Demultiplexer for long-read single-cell RNA-seq.
rad_haplotyper 1.1.9 Perl XX A program for building SNP haplotypes from RAD sequencing data
radiant 1.1.5 GPL-3.0-or-later XX 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 XX The radsex software is part of RADSex, a computational workflow for the...
radte 0.2.3 MIT X Reconciliation-Assisted Divergence Time Estimation for gene families.
radtk 0.2.0 BSD-3-Clause XX A collection of tools for working with RAD files.
ragout 2.3 GPLv3 XX Chromosome-level scaffolding using multiple references
ragtag 2.1.0 doc dev MIT X Fast reference-guided genome assembly scaffolding
rainbow 2.0.4 doc GPL-2.0-or-later XX 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 XXX a reference-based tool for rapid and sensitive extraction of one...
randfold 2.0.1 doc GPL-2.0-or-later XX Minimum free energy of folding randomization test software.
rapclust 0.1.2 BSD XXX Accurate, Fast and Lightweight Clustering of de novo Transcriptomes...
rapgreen 1.0 doc GPLv3 X Manipulate and annotate phylogenetic trees
rapid 1.0 GPL2 XXX Read Alignment, Analysis, and Differential Pipeline (RAPID) is a set of...
rapidnj 2.3.2 dev GPL-2-only XX RapidNJ is an algorithmic engineered implementation of canonical...
rapidshapes 2.1.0 GPL-3.0-or-later XX 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 XX 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 20180710 doc dev GPL-2.0-or-later XX Scaffolding with RNA-seq read alignment.
rastair 0.8.2 dev GPL-3.0-or-later XX Rust tool for TAPS-based methylation calling.
rasusa 2.2.2 MIT XX 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 1.1.0 dev GPL3 X Rapid Annotation Transfer Tool
rattle 1.0 doc dev GPL-3.0-or-later XX Reference-free reconstruction and quantification of transcriptomes from...
raven-assembler 1.8.3 doc dev MIT XX 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 XX Phylogenetics - Randomized Axelerated Maximum Likelihood.
raxml-ng 1.2.2 AGPL-3 XX RAxML Next Generation: faster, easier-to-use and more flexible
ray 2.3.1 GPL3 XX Parallel genome assemblies for parallel DNA sequencing
razers3 3.5.8 doc dev GPL-3.0-only XX RazerS 3 - Faster, fully sensitive read mapping.
rbpbench 1.0.6 MIT X Evaluate CLIP-seq and other genomic region data using a comprehensive...
rcorrector 1.0.7 doc dev GPL-3.0-only XX 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 0.0.8 doc dev MIT XX A general purpose, multithreaded read analysis and manipulation tool.
rdfextras 0.4 BSD XX RDFExtras provide tools, extra stores and such for RDFLib.
rdflib 4.2.2 BSD XX RDFLib is a pure Python package work working with RDF
rdflib-jsonld 0.4 BSD XX rdflib extension adding JSON-LD parser and serializer
rdkit 2016.03.3 BSD X None
rdock 2013.1 doc dev LGPLv3 X A Fast, Versatile and Open Source Program for Docking Ligands to...
rdp-readseq 2.0.2 GPL XXX Java based common sequence file format reader and sequence file manipulation.
rdp_classifier 2.14 GPL-2.0-only XXX Naive Bayesian classifier that can rapidly and accurately provide...
rdptools 2.0.3 Creative XXX Metaproject for RDP Tools
rdrpcatch 0.0.9 dev MIT X RNA virus RdRp sequence scanner.
reactome-cli 1.0.0 Apache-2.0 X Reactome CLI bioconda
read-it-and-keep 0.3.0 MIT XX Read contamination removal
read2tree 2.0.1 dev MIT X Building phylogenetic trees directly from sequencing reads.
readfq 2015.08.30 dev MIT XX 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 XXX 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 XX An assembly tool for 16S ribosomal RNA recovery from metagenomic data
real 1.0 file XX REad ALigner for Next-Generation sequencing reads.
realphy 1.13 No X The Reference sequence Alignment based Phylogeny
reaper 16.098 GPL3 XX Tool for demultiplexing, trimming and filtering sequencing data.
rearr 1.0.4 doc dev MIT X Chimeric alignment of CRISPR-seq
rebaler 0.2.0 GPL-3.0 XXX Reference-based long read assemblies of bacterial genomes
rebar 0.2.1 Apache-2.0 XX 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 1.16.1 doc dev AGPL-3.0-or-later X Robust comparative analysis and contamination removal for metagenomics.
recgraph 1.0.0 MIT XX 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 doc dev GPL-2.0-or-later XX The RECON package performs de novo identification and classification of...
recontig 1.5.0 MIT XX recontig is a D program and python package that provides fast...
recur 1.0.0 doc dev GPL-3.0-only X Detect recurrent amino-acid substitutions from multiple-sequence alignments.
recycler 0.7 BSD-3-Clause XXX Recycler is a tool designed for extracting circular sequences from de...
red 2018.09.10 Custom XX Red (RepeatsDetector): an intelligent, rapid, accurate tool for...
reditools3 3.5 dev GPL-3.0-or-later X REDItools3 is an RNA editing detection tool implemented in Python3 for...
reduce 4.15 doc dev BSD-4-Clause-UC XX 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 dev GPL-3.0-or-later XX 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 1.6.0 dev Apache-2.0 X Metabolic modeling package.
refseq-plasmid-dl 0.1.0 GPL-3.0-only X A command-line tool to download and curate RefSeq plasmid sequences from NCBI.
refseq_masher 0.1.2 doc dev Apache XXX refseq_masher finds what NCBI RefSeq genomes match or are contained...
regain-cli 1.7.1 MIT X Bayesian-network pipeline for ARG/virulence co-occurrence analysis.
regenie 4.1.2 doc dev MIT XX Regenie is a C++ program for whole genome regression modelling of large...
regex 2016.06.24 Python XX 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 doc dev MIT XX Tools that integrate DNA-seq and RNA-seq data to help interpret...
relecov-tools 1.7.4 dev GPL-3.0-or-later X Tools for managing and processing of relecov data.
relion 5.0.1 doc dev GPL-2.0-or-later XX Image-processing software for cryo-electron microscopy.
relocate2 2.0.1 unknown XXX a high resolution transposable element insertion sites mapping tool for...
remag 0.3.4 doc dev MIT X Recovery of high-quality eukaryotic genomes from complex metagenomes
remurna 1.0 doc LicenseRef-HHS- X Measurement of Single-Nucleotide Polymorphism-induced Changes of RNA...
rename 1.601 GNU XXX Perl-powered file rename script with many helpful built-ins
renano 1.3 MIT XX 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 0.5.1 doc dev MIT XX A fast lossless FASTQ compressor with ultra-high compression ratio.
reparation_blast 1.0.9 GPL3 XX A pipeline that detects novel open reading frames with ribseq data for bacteria.
repdenovo 0.0.1 MIT XX REPdenovo is designed for constructing repeats directly from sequence reads.
repeatafterme 0.0.7 doc dev CC0 XX A package for the extension of repetitive DNA sequences.
repeatmasker 4.2.2 doc dev Open XXX RepeatMasker is a program that screens DNA sequences for interspersed...
repeatmodeler 2.0.7 doc dev Open XXX RepeatModeler is a de-novo repeat family identification and modeling package.
repeatscout 1.0.7 doc dev CC0 XX De novo identification of repeat families in large genomes.
repenrich 1.2 Custom XXX 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 0.3.5 doc dev 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 XXX 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 XX Persistent cache for requests library
requests-mock 1.0.0 Apache XX Mock out responses from the requests package
requests-toolbelt 0.5.0 Apache XX A toolbelt of useful classes and functions to be used with python-requests
rerconverge 0.3.0 GPL-3 XX RERconverge is a set of software written in R that estimates the...
reseek 2.6.1 doc dev GPL-3.0-only XX Protein structure alignment and search algorithm.
reseq 1.1 MIT X ReSeq Illumina/BGI simulator
resfinder 4.7.2 doc dev Apache-2.0 X ResFinder identifies acquired antimicrobial resistance genes in total...
resistify 1.3.0 doc dev GPL-3.0-or-later X A resistance gene annotation tool.
resmico 1.2.2 doc dev MIT XX Increasing the quality of metagenome-assembled genomes with deep learning
retry_decorator 1.1.1 MIT XXX Retry Decorator
revbayes 1.3.2 doc dev GPL-3.0-or-later XX Bayesian Phylogenetic Inference Using Graphical Models and an...
reveal 0.1 MIT XX Graph based multi genome aligner
reviewer 0.2.7 GPL-3.0 XX 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
revtag 1.0.0 doc dev MIT XX Reverse (and complement) array-like SAM tags for negative facing alignments.
revtrans 1.4 GPLv2 XXX revtrans - performs a reverse translation of a peptide alignment.
rfmix 2.03.r0.9505bfa dev Free XX 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 6.0.5 https://card.mc XXX This tool provides a preliminary annotation of your DNA sequence(s)...
rgt 1.0.2 doc dev GPL-3.0-or-later XX Toolkit to perform regulatory genomics data analysis
rhocall 0.5.1 doc dev GPLv3 XX Call regions of homozygosity and make tentative UPD calls.
rhotermpredict 3.4 dev AGPL-3.0-or-later X RhoTermPredict (Barrick Lab Fork)
riassigner 0.5.0 dev MIT X GC-MS retention index calculation
riblast 1.2.0 MIT XX RIblast is ultrafast RNA-RNA interaction prediction software.
ribocode 1.2.15 MIT XXX 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 0.3.2 GPL-3.0-or-later X Accurate and rapid RiboRNA sequences Detector based on deep learning
ribodiff 0.2.2 GPL XXX 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 0.3.10 dev 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 XX Plot read counts of RiboSeq data from BAM format alignment files
riboraptor 0.2.2 doc dev BSD XXX Python package to analyse ribosome profiling data
riborex 2.4.0 GPL-3 XXX Riborex is a R package for identification of differential translation...
riboseed 0.4.90 dev MIT XXX 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 1.5 doc dev MIT X Ribosomal DNA assembly tool.
ribotish 0.2.8 GPL-3.0-or-later XX Ribo TIS Hunter (Ribo-TISH) identifies translation activities using...
ribotools 2.0.0 doc dev MIT X Ribotools: a toolbox for translation efficiency (TE) and differential...
ribotricer 1.4.0 GNU XXX 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 XX 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 XX rmap is a short reads mapper for next-generation sequencing data
rmath4 4.3.1 GPL-2.0 XX standalone Rmath library from R
rmats 4.3.0 Free XX 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 XXX rmats2sashimiplot
rmblast 2.14.1 doc OSL-2.1 XX 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 0.1.8 doc dev MIT X Python package to perform rMLST through the PubMLST API.
rna-cd 0.2.0 doc dev GNU X RNA contamination detector
rna-seqc 2.4.2 doc dev BSD-3-Clause XXX Fast, efficient RNA-Seq metrics for quality control and process optimization.
rnaalishapes 2.5.0 GPL-3.0-or-later XX 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 1.3.3 doc dev GPL-3.0-or-later XX The RNAblueprint library solves the problem of uniformly sampling...
rnabob 2.2.1 XX fast RNA motif searching
rnabridge-align 1.0.1 dev BSD-3-Clause XX A tool to construct the alignments of entire fragments given the...
rnabridge-denovo 1.0.1 BSD-3-Clause XX A tool to construct the alignments of entire fragments given the...
rnachipintegrator 3.0.0 doc dev Artistic XXX Analyse genes against peak data, and vice versa
rnaclust 1.3 GPL-2.0 XX A tool for clustering of RNAs based on their secondary structures using LocARNA
rnacode 0.3.1 doc dev Unknown XX RNAcode - Analyze the protein coding potential in multiple sequence...
rnahybrid 2.1.2 GPL-2 XX RNAhybrid is a tool for finding the minimum free energy hybridization...
rnalien 1.8.0 GPL-3 XX 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 XX rnaQUAST is a tool for evaluating RNA-Seq assemblies using reference...
rnaredprint 0.3 doc dev GPL-3.0-or-later XX Tree-decomposition based dynamic programming algorithm for multiple...
rnasamba 0.2.5 GPL-3 XXX A tool for computing the coding potential of RNA transcript sequences...
rnashapes 3.4.0 doc dev GPL-3.0-or-later XX RNAshape abstraction maps structures to a tree-like domain of shapes,...
rnasketch 1.5 GPL3 XX RNAsketch Library for designing RNA molecules. Glue between...
rnasnp 1.2 RTH XX Efficient detection of local RNA secondary structure changes induced by SNPs.
rnastructure 6.4 GPL-2.0-only XX 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 doc dev MIT-like XX Predicting structural noncoding RNAs.
rnftools 0.4.0.0 MIT XXX RNF framework for NGS: simulation of reads, evaluation of mappers,...
roadies 0.1.10 doc dev MIT XX Reference-free Orthology-free Alignment-free DIscordance aware...
roary 3.13.0 GPL-3.0 XX Rapid large-scale prokaryote pan genome analysis
roary2fripan.py 0.1 GPLv2 XXX 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 XX 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 XX 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 dev MIT XX Incremental construction of FM-index for DNA sequences.
ropebwt3 3.10 doc dev MIT XX Constructs the FM-index of a large DNA sequence set and searches for...
roprofile 1.4.5 GPLv3 XX Generation of pan-genome profile files using Roary output.
roprofile.py 1.4.5 GPLv3 XX 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 XX Simple program to rotate a circular sequence to start at a given...
rpbp 4.0.1 doc dev MIT XX 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 XXX Calculates gene expression from a read mapping file
rpsbproc 0.5.0 Public XX RpsbProc, the post-RPSBLAST Processing Utility.
rpy2 2.7.8 GNU XX Python interface to the R language (embedded R)
rrikindp 0.0.2 doc dev GPL-3.0-only XX Evaluation of thermodynamic and kinetic features of RNA-RNA interactions.
rrmscorer 1.0.11 doc dev MIT X RRMScorer (RRM-RNA score predictor) predicts how likely a single RRM is...
rs3 0.0.18 Apache-2.0 X Predict the activity of CRISPR sgRNAs
rsa 3.1.4 Apache XX Pure-Python RSA implementation
rsat-core 2025.04.04 GNU XX Regulatory Sequence Analysis Tools (RSAT)
rscape 2.0.4.a GPLv3 XX R-scape (RNA Structural Covariation Above Phylogenetic Expectation)...
rseg 0.4.9 doc dev GPL-3.0-or-later X The RSEG software package is used to analyze ChIP-Seq data, especially...
rsem 1.3.3 doc dev GPL-3.0-or-later XX RSEM is a software package for estimating gene and isoform expression...
rseqc 5.0.4 doc dev GPL-2.0-or-later XXX QC package for RNA-seq data.
rsidx 0.3.1 dev BSD-3-Clause X Library for indexing VCF files for random access searches by rsID.
rsrq 1.1.0 GNU XX A minimal Redis-backed queue system.
rsv-typer 0.5.0 MIT X Genotyping RSV samples from nanopore sequencing data
rtg-core 3.13 doc dev BSD-2-Clause X RealTimeGenomics Core -- Software for alignment and analysis of...
rtg-tools 3.13 doc dev BSD-2-Clause XXX RealTimeGenomics Tools -- Utilities for accurate VCF comparison and...
rtk 0.93.2 dev GPL-2.0-or-later XX rtk - rarefaction toolkit for OTU tables.
rtk2 2.11.2 dev GPL-2.0-or-later XX rtk2 - a CLI rarefaction toolkit for OTU tables
ruby 2.2.3 BSD XX Ruby is a dynamic, reflective, object-oriented, general-purpose...
ruby-dna-tools 1.0 GPL-2.0 XXX Various libraries containing useful functions for working with DNA...
rucs 1.0.3 doc dev Apache-2.0 X RUCS is a bioinformatics tool developed to ease the task of designing...
ruffus 2.8.4 MIT XXX Light-weight Python Computational Pipeline Management
rukki 0.3.0 doc dev Public XX 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.
ruranges 0.0.15 dev MIT XX Rust-backed interval kernels exposed to Python/NumPy.
rust-bio-tools 0.42.2 dev MIT XX A growing collection of fast and secure command line utilities for...
rust-gtars 0.5.2 doc dev BSD-2-Clause XX Performance-critical tools to manipulate, analyze, and process genomic...
rust-mdbg 1.0.1 MIT XX An ultra-fast minimizer-space de Bruijn graph (mdBG) implementation,...
rust-ncbitaxonomy 1.0.7 doc MIT XX 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...
rust-proseg 2.0.6 doc GPL-3.0-or-later XX A Rust crate for running Proseg, a cell segmentation method for in situ...
rustybam 0.1.34 doc dev MIT XX Mitchell Vollger's bioinformatics rust utilities.
rustynuc 0.3.1 MIT XX Quick analysis of pileups for likely 8-oxoG locations
rustyread 0.4.1 MIT XX Rustyread, a long-read simulator
rvtests 2.0.7 GPL XX Rare variant test software for next generation sequencing data
rxdock 2013.1.1_148c5bd1 dev LGPL-3.0 XX RxDock is a fork of rDock (GitLab), a fast, versatile and open-source...
ryuto 1.6.3 BSD XX Network-Flow based Transcriptome Reconstruction
s3gof3r 0.5.0 MIT XX Fast, concurrent, streaming access to Amazon S3, including gof3r, a CLI
s4pred 1.2.1 dev GPL-3.0-or-later X Accurate prediction of a protein's secondary structure from its...
sabre 1.000 MIT XX A barcode demultiplexing and trimming tool for FastQ files
saccharis 2.0.5 dev GPL-3.0-or-later X SACCHARIS Bioinformatics Pipeline
sadie-antibody 2.0.0 dev MIT X The Complete Antibody Library
safesim 0.1.6.8d44580 Apache-2.0 XX SafeSeqS variant simulator
saffrontree 0.1.2 dev GPL-3.0-or-later XXX Reference-free rapid phylogenetic tree construction from raw read data.
sage-proteomics 0.14.7 doc dev MIT XX 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 0.4.8 doc dev https://github. XX 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 XX Highly-accurate & wicked fast transcript-level quantification from...
salsa2 2.3 MIT XX 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 XX 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 XX 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 XX Tools for working with SAM/BAM data.
samblaster 0.1.26 doc dev MIT XX Mark duplicates in and extract discordant and split reads from SAM files.
samclip 0.4.0 GPL-3.0 XXX Filter SAM file for soft and hard clipped alignments
samcut 0.1.1 MIT XX samcut is `cut` for sam. Select (cut) columns from the output of...
samestr 1.2025.111 doc dev AGPL-3.0-or-later X SameStr identifies shared strains between pairs of metagenomic samples...
samhaplotag 0.0.4 MIT XX 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
sample_grouping 1.0.0 dev GPL-3.0-only X A tool for merging reads based on metadata groups.
samplot 1.3.0 MIT X Plot structural variant signals from BAMs and CRAMs.
samrefiner 1.4.2.1 dev GPL-3.0-or-later X A program for gathering variant information from a SAM formated files.
samshee 0.2.12 MIT X A schema-agnostic parser and writer for illumina sample sheets v2.
samsift 0.3.1 dev MIT XXX Advanced filtering and tagging of SAM/BAM alignments using Python expressions.
samsifter 1.0.0 GNU XX Workflow editor for metagenomic analysis
samstats 0.2.2 MIT X SAM file alignment statistics at the read level
samstrip 0.2.1 MIT XX Strip SAM files of data not needed for alignment computations.
samsum 0.1.4 dev GPL-3.0-or-later XX A light-weight python package for summarizing sequence coverage from...
samtools 1.23 dev MIT XX Tools for dealing with SAM, BAM and CRAM files
samwell 0.0.4 MIT XX 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 XX 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 0.2.5 BSD-3-Clause XX Structural variant annotation
sap 1.1.3 GPL-3.0-only XX Pairwise structure alignment via double dynamic programming
sapling 1.0.0 doc dev BSD-3-Clause X Inferring and Summarizing Tumor Phylogenies from Bulk DNA Data
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.
sassy 0.1.8 MIT XX Fast approximate string searching
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 XX SATIVA Semi-Automatic Taxonomy Improvement and Validation Algorithm
satrap 0.2 file XX 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 1.3.6 dev Apache-2.0 X SAVANA: a somatic structural variant caller for long-read data.
savont 0.2.0 dev MIT XX Amplicon sequencing variants (ASVs) and taxonomic profiling from modern...
savvy 2.1.0 dev MPL-2.0 XX Interface to various variant calling formats.
sawfish 2.2.1 Pacific X Joint structural variant and copy number variant caller for HiFi sequencing 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 XXX SBpipe is a collection of pipelines for systems modelling of biological...
sbt 0.13.12 BSD XX None
sc-musketeers 0.4.2 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 XXX 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 XX Scala combines object-oriented and functional programming in one...
scallop 0.10.5 dev BSD-3-Clause XX Scallop is a reference-based transcriptome assembler for RNA-seq.
scallop-lr 0.9.2 BSD XX Scallop-LR is a reference-based transcriptome assembler for long-reads...
scallop-umi 1.1.0 BSD-3-Clause XX A reference-based transcript assembler for linked-reads RNA-seq data.
scallop2 1.1.2 dev BSD-3-Clause XX 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 doc MIT XX Sensitive detection of INDELs (INsertions and DELetions).
scanindel 1.3 GNU XX 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 XXX Single-Cell Analysis in Python. Scales to >1M cells.
scanpy-cli 0.2.0 MIT X CLI for Scanpy
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 1.0.1 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
scatac-fragment-tools 0.1.4 doc MIT XX Tools for working with scATAC-seq fragment files.
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 XXX Dong X et al. Accurate identification of single-nucleotide variants in...
sccellfie 0.5.0 MIT X A tool for inferring metabolic activities from single-cell and spatial...
sccmec 1.2.0 MIT X A tool for typing SCCmec cassettes in assemblies
scelestial 1.2 GPL XX 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
scenicplus 1.0a2 OTHER X SCENIC+ is a python package to build gene regulatory networks (GRNs)...
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 XXX The single cell genotyper (SCG): "Roth A, McPherson A, Laks E,...
scglue 0.4.0 doc dev MIT X Graph-linked unified embedding for unpaired single-cell multi-omics...
schavott 0.5.0 MIT XXX Assembly and scaffolding of bacterial genomes in real time using...
schema 0.7.0 MIT XXX Simple data validation library
schema-salad 2.7.20180809223002 Apache-2.0 XXX Schema Annotations for Linked Avro Data (SALAD)
schemarefinery 0.4.0 doc dev GNU X Tool to refine cg/wgMLST Schemas.
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 XX Evaluating single-cell data integration methods
scikit-allel 0.20.3 MIT X None
scikit-bio 0.4.2 BSD XX Data structures, algorithms and educational resources for bioinformatics.
scikits-datasmooth 0.7.1 BSD XXX Scikits data smoothing package
sciphi 0.1.7 GNU XX Single-cell mutation identification via phylogenetic inference
sciphin 1.0.1 GNU X Single-Cell mutation Identification via finite-sites Phylogenetic Inference
scirpy 0.22.4 dev BSD-3-Clause X A Scanpy extension for analyzing single-cell T-cell and B-cell receptor...
scispacy 0.6.2 doc dev Apache-2.0 X A full SpaCy pipeline and models for scientific/biomedical documents.
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 0.1.15 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 XXX Microbial pan-GWAS using the output from Roary
scoop 0.7.2.0 doc dev LGPL-3.0-only XXX Scalable COncurrent Operations in Python.
scoring-matrices 0.3.3 doc dev MIT XX 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 doc GPL-3.0-only X Tools for loading and preprocessing biological matrices in Python.
scramble 1.0.2 CC XX 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 1.4.2 MIT X SCReadCounts is a computational tool for a cell-level assessment of the...
screamingbackpack 0.2.333 GPLv3 XXX ScreamingBackpack
screed 1.0.4 BSD XXX Screed is a biological sequence parsing and storage/retrieval library...
scripps-msms 2.6.1 doc Free XX Fast algorithm for computing molecular surfaces
scrm 1.7.4 GPLv3+ XX 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 XX Read depletion/extraction and database cleaning using k-mer and...
scrublet 0.2.3 MIT XXX 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 XX 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...
scxmatch 0.1.0 MIT X Python implementation for single-cell cross match test, an efficient...
sdeper 1.7.1 doc dev MIT X Spatial Deconvolution method with Platform Effect Removal
sdm 3.10 dev GPL-3.0-or-later XX sdm - simple demultiplex tool for FASTQ demultiplexing and dereplication.
sdrf-pipelines 0.0.33 doc dev Apache-2.0 X Translate, convert SDRF to configuration pipelines
sdust 0.1 dev Unknown XX Symmetric DUST for finding low-complexity regions in DNA sequences.
seabreeze-genomics 1.5.0 doc dev MIT X Analyzing Structural Variation Between Bacterial Genome Assemblies.
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 4.3.15 doc dev Apache-2.0 XXX User-friendly graphical tool for using proteomics identification search engines.
secapr 2.2.8 MIT XXX Process sequence-capture FASTQ files into alignments for phylogenetic...
secedo 1.0.7 dev MIT XX SNV-based clustering for single-cell sequencing data.
secimtools 22.3.23 MIT XXX Metabolomics tools from the SECIM project
seedme 1.2.4 GPL XXX 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 XX 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 doc GPL-3.0-or-later XX Short read mapping with gaps.
segmentation-fold 1.7.0 GNU XX 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 XXX a python package for analyzing genomic segmentations
segul 0.22.1 MIT XX An ultrafast and memory efficient tool for phylogenomics
segway 3.0.4 GPL2 XXX 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 0.24.3 doc dev GPL-3.0-only XXX SEISMIC-RNA software by the Rouskin Lab.
selam 0.9 GPL3 XX 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 dev BSD XX 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 XX 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 XX SeMeta is a new software for taxonomic assignment of metagenomic reads....
semibin 2.2.1 doc MIT X Metagenomic binning with siamese neural networks
semidbm 0.5.1 BSD XXX Cross platform (fast) DBM interface in python
sensv 1.0.4 AGPLv3 X SENSV
sentieon 202503.01 Commercial XX Accelerated performance bioinformatics tools for mapping and variant calling
sepp 4.5.6 doc dev GPL-3.0-or-later XX 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 XX Seq-Gen is a program that will simulate the evolution of nucleotide or...
seq-hasher 0.2.0 MIT XX Compute hash digests for DNA sequences in a FASTA file, with support...
seq-seq-pan 1.1.0 FreeBSD XX 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 XXX Cohort based copy number calling in gene regions
seq2hla 2.3 MIT XXX 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 1.2.4 doc dev MIT X Automated preprocessing of Next-Generation-Sequencing data.
seq2squiggle 0.3.4 MIT X End-to-end simulation of nanopore sequencing signals with feed-forward...
seqan 2.4.0 BSD-3-Clause XXX SeqAn is an open source C++ library of efficient algorithms and data...
seqan3 3.4.0 doc dev BSD-3-Clause XXX SeqAn3 is the new version of the popular SeqAn template library for the...
seqan_tcoffee 1.13.8 doc dev GPL-3.0-or-later XX SeqAn::T-Coffee - Multiple Sequence Alignment.
seqbuster 3.5 MIT XX miRNA and isomiR annotation
seqchromloader 0.9.1 doc dev MIT X Sequence and chromatin dataloader for deep learning.
seqcluster 1.2.9 MIT XXX small RNA analysis from NGS data
seqcomplexity 0.1.2 MIT XX Calculates Per-Read and Total Sequence Complexity from FastQ file.
seqerakit 0.5.6 Apache-2.0 X Automate creation of Seqera Platform resources
seqfold 0.9.0 MIT X Predict the minimum free energy and structure of nucleic acids.
seqforge 2.0.0 MIT X SeqForge: A genomics toolkit for FASTA processing, BLAST orchestration,...
seqfu 1.23.0 GPL-3.0-only XXX 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 2.12.0 doc dev MIT XX A cross-platform and ultrafast toolkit for FASTA/Q file manipulation.
seqlib 1.2.0 doc dev Apache-2.0 XX 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 XXX Python port of the R Bioconductor `seqlogo` package
seqmagick 0.8.6 GNU XXX Tools for converting and modifying sequence files from the command-line
seqmap 1.0.13 Custom XX SeqMap is a tool for mapping large amount of oligonucleotide to the genome.
seqnado 0.7.6 GPL-3.0-or-later X Pipelines for genomics analysis
seqprep 1.3.2 doc dev MIT XX Tool for stripping adaptors and/or merging paired reads with overlap...
seqscreen 4.5 GPL3 X SeqScreen was created to sensitively assign taxonomic classifications,...
seqsero2 1.3.2 dev GPL-2.0-or-later X Salmonella serotype prediction from genome sequencing data.
seqsero2s 1.1.4 dev GPL-2.0-or-later X Simplified Salmonella serotype prediction from genome sequencing data
seqsizzle 0.3.0 AGPL-3.0-or-later XX A pager for viewing FASTQ files with fuzzy adaptor matching and coloring.
seqspec 0.4.0 MIT X File format that describes data generated from genomics experiments. ...
seqstats 1.0.0 MIT XX 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 1.5 doc dev MIT XX Seqtk is a fast and lightweight tool for processing sequences in the...
sequali 1.0.2 doc dev AGPL-3.0-or-later XX Fast sequencing quality metrics
sequana 0.19.5 doc dev BSD-3-Clause XXX A set of standalone application and snakemake pipelines dedicated to...
sequana_pipetools 1.3.0 doc BSD-3-Clause X A set of tools to help building or using Sequana pipelines
sequencetools 1.6.0.0 MIT XX A tool (pileupCaller) for processing ancient DNA sequencing data
sequenoscope 1.0.0 doc dev Apache-2.0 X Sequenoscope - A Modular Pipeline for ONT Adaptive Sampling and...
sequenticon 0.1.8 doc dev MIT X Generate human-friendly icons from DNA sequences.
sequenza-utils 3.0.0 GNU XX Analysis of cancer sequencing samples, utilities for the R package sequenza
sequip 0.11 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.
seqwin 0.2.0 dev GPL-3.0-only X Ultrafast identification of signature sequences in microbial genomes
seqwish 0.7.11 MIT X Alignment to variation graph inducer
seqyclean 1.10.09 MIT XX 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 XXX 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 XX Motif finding with modified MCMC
setuptools_cython 0.2.1 http://www.gnu. XXX 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 XXX SBG API python client bindings
severus 1.6 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 XX Extract 454 Genome Sequencer reads from a SFF file and convert them...
sfld 1.1 dev Apache XX SFLD pre/post-processing
sfold 2.2 OTHER X Software for Statistical Folding of Nucleic Acids
sfs 0.1.0 MIT XX CLI tool for site frequency spectra.
sfs_code 20150910 file XX This article introduces a new forward population genetic simulation...
sga 0.10.15 dev GPL-3.0-or-later XX 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 XX Personalized haplotype construction and crossover calling in...
sgdemux 1.2.0 For XX Tool for demultiplexing sequencing data generated on Singular...
sglearn 1.2.5 MIT X Python package for featurizing sgRNAs for machine learning
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 XX 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 XXX 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 XX Mapping-free filtering of useless RNA-Seq reads
shasta 0.14.0 doc dev MIT XX De novo assembly from Oxford Nanopore reads.
shellescape 3.4.1 MIT XXX Shell escape a string to safely use it as a token in a shell command...
sherpas 1.0.2 MIT XX Screening Historical Events of Recombination in a Phylogeny via...
shiba 0.8.1 doc dev MIT X A versatile method for systematic identification of differential RNA...
shiba2sashimi 0.1.7 doc dev MIT X A utility for creating sashimi plot from Shiba output
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 XXX SHIVER - Sequences from HIV Easily Reconstructed
shmlast 1.6 BSD-3-Clause XXX conditional reciprocal best hits with LAST
shorah 1.99.2 GPLv3 XX The Short Reads Assembly into Haplotypes (ShoRAH) program for inferring...
short-read-connector 1.2.0 dev AGPL-3.0-or-later XX Short read connector enables the comparisons of two read sets.
shortcut 1.0 MIT X ShortCut Small RNA-seq data trimmer and quality control tool
shortreadconnector 1.1.3 GNU XX Short read connector enables the comparisons of two read sets
shortseq 0.0.1 MIT XX \ ShortSeqs are compact and efficient Python objects that hold short...
shortstack 4.1.2 MIT XXX ShortStack: Comprehensive annotation and quantification of small RNA genes
shorttracks 1.3 dev MIT X ShortTracks : Useful length- and strand-based coverage files (bigwig)...
shovill 1.4.2 GPL2 XXX 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...
showali 1.0.1 Unlicense XX Minimalistic TUI viewer for aligned biological sequences (FASTA, ALN,...
showit 1.1.4 MIT X simple and sensible display of images in python
shustring 2.6 GPL-2 XX 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 XX Genome comparison via de Bruijn graph.
sibeliaz 1.2.7 doc dev Custom XX A fast whole-genome aligner based on de Bruijn graphs.
sicer 1.1 MIT XXX A clustering approach for identification of enriched domains from...
sicer2 1.0.3 dev MIT XX Redesigned and improved ChIP-seq broad peak calling tool SICER.
sickle 0.7.0 BSD XX A lightweight OAI client library for Python
sickle-trim 1.33 doc dev MIT XX Windowed Adaptive Trimming for fastq files using quality.
sideretro 1.1.6 GPL-3.0-only XX A pipeline for detecting Somatic Insertion of DE novo RETROcopies
sidr 0.0.2a2 MIT X Sequence Idenification using Decision tRees; a tool to classify DNA...
sierra-local 0.4.3 doc GPLv3 X sierra-local is a Python3 implementation of the Stanford HIVdb Sierra...
sierrapy 0.4.3 MIT X A Client of HIVdb Sierra GraphQL Webservice.
sift4g 2.0.0 doc dev GPL-3.0-or-later XX 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 1.0.3 BSD-2-Clause X SigProfilerAssignment - Assignment of known mutational signatures to...
sigprofilerextractor 1.2.5 dev BSD-2-Clause X Extracts mutational signatures from mutational catalogues.
sigprofilermatrixgenerator 1.3.3 dev BSD-2-Clause X SigProfiler matrix generator tool.
sigprofilerplotting 1.4.2 doc dev BSD-2-Clause X SigProfiler plotting tool.
sim4db 2008 GPL-3.0-or-later XX 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 XX A customized PyTorch-BigGraph (PBG) package for `simba`
simbac 0.1a GPL-3.0 XX SimBac simulates bacterial genomes with the clonal genealogy under a...
simka 1.5.3 AGPL-3.0-or-later XX Simka and simkaMin are de novo comparative metagenomics tools. Simka...
simlord 1.0.4 MIT XXX SimLoRD is a read simulator for long reads from third generation...
simphyni 1.0.0 MIT X SimPhyni: a tool for phylogenetic trait simulation and inference.
simple_sv_annotation 2019.02.18 MIT XXX Simplify snpEff annotations for interesting cases
simpleaf 0.19.5 doc dev BSD-3-Clause XX A rust framework to make using alevin-fry even simpler.
simplejson 3.8.1 MIT XX 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 XX Reference based multiple sequence alignment
sincei 0.5.2 MIT X A user-friendly toolkit for QC, counting, clustering and plotting of...
singlecell-barcodes 0.2 MIT XXX 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 0.20.3 doc dev GPL-3.0-or-later X At heart, SingleM is a tool for profiling shotgun metagenomes. It was...
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 5.0.1 MIT X Tools for stable isotopic mass spectrometry-based metaproteomics
sirius-csifingerid 5.8.6 doc dev AGPL-3.0-only XX SIRIUS (CLI + GUI) LC-MS/MS data analyses framework. Includes: SIRIUS,...
sis 0.1.2 GPLv2+ XXX A tool that uses mummer to scaffold small genomes.
sistem 1.0.4 doc dev GPL-3.0-only X A tool for simulating tumor growth, metastasis, and DNA-seq data.
sistr_cmd 1.1.3 dev Apache-2.0 XX Salmonella In Silico Typing Resource (SISTR) commandline tool for...
sixgill 0.2.4 dev Apache XXX 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 doc dev GPL-3.0-or-later XX SKA (Split Kmer Analysis).
ska2 0.5.0 dev Apache-2.0 XX SKA (Split Kmer Analysis) version 2.
skani 0.3.1 MIT XX skani is a fast and robust tool for calculating ANI between metagenome...
skc 0.1.0 MIT XX Shared k-mer content between two genomes
skder 1.3.4 dev BSD-3-Clause XX skDER & CiDDER: efficient & high-resolution dereplication...
skesa 2.5.1 doc dev Public XX Strategic Kmer Extension for Scrupulous Assemblies & Sequence...
sketchlib 0.2.4 Apache-2.0 XX Fast sequence distance estimates
sketchy 0.6.0 MIT XX Real-time lineage hashing and genotyping of bacterial pathogens
skewer 0.2.2 MIT XX A fast and accurate adapter trimmer for paired-end reads.
skmer 3.3.0 BSD-3-Clause XXX 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 XX Slamdunk is a software tool for SLAMseq data analysis.
slamem 0.8.5 GPL-3.0 XX 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 doc dev Artistic XX 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 XX slimfastq would efficiently compresses/decompresses fastq files
slimm 0.3.4 https://github. XX SLIMM - Species Level Identification of Microbes from Metagenomes
slivar 0.3.3 doc dev MIT XX filter/annotate variants in VCF/BCF format with simple expressions.
slncky 1.0.4 MIT XXX slncky is a tool for lncRNA discovery from RNA-Seq data. slncky filters...
sloika 2.0.1 Mozilla XX Sloika is Oxford Nanopore Technologies' software for training...
slow5curl 0.2.1 MIT XX Tool for accessing remote BLOW5 files.
slow5tools 1.3.0 dev MIT XX 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...
smakcr 0.1.0 MIT XX Count short k-mers fast
smallgenomeutilities 0.5.2 GNU XXX A collection of scripts that are useful for dealing with viral RNA NGS data.
smalt 0.7.6 doc GPL-3.0-or-later XX SMALT aligns DNA sequencing reads with a reference genome.
smartdenovo 1.0.0 GPLv3 XX Ultra-fast de novo assembler using long noisy reads
smartmap 1.0.0 MIT XX SmartMap: Bayesian Analysis of Ambiguously Mapped Reads
smashbenchmarking 1.0.1 BSD XX 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 XXX 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 XX Strain-level Metagenomic Estimation of Growth rate (SMEG) measures...
smetana 1.2.1 doc dev Apache-2.0 X Species METabolic interaction ANAlysis (SMETANA) is a python-based...
smhasher 0.150.1 MIT XX Python extension for smhasher hash functions
smina 2017.11.9 GNU XX A fork of AutoDock Vina that is customized to better support scoring...
smithwaterman 1.0.0 dev MIT XX Smith-waterman-gotoh alignment algorithm.
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 0.8.2 doc dev 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 0.5.3 dev Apache-2.0 XX Inference of ploidy and heterozygosity structure using whole genome...
smudgeplot_rn 0.2.5_RN Apache-2.0 XX Inference of ploidy and heterozygosity structure using whole genome...
snakealtpromoter 1.0.5 dev MIT X A comprehensive pipeline for differential alternative promoter analysis.
snakeatac_env 0.1.1 doc GPL-3.0-or-later X snakemake based ATACseq pipeline
snakebids 0.15.0 dev MIT X BIDS integration into snakemake workflows.
snakedeploy 0.15.0 dev MPL-2.0 X Helper for deploying published Snakemake pipelines.
snakefmt 0.11.2 doc dev MIT X The uncompromising Snakemake code formatter.
snakelines 1.1.8 CC X Computational pipelines for processing of paired-end sequencing reads.
snakemake 9.14.5 doc dev MIT XXX A popular workflow management system aiming at full in-silico reproducibility.
snakemake-executor-plugin-aws-batch 0.2.1 MIT X A Snakemake executor plugin for submitting jobs to AWS Batch.
snakemake-executor-plugin-azure-batch 0.1.3 MIT X A Snakemake executor plugin for submitting jobs to Microsoft Azure Batch.
snakemake-executor-plugin-cannon 1.9.2.post2 dev MIT X A Snakemake executor plugin for submitting jobs to the Cannon cluster...
snakemake-executor-plugin-cluster-generic 1.0.9 MIT X Generic cluster executor for Snakemake
snakemake-executor-plugin-cluster-sync 0.1.5 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 0.5.1 dev 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 2.0.3 dev MIT X A Snakemake executor plugin for submitting jobs to a SLURM cluster.
snakemake-executor-plugin-slurm-jobstep 0.4.0 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 1.22.0 dev MIT X Common functions and classes for Snakemake and its plugins.
snakemake-interface-executor-plugins 9.3.9 dev MIT X This package provides a stable interface for interactions between...
snakemake-interface-logger-plugins 2.0.0 MIT X This package provides a stable interface for interactions between...
snakemake-interface-report-plugins 1.3.0 MIT X This package provides a stable interface for interactions between...
snakemake-interface-scheduler-plugins 2.0.2 MIT X This package provides a stable interface for interactions between...
snakemake-interface-storage-plugins 4.3.2 dev MIT X This package provides a stable interface for interactions between...
snakemake-logger-plugin-snkmt 0.1.5 dev MIT X Snakemake logger plugin that writes logs to SQLite database.
snakemake-minimal 9.14.5 doc dev MIT XXX A popular workflow management system aiming at full in-silico reproducibility.
snakemake-scheduler-plugin-firstfit 0.1.2 dev MIT X A Snakemake scheduler plugin that selects the first jobs that fit...
snakemake-storage-plugin-azure 0.4.4 MIT X A Snakemake storage plugin to read and write from Azure Blob Storage
snakemake-storage-plugin-cached-http 0.1.0 MIT X Snakemake storage plugin for downloading files via HTTP with caching...
snakemake-storage-plugin-fs 1.1.3 dev MIT X A Snakemake storage plugin that reads and writes from a locally mounted...
snakemake-storage-plugin-ftp 0.1.3 MIT X A Snakemake plugin for handling input and output via FTP
snakemake-storage-plugin-gcs 1.1.4 MIT X A Snakemake storage plugin for Google Cloud Storage
snakemake-storage-plugin-http 0.3.0 MIT X Snakemake storage plugin for donwloading input files from HTTP(s).
snakemake-storage-plugin-irods 0.3.1 dev MIT X A Snakemake plugin for handling input and output on iRODS.
snakemake-storage-plugin-s3 0.3.6 doc MIT X A Snakemake storage plugin for S3 API storage (AWS S3, MinIO, etc.)
snakemake-storage-plugin-sftp 0.1.3 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-xrootd 0.4.1 MIT X A Snakemake storage plugin for XRootD storage
snakemake-storage-plugin-zenodo 0.1.5 MIT X A Snakemake storage plugin for reading from and writing to zenodo.org
snakemake-wrapper-utils 0.8.0 dev 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 XXX Making Snakemake workflows into full-fledged command line tools since 1999.
snakesee 0.4.1 doc dev MIT X A terminal UI for monitoring Snakemake workflows
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 2017_03_01 doc dev MIT XX Semi-HMM-based Nucleic Acid Parser - a gene prediction tool.
snap-aligner 2.0.5 doc dev Apache-2.0 XX Scalable Nucleotide Alignment Program -- a fast and accurate read...
snapatac2 2.8.0 doc dev MIT XX SnapATAC2: Single-cell epigenomics analysis pipeline.
snapgene-reader 0.1.23 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 XX Identify regulatory non-coding SNPs (rSNPs)
sniffles 2.7.2 doc dev MIT XXX 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 XXX 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
snkmt 0.2.4 dev MIT X A TUI for monitoring Snakemake workflows in real-time.
snmf 1.2 GNU XX Fast and efficient program for estimating individual admixture...
snns 4.3 LGPL X Stuttgart Neural Network Simulator (SNNS)
snoscan 1.0 doc GNU XX 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 1.2.0 dev GPL-3.0-or-later XX 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 XXX Script and functions for SNP matrix construction
snp-sites 2.5.1 doc dev GPL-3.0-or-later XX 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 5.4.0a LGPLv3 XXX 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 XX A fast and memory-efficient tool for SNP extraction from genomic alignments.
snpiphy 0.5 GPLv3 XX An automated snp phylogeny pipeline
snpomatic 1.0 GPL3 XX SNP-o-matic is a fast, stringent short-read mapping software.
snpsift 5.4.0a LGPLv3 XXX Toolbox that allows you to filter and manipulate annotated files
snpsplit 0.6.0 GPL-3.0-or-later XXX 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 XX SOAPaligner/soap2 is an updated version of SOAP software for short...
soapcoverage 2.7.7 GPL XX SOAPcoverarge can calculate sequencing coverage or physical coverage as...
soapdenovo-trans 1.04 doc dev GPLv3 XX SOAPdenovo-Trans is a de novo transcriptome assembler basing on the...
soapdenovo2 2.40 GPL XX SOAPdenovo is a novel short-read assembly method that can build a de...
soapdenovo2-errorcorrection 2.0 GNU XX Error correction for soapdenovo2.
soapdenovo2-gapcloser 1.12 GPL-3.0-or-later XX A tool named GapCloser for SOAPdenovo.
soapdenovo2-prepare 2.0 GPL-3.0 XX 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 XXX A Python SOCKS module
socru 2.2.5 GPLv3 XXX 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,...
soi 1.2.3 GPL-3.0-or-later X Orthology Index (OrthoIndex or OI) determines the orthology of a syntenic block.
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 2.34.0 doc dev MIT XXX The SolveBio Python client.
somalier 0.3.1 doc dev MIT XX Fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs.
somatic-sniper 1.0.5.0 MIT XX A tool to call somatic single nucleotide variants.
somaticseq 3.11.1 dev BSD-2-Clause XX An ensemble approach to accurately detect somatic mutations.
sompy 0.1.1 MIT XXX Numpy based SOM Library.
sonicparanoid 2.0.9 doc dev GPL-3.0-only XX SonicParanoid: fast, accurate, and comprehensive orthology inference...
sonlib 2.0.dev88 MIT XXX 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 2.1.11 doc dev BSD-3-Clause X Spatial-omics pipeline and analysis.
sorted_nearest 0.0.41 dev BSD-3-Clause XX Find nearest interval.
sortmerna 4.3.7 doc dev LGPL-3.0-only XX 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 4.9.4 doc dev BSD-3-Clause XXX Quickly search, compare, and analyze genomic and metagenomic data sets.
spacedust 2.e56c505 GPL-3 XX De novo discovery of conserved gene clusters in microbial genomes with Spacedust
spacepharer 5.c2e680a GPL-3 XX SpacePHARER: Sensitive identification of phages from CRISPR spacers in...
spacerextractor 0.9.8 doc dev GPL-3.0-or-later X Extract CRISPR spacers from metagenome short reads.
spacerplacer 1.0.1 dev GPL-3.0-only X SpacerPlacer is a powerful software for reconstructing ancestral CRISPR...
spades 4.2.0 doc dev GPL-2.0-only XX 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 3.0.7 doc dev GPL-2.0-or-later XX Map and align a set of cDNA/EST or protein sequences onto a genome.
spanki 0.5.1 GPLv3 XX Spanki is a set of tools to facilitate analysis of alternative splicing...
spapros 0.1.6 doc dev MIT X Probe set selection for targeted spatial transcriptomics.
sparc 20160205 dev MIT XX 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 XX Approximate k-nearest neighbors search on sparse datasets
sparseassembler 20160205 dev GPL-3.0-or-later XX A sparse k-mer graph based, memory-efficient genome assembler.
sparsehash 2.0.2 X None
spatialleiden 0.4.0 doc GPL-3.0-or-later 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 XX Spectral clustering for biological sequences
spec2vec 0.9.1 doc dev Apache-2.0 X Word2Vec based similarity measure of mass spectrometry data.
spectacle 1.4 GPL-3.0 XX This software implements a spectral learning algorithm for hidden...
spectra-cluster-cli 1.1.2 Apache-2.0 XXX This is a stand-alone implementation of the new updated PRIDE Cluster...
spectral_hk 0.1 dev PUBLIC XX NCGC Spectral HashKey.
spectrassembler 0.0.1a1 MIT XX Tool (experimental) to compute layout from overlaps with spectral algorithm
spectrum_utils 0.5.0 doc dev Apache-2.0 X Mass spectrometry utility functions.
spestimator 0.1.0.232 MIT X A tool to predict bacterial species from fasta files using RefSeq 16S.
sphae 1.5.3 doc dev MIT X Phage toolkit
sphinx-argparse 0.1.15 MIT XX Sphinx extension that automatically document argparse commands and options
sphinxcontrib-programoutput 0.8 BSD XX Sphinx extension to include program output
spine 0.3.2 GPL-3.0 XXX 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 XX 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 XX A tool to convert spliced BAM alignments into GFF2 format
splicemap 3.3.5.2 doc Custom XX Detects splice junctions from RNA-seq data. This method does not depend...
splitcode 0.31.6 doc dev BSD-2-Clause XX Flexible parsing, interpretation, and editing of technical sequences.
splitmem 1.0 Apache XX Graphical pan-genome analysis with suffix skips
splitp 0.2.0 BSD-3-Clause XX splitp is a streaming read pre-preprocessor.
splitubam 0.1.1 dev MIT XX Split one ubam into multiple, per line, fast
spoa 4.1.5 doc dev MIT XX SIMD partial order alignment tool/library.
spotyping 2.1 GPL-3 XXX 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 XX Plugins! Easy!
sprinter 1.0.0 doc dev ACADEMIC X Single-cell Proliferation Rate Inference in Non-homogeneous Tumours...
spydrpick 1.2.0 GNU XX Mutual information based detection of pairs of genomic loci co-evolving...
sqlalchemy-datatables 2.0.1 MIT XXX 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 XX Command-line tools for the analysis of high-throughput sequencing data
squeakr 0.8 dev BSD-3-Clause XX 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 dev BSD-3-Clause XX Detector for fusion-gene and non-fusion-gene transcriptomic structural...
squigualiser 0.6.4 MIT X Visualise ONT raw signals
squigulator 0.4.0 MIT XX A tool for simulating nanopore raw signal data
squire 0.9.9.92 GNU X Quantitative, locus-specific view of transposable element expression.
squirrel 1.3 doc dev GPL-3.0-only X Some QUIck Reconstruction to Resolve Evolutionary Links.
squizz 0.99d GPL-2.0-only XX Squizz is a sequence/alignment format checker, but it has some...
sr2silo 1.6.1 doc dev MIT X Short-read to SILO format converter.
sra-human-scrubber 2.2.1 Public X An SRA tool identifies and removes any significant human read, and...
sra-tools 3.2.1 doc dev Public XX The SRA Toolkit and SDK from NCBI.
sracat 0.2 dev BSD-3-Clause XX a command-line tool for extracting unordered read data from SRA files
srahunter 0.0.9 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
srf-n-trf 0.1.2 dev MIT XX Extract specific monomers, motifs, and regions from srf and trf output
srnamapper 1.0.12 dev GPL-3.0-or-later XX Mapping small RNA data to a genome.
srnaminer 1.1.2 dev CC X sRNAminer: a Multifunctional Toolkit for Next Generation Sequencing...
srnapipe 1.2.1 dev Academic XXX Pipeline for bioinformatic in-depth exploration of small RNA-seq data.
srprism 2.4.24 Public XX SRPRISM - Short Read Alignment Tool
srst2 0.2.0 BSD XXX Short Read Sequence Typing for Bacterial Pathogens
ssake 4.0 GPL-2.0 XXX SSAKE is a genomics application for de novo assembly of millions of...
sscocaller 0.2.2 doc dev MIT XX Haplotyping single-cell DNA sequenced gamete cells.
ssdrippipeline 0.0.5 doc dev GPL3 X Useful tools for the analysis of ssDRIP-seq data
sshash 4.0.0 MIT XX SSHash is a compressed dictionary data structure for k-mers (strings of...
sshmm 1.0.7 GPL-3.0 X ssHMM is an RNA motif finder that recovers sequence-structure motifs...
ssm 1.4 doc GPL-3.0-or-later XX Secondary-structure matching, tool for fast protein structure alignment
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 XX 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 doc GPL-3.0-or-later XX Stacks is a software pipeline for building loci from short-read sequences.
stacks_summary 1.1 GNU XX Stacks reports generator
staden_io_lib 1.15.1 doc dev BSD-3-Clause XX 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 XXX 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 XX An RNA-seq read aligner.
star-fusion 1.15.1 doc dev BSD-3-Clause XXX STAR-Fusion fusion variant caller. All dependencies required to run...
staramr 0.11.1 doc dev Apache XXX Scan genome contigs against the ResFinder and PointFinder databases
starcatpy 1.0.9 dev MIT X Implements *CellAnnotator (aka *CAT/starCAT), annotating scRNA-Seq with...
starcode 1.4 dev GPL-3.0-or-later XX Starcode: sequence clustering based on all-pairs search.
stare-abc 1.0.5 MIT XX Calculate Gene-TF affinities via enhancer-gene interactions
starfish 0.3.4 doc dev MIT X Standardized analysis pipeline for image-based transcriptomics.
stark 0.1.1 dev MIT XX A tool for bluntifying a bidirected de bruijn graph by removing overlaps.
starseqr 0.6.7 ../../LICENSE XX RNA Fusion Detection and Quantification
start-asap 1.3.0 MIT X Prepare project directory and project sheet for ASA3P
steamboat 1.1.1 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+ XXX STELLAR is a tool for finding pairwise local alignments between long...
stellarscope 1.5 doc dev MIT XX Single-cell Transposable Element Locus Level Analysis of scRNA Sequencing.
stemcnv-check 1.0.0 doc dev MIT X StemCNV-check: CNV Based Quality Control Workflow for Stem Cell SNP Array Data.
stereogene 2.20 Artistic-2.0 XX 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 1.5.6 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 XX 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 XX Strain Genome Explorer: a tool suite for tracking and characterizing...
strainr2 2.3.0 MIT XX 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 XX The STR Allele Identification Tool
strandphaser 1.0.2 MIT X Phase Strand-seq data
strangepg 0.9.4 MIT XX Strange pangenome-scale interactive graph visualizer
stranger 0.10.0 doc dev MIT X Annotate VCF files with STR variants with pathogenicity implications.
strawc 0.0.2.1 dev MIT XX Straw bound with pybind11.
strcount 0.1.1 MIT X A package to count the number of repeats in a Short Tandem Repeat...
strdust 0.14.0 doc dev MIT XX Tandem repeat genotyper for long reads.
stream 1.1 AGPL-3 XXX STREAM-Single-cell Trajectories Reconstruction, Exploration And Mapping
stream_atac 0.3.5 AGPL-3 XXX STREAM-Single-cell Trajectories Reconstruction, Exploration And Mapping...
strelka 2.9.10 GPL-3.0 XX 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 XX A program to evaluate protein multiple sequence alignments using a...
stringdecomposer 1.1.2 dev GPL-2.0-or-later X A tool for decomposing of strings into a set of given monomers.
stringmeup 0.1.5 dev MIT X A post-processing tool to reclassify Kraken 2 output based on the...
stringmlst 0.6.3 CC XXX Fast k-mer based tool for multi locus sequence typing (MLST) directly...
stringtie 3.0.3 doc dev MIT XX 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 1.3.0 doc dev MIT X StripePy recognizes architectural stripes in 3C and Hi-C contact maps...
strling 0.6.0 MIT X STRling (pronounced like “sterling”) is a method to detect large STR...
strobealign 0.17.0 MIT XX Align short reads using dynamic seed size with strobemers
strobemap 0.0.2 GPL-3.0 XX Efficient string matching using strobemers
structure 2.3.4 MIT XX The program structure is a free software package for using multi-locus...
structure-threader 1.3.11 dev GPL-3.0-only X A program to parallelize runs of 'Structure',...
structureharvester 0.6.94 MIT XXX 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 XXX Strudel is a graphical tool for visualizing genetic and physical maps...
strvctvre 1.10 doc dev MIT X StrVCTVRE, a structural variant classifier for exonic deletions and duplications
sts-smctc 1.0 GPL-3.0 X A C++ template class library for the efficient and convenient...
stxtyper 1.0.25 dev Public XX Accurately type both known and unknown Shiga toxin operons from...
submission-excel2xml 3.6.2 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 2.1.1 doc dev GPL-3.0-only XX High-performance read alignment, quantification, and mutation discovery.
subset-bam 1.1.0 doc dev MIT XX A tool to subset a 10x Genomics BAM file based on a tag, most commonly...
suchtree 1.3 doc dev BSD XX A python library for doing fast, thread-safe computations on phylogenetic trees
suds-jurko 0.6 GNU XX Lightweight SOAP client (Jurko's fork)
suma_package 1.0.00 CeCILL X Fast and exact comparison of sequences
sumaclust 1.0.31 CeCILL XX Sumaclust clusters sequences in a way that is fast and exact at the...
sunbeamlib 5.2.2 doc dev MIT X A robust, extensible metagenomic sequencing pipeline.
super-focus 1.6 dev GPL-3.0 XXX 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 0.3.5 dev MIT XX Rapid interval intersections.
superstr 1.0.1 GPL-2.0 XX A lightweight, alignment-free utility for detecting repeat-containing...
suppa 2.4 MIT XXX A tool to study splicing across multiple conditions at high speed and accuracy.
sure 2.0.1 GNU XXX utility belt for automated testing in python for python
surpyvor 0.15.0 MIT X Evaluating, merging and plotting SV vcf files
survindel2 1.1.4 dev GPL-3.0-only XX A CNV caller for Illumina paired-end WGS data.
survivor 1.0.7 dev MIT XX Toolset for SV simulation, comparison and filtering.
suvtk 0.1.6 doc GPL-3.0-or-later X Tool to submit viral sequences to Genbank.
sv2 1.4.3.4 MIT XX Support Vector Structural Variation Genotyper
svaba 1.2.0 GPLv3 XX Structural variation and indel detection by local assembly
svanalyzer 0.36 CC0 X SVanalyzer: tools for the analysis of structural variation in genomes
svarp 1.1.1 doc dev MIT X Pangenome-based structural variant discovery (SVarp)
svclone 1.1.4 dev BSD-3-Clause X Computational method for inferring cancer cell fraction of tumour SVs from WGS.
svdb 2.8.3 doc dev MIT XX Structural variant database software.
svdss 2.1.0 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 XX 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 XX 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 2.5 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 doc Modified XX SVMLight Library by Thorsten Joachim.
svpg 1.3.0 dev MIT X Pangenome-based structural variation caller
svseq2 2 doc CC-PDDC XX 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 XX Utilities for consolidating, filtering, resolving, and annotating...
svtools 0.5.1 MIT XXX Tools for processing and analyzing structural variants
svtopo 0.3.0 Pacific X Complex structural variant visualization for HiFi sequencing data:...
svtopovz 0.3.0 dev Pacific X Complex structural variant visualization for HiFi sequencing data:...
svtyper 0.7.1 MIT XXX Bayesian genotyper for structural variants
svtyper-python3 0.7.1 MIT X Bayesian genotyper for structural variants
svviz 1.6.2 MIT XXX A read visualizer for structural variants
svync 0.3.0 MIT XX A tool to standardize VCF files from structural variant callers
swalign 0.3.7 BSD XXX Smith-Waterman local aligner
swarm 3.1.6 doc dev AGPL-3.0-or-later XX A robust and fast clustering method for amplicon-based studies.
sweepfinder2 1.0 doc Unknown XX A program written in C that can perform genomic scans for recent...
swga 0.4.4 GPL-3.0 XX Select primer sets for selective whole genome amplification (SWGA)
swiftlink 1.0 GPLv3 XX A multipoint parametric linkage analysis tool for large consanguineous...
swipe 2.1.1 dev AGPL-3.0 XX Tool for performing rapid local alignment searches in amino acid or...
switchtfi 0.1.0 doc dev GPL-3.0-only X Implementation of the SwitchTFI method as presented in:...
sword 1.0.4 GPL3 XX SWORD - a highly efficient protein database search
sylph 0.9.0 doc dev MIT XX sylph quickly enables querying of genomes against even low-coverage...
sylph-tax 1.8.0 doc dev MIT X Integrating taxonomic information into the sylph metagenome profiler.
symbiontscreener 1.0.0 GPL-3.0-only XX Symbiont-Screener is a reference-free approach to identifying...
synapseclient 4.10.0 doc dev Apache-2.0 XXX Python client for Synapse.
syngap 1.2.5 dev CC-BY-NC-SA-4.0 X SynGAP: Synteny-based Gene structure Annotation Polisher
syny 1.3.1 MIT X Genome collinearity inferences
syri 1.7.1 doc dev MIT XX Synteny and rearrangement identifier between whole-genome assemblies.
t-coffee 13.46.2.7c9e712d doc dev GPL-2.0-only XX 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 1.0.9 doc dev MIT XX 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 XXX C library and command line tools for high-throughput sequencing data formats.
tabixpp 1.1.2 dev MIT XX A C++ wrapper around the tabix project, a generic indexer for...
table2asn 1.28.1179 doc Public XX table2asn is a command-line program that creates sequence records for...
tablet 1.17.08.17 BSD-2-Clause XX Tablet is a lightweight, high-performance graphical viewer for next...
tabview 1.4.3 MIT XXX A curses command-line CSV and list (tabular data) viewer
taco 0.7.3 MIT XX 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 XX TADbit is a complete Python library to deal with all steps to analyze,...
tadlib 0.4.5.post1 dev GPL-3.0-or-later 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 XXX TADtool is an interactive tool for the identification of meaningful...
taeper 0.1.0 MIT XXX 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.
tagdust2 2.33.1 GPL-3.0-only XX Tool to extract high confidence reads from sequencing data
tagger 1.1 doc dev BSD-2-Clause 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
tagra 0.2.5 dev MIT X TaGra: TAbular data preprocessing to GRAph representation.
tajimas_d 2.0.4 doc dev GPL-3.0-or-later X Computes Tajimas D, the Pi- or Watterson-Estimator for multiple sequences.
takeabreak 1.1.2 GNU XX 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...
tandemtwister 0.2.0 doc BSD-3-Clause-No X Detection of interleaved and embedded tandem repeats from long reads
tango 0.5.7 MIT X Assign taxonomy to metagenomic contigs
tantan 51 doc dev GPL-3.0-or-later XX 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 XX Pre-processor for bioinformatics cluster job submission
targetdb 1.3.3 doc dev GPL-3.0-or-later X Package with an application to generate report on potential drug targets.
targetfinder 1.7 MIT XXX Plant small RNA target prediction tool
targetscan 7.0 MIT X Search for predicted microRNA targets in mammals
targqc 1.8.1 GNU XXX Target capture coverage QC
taseq 1.1.1 MIT X Downstream analysis for targetted amplicon sequencing.
tasmanian-mismatch 1.0.9 dev LGPL-2.1-or-later X Tasmanian tool to analyze mismatches at read and position in high...
tassel 5.2.89 LGPL XX 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 XX Taxator-tk sequence taxonomic annotaion
taxburst 0.3.2 BSD-3-Clause X sunburst plots for taxonomy
taxmapper 1.0.2 MIT XX Analysis pipeline for metagenomic, microeukaryotic sequencing data.
taxmyphage 0.3.6 MIT X Script to assign taxonomy to a bacteriophage at the genus and species level
taxoniumtools 2.1.17 GPL-3.0-only X Taxonium is a tool for exploring trees, including those with millions...
taxonkit 0.20.0 MIT XX A Cross-platform and Efficient NCBI Taxonomy Toolkit
taxonomy 0.10.1 doc dev MIT XX 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 0.2.1 doc dev 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 0.12.0 GPL-3.0 XXX Tools for taxonomic naming and annotation
tb-ml 0.1.1 GPL3 X A simple tool for creating machine learning antimicrobial resistance...
tb-profiler 6.6.6 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 XX tbl2asn is a program that automates the creation of sequence records...
tbl2asn-forever 25.7.2f Public XX tbl2asn is a program that automates the creation of sequence records...
tbox-scan 1.0.2 doc dev 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 XX 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 XX TCLAP is a small, flexible library that provides a simple interface for...
td2 1.0.6 doc MIT X TD2: a tool to find protein coding regions in transcripts.
tdrmapper 1.1 academic XX 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 1.3.1 doc dev GPL-3.0-or-later XX Tedna is a lightweight de novo transposable element assembler.
tefinder 2.32 dev CeCILL XX Programs for transposable element search and annotation in large...
telescope 1.0.3 MIT XX Single locus resolution of Transposable ELEment expression.
teloclip 0.3.4 doc dev MIT XXX A tool for the recovery of unassembled telomeres from soft-clipped read...
telogator2 2.2.3 doc dev MIT X Analyze allele-specific telomere length from PacBio and Nanopore reads
telometer 1.1 dev MIT X A simple regular expression based method for measuring individual,...
teloscope 0.1.3 doc dev MIT XX 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 XX 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 XX TEPID uses paired-end illumina sequencing reads to identify novel TE variants.
terminus 0.1.0 BSD XX Terminus enables the discovery of data-driven, robust transcript groups...
terrace 1.1.2 BSD-3-Clause XX TERRACE is an assembler for circular RNAs.
tesorter 1.5.1 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 XXX 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 1.6.2 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 XXX streamlined version of stdlib fileinput
tf-comb 1.1 doc dev MIT XX Transcription Factor Co-Occurrence using Market Basket analysis
tgsgapcloser 1.2.1 doc dev GPL-3.0-only XX A gap-closing software tool that uses error-prone long reads generated...
tgt 1.4.3 GPL-3.0+ XXX TextGridTools -- Read, write, and manipulate Praat TextGrid files
tgtools 0.0.4 doc dev MIT X A command-line tool to help manipulate transjson files which are used...
tgv 0.1.0 doc dev MIT XX Explore genomes in the terminal. Light, blazing fast 🚀, vim-motion.
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...
themis 0.1.0 GPL-3.0-or-later X Themis: metagenomic profiler
thermorawfileparser 1.4.5 doc dev Apache XXX 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 XX Estimate tumor purity and clonal/subclonal copy number aberrations...
tiberius 1.1.7 doc dev MIT X Tiberius is a deep learning gene-finder.
tiddit 3.9.4 doc dev GPL-3.0-only XX TIDDIT - structural variant calling.
tidehunter 1.5.5 dev MIT XX 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 XX Identify and find telomeres, or telomeric repeats in a genome.
tidyp 1.04 BSD-like XX Program for cleaning up and validating HTML
tigmint 1.2.10 doc dev GPL-3.0 XXX 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 XX The Tinker molecular modeling software is a complete and general...
tinscan 0.2.1 doc dev MIT XXX Find alignment signatures characteristic of transposon insertion sites.
tiny-count 1.5.0 GPLv3 XX \ A precision counting tool for hierarchical classification and...
tinyalign 0.2.2 MIT XX 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 XXX 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 XX Predict plasmids from uncorrected long read data.
tir-learner 3.0.7 doc dev GPL-3.0-or-later X An ensemble pipeline for terminal inverted repeat (TIR) transposable...
tirank 0.1.3 doc dev MIT X A comprehensive analysis tool for transferring phenotype of bulk...
tirmite 1.2.0 dev MIT XXX Map TIR-pHMM models to genomic sequences for annotation of MITES and...
tissuumaps 3.2.1.14 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 XX TM-align sequence-order independent protein structure alignment.
tmb 1.5.0 doc dev 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...
tmscoring 0.4.post0 doc dev BSD X Python implementation of the TMscore program.
tn93 1.0.15 doc dev MIT XX This is a simple program meant to compute pairwise distances between...
tntblast 2.66 doc dev BSD XX Searching DNA/RNA sequence databases with PCR and/or probe queries
tobias 0.17.3 doc dev MIT XX Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal.
toil 7.0.0 doc dev Apache-2.0 XXX 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
tomm40_wgs 1.0.1 dev GPL-2.0-or-later X TOMM40_WGS: Genotyping TOMM40’523 Poly-T Polymorphisms Using...
tooldistillator 1.0.4 doc dev GPLv3 X Tool to extract and aggregate information from different tool outputs...
toolshed 0.4.6 MIT XXX flexible and easy file manipulation
topas 1.0.1 CC-BY X This toolkit allows the efficient manipulation of sequence data in...
tophat 2.1.2 doc dev Boost XX A spliced read mapper for RNA-Seq.
tophat-recondition 1.4 BSD-2-Clause XXX Post-processor for TopHat unmapped reads
toposort 1.4 Apache XX None
tortoize 2.0.16 doc dev BSD-2-Clause XX Application to calculate ramachandran z-scores.
toulligqc 2.7.1 doc dev GPL-3.0-or-later XXX A post sequencing QC tool for Oxford Nanopore sequencers.
tower-cli 0.18.0 doc dev Apache-2.0 XXX The Tower CLI an interface to Nextflow Tower via the CLI.
tpmcalculator 0.0.5 dev Public XX 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 XX A Fast, Extensible Progress Meter
tr-trimmer 0.4.0 MIT XX 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 XXX Tracer is a program for analysing the trace files generated by Bayesian...
trackhub 1.0 MIT XXX 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 0.5.7 doc BSD-3-Clause X The trackplot is a tool for visualizing various next-generation...
tracs 1.0.1 doc MIT XX Tracs - Fast pairwise transmission inference from single genome and/or...
tracy 0.8.1 doc dev BSD-3-Clause XX 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 XXX de novo assembly of RNA-Seq data using ABySS
transanno 0.4.5 GPL-3.0-only XX accurate VCF/GFF3/GTF LiftOver tool for new genome assemblies
transannot 4.0.0 doc dev GPL-3.0-or-later XX TransAnnot: a fast transcriptome annotation pipeline.
transcomb 1.0 XX 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 doc dev Broad XXX TransDecoder identifies candidate coding regions within transcript...
transgenescan 1.3.0 GPL-3.0-only XX 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 3.3.20 dev GPL-3.0-only XXX TRANSIT
translate-gard 1.0.4 MIT X Converts HyPhy 2.3.2 GARD output to JSON
translatorx 1.1 unknown XXX 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 dev MIT XX Command-line tools used by transrate for processing bam files.
transtermhp 2.09 doc GPL-3.0-or-later XX TransTermHP finds rho-independent transcription terminators in...
trawler 2.0 GPLv2 XXX Trawler is a motif discovery tool used to identify enriched motifs in a...
tree-qmc 3.0.4 MIT XX TREE-QMC is a quartet-based method for estimating species trees from gene trees.
treebest 1.9.2.post1 doc GPLv2 XX TreeBeST: Tree Building guided by Species Tree, used in the Ensembl...
treecluster 1.0.5 GPL-3.0-only X Identify clusters in phylogenetic trees based on a distance threshold...
treekin 0.5.1 GPL XX Compute folding dynamics on coarse grained version of an energy...
treemaker 1.4 BSD-3-Clause XXX A python tool for generating a Newick formatted tree from alist of...
treemix 1.13 GPLv3 XX TreeMix is a method for inferring the patterns of population splits and...
treeqmc 3.0.1 dev MIT XX TREE-QMC is a quartet-based method for estimating species trees from gene trees.
treerecs 1.2 AGPL XX 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 XX TreeSAPP is a functional and taxonomic annotation tool for microbial...
treeshrink 1.3.9 doc dev GPL-3.0-or-later X An algorithm for detecting (and removing) abnormally long branches in...
treesimulator 0.2.27 doc dev GPL-3.0-only 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
treeswirl 2.0.0 doc dev MPL-2.0 XX TreeSwirl: A tool to infer locus-specific population mixtures from...
treetime 0.11.4 doc dev MIT XXX Maximum-Likelihood dating and ancestral inference for phylogenetic trees
trf 4.10.0rc2 doc dev AGPL-3.0-or-later XX Tandem Repeats Finder is a program to locate and display tandem repeats...
trgt 5.0.0 Pacific XX Tandem repeat genotyping and visualization from PacBio HiFi data
tribal 0.1.1 doc BSD-3-Clause XX TRIBAL is a package to infer B cell lineage trees from single-cell RNA...
triform2 0.0.5 GNU XX Improved sensitivity, specificity and control of false discovery rates...
trim-galore 0.6.10 dev GPL-3.0-only XXX Trim Galore! is a wrapper script to automate quality and adapter...
trim_isoseq_polya 0.0.3 BSD-3-Clause-Clear XX Trims polyA tails from IsoSeq FASTA files
trimadap r11 dev MIT XX Fast but inaccurate adapter trimmer for Illumina reads.
trimal 1.5.1 doc dev GPL-3.0-or-later XX 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 0.40 doc dev GPL-3.0-or-later XXX 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 XX Trinity assembles transcript sequences from Illumina RNA-Seq data.
trinotate 4.0.2 BSD-3-Clause XXX Trinotate is a comprehensive annotation suite designed for automatic...
triqler 0.9.1 doc dev Apache-2.0 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 XXX tRNA analysis pipeline
trnascan-se 2.0.12 doc dev GPL-3.0-or-later XX 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 XXX For NGS experiments using unique molecular identifiers (UMIs),...
trust4 1.1.7 doc dev MIT XX TCR and BCR assembly from bulk or single-cell RNA-seq data.
truvari 5.4.0 doc dev MIT XXX Structural variant comparison tool for VCFs.
trycycler 0.5.6 doc dev GPL-3.0-or-later 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 doc GPL-2.0-or-later XX TSSAR is a Web Service for predicting bacterial Transcription Start...
tssv 1.1.2 doc dev MIT XX Targeted characterisation of short structural variation.
tsumugi 0.5.0 doc dev MIT X TSUMUGI: Phenotype-driven gene network identifier
tsv-utils 2.2.0 doc dev BSL-1.0 XX eBay's TSV Utilities
tttrlib 0.25.1 doc dev BSD-3-Clause XX A file format agnostic library for time-resolved imaging and spectroscopic data.
turbocor 0.1.1 MIT XX A command line tool to compute very large correlation matrices.
twilight 0.2.3 doc dev MIT XX TWILIGHT: A high throughput tool for tall and wide multiple sequence alignment.
twobitreader 3.1.7 Artistic XXX A fast python package for reading .2bit files (used by the UCSC genome browser)
twopaco 1.1.0 dev Custom XX 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 XX Type Hints for Python
tyto 1.4 Apache-2.0 X Tyto (Take Your Terms from Ontologies) provides a handy interface for...
uchime 4.2 doc MIT XX UCHIME2 is an algorithm for detecting chimeric sequences.
ucsc-addcols 482 doc dev Varies; XX Sum columns in a text file.
ucsc-ameme 482 doc dev Varies; XX Find common patterns in DNA.
ucsc-autodtd 482 doc dev Varies; XX Give this a XML document to look at and it will come up with a DTD.
ucsc-autosql 482 doc dev Varies; XX Create SQL and C code for permanently storing.
ucsc-autoxml 482 doc dev Varies; XX Generate structures code and parser for XML file from DTD-like spec.
ucsc-ave 357 varies; X Compute average and basic stats
ucsc-avecols 482 doc dev Varies; XX Average together columns.
ucsc-axtchain 482 doc dev Varies; XX Chain together axt alignments.
ucsc-axtsort 482 doc dev Varies; XX Sort axt files.
ucsc-axtswap 482 doc dev Varies; XX Swap source and query in an axt file.
ucsc-axttomaf 482 doc dev Varies; XX Convert from axt to maf format.
ucsc-axttopsl 482 doc dev Varies; XX Convert axt to psl format.
ucsc-bamtopsl 482 doc dev Varies; XX Convert a bam file to a psl and optionally also a fasta file that...
ucsc-bedclip 482 doc dev Varies; XX Remove lines from bed file that refer to off-chromosome locations.
ucsc-bedcommonregions 482 doc dev Varies; XX Create a bed file (just bed3) that contains the regions common to all inputs.
ucsc-bedcoverage 482 doc dev Varies; XX Analyse coverage by bed files - chromosome by chromosome and genome-wide.
ucsc-bedextendranges 482 doc dev Varies; XX Extend length of entries in bed 6+ data to be at least the given...
ucsc-bedgeneparts 482 doc dev Varies; XX Given a bed, spit out promoter, first exon, or all introns.
ucsc-bedgraphpack 482 doc dev Varies; XX Pack together adjacent records representing same value.
ucsc-bedgraphtobigwig 482 doc dev Varies; XX Convert a bedGraph file to bigWig format.
ucsc-bedintersect 482 doc dev Varies; XX Intersect two bed files.
ucsc-beditemoverlapcount 482 doc dev Varies; XX Count number of times a base is overlapped by the items in a bed file.
ucsc-bedjointaboffset 377 varies; XX given a bed file and tab file where each have a column with matching...
ucsc-bedpileups 482 doc dev Varies; XX Find (exact) overlaps if any in bed input.
ucsc-bedremoveoverlap 482 doc dev Varies; XX Remove overlapping records from a (sorted) bed file.
ucsc-bedrestricttopositions 482 doc dev Varies; XX Filter bed file, restricting to only ones that match chrom/start/ends...
ucsc-bedsort 482 doc dev Varies; XX Sort a .bed file by chrom,chromStart.
ucsc-bedtobigbed 482 doc dev Varies; XX Convert bed file to bigBed. (BigBed version: 4)
ucsc-bedtogenepred 482 doc dev Varies; XX Convert bed format files to genePred format.
ucsc-bedtopsl 482 doc dev Varies; XX Convert bed format files to psl format.
ucsc-bedweedoverlapping 482 doc dev Varies; XX Filter out beds that overlap a 'weed.bed' file.
ucsc-bigbedinfo 482 doc dev Varies; XX Show information about a bigBed file.
ucsc-bigbednameditems 482 doc dev Varies; XX Extract item of given name from bigBed.
ucsc-bigbedsummary 482 doc dev Varies; XX Extract summary information from a bigBed file.
ucsc-bigbedtobed 482 doc dev Varies; XX Convert from bigBed to ascii bed format.
ucsc-bigmaftomaf 482 doc dev Varies; XX Convert bigMaf to maf file.
ucsc-bigpsltopsl 482 doc dev Varies; XX Convert bigPsl file to psl.
ucsc-bigwigaverageoverbed 482 doc dev Varies; XX Compute average score of big wig over each bed, which may have introns.
ucsc-bigwigcat 482 doc dev Varies; XX Merge non-overlapping bigWig files.
ucsc-bigwigcluster 482 doc dev Varies; XX Cluster bigWigs using a hacTree.
ucsc-bigwigcorrelate 482 doc dev Varies; XX Correlate bigWig files, optionally only on target regions.
ucsc-bigwiginfo 482 doc dev Varies; XX Print out information about bigWig file.
ucsc-bigwigmerge 482 doc dev Varies; XX Merge together multiple bigWigs into a single output bedGraph.
ucsc-bigwigsummary 482 doc dev Varies; XX Extract summary information from a bigWig file.
ucsc-bigwigtobedgraph 482 doc dev Varies; XX Convert from bigWig to bedGraph format.
ucsc-bigwigtowig 482 doc dev Varies; XX Convert bigWig to wig. This will keep more of the same structure of the...
ucsc-blasttopsl 482 doc dev Varies; XX Convert blast alignments to PSLs.
ucsc-blat 482 doc dev Varies; XX Standalone BLAT v. 39x1 fast sequence search command line tool.
ucsc-calc 357 varies; X Little command line calculator
ucsc-catdir 482 doc dev Varies; XX Concatenate files in directory to stdout.
ucsc-catuncomment 482 doc dev Varies; XX Concatenate input removing lines that start with '#'.
ucsc-cell-browser 1.2.16 doc dev GPL-3.0-or-later X A browser for single-cell data, main site at http://cells.ucsc.edu....
ucsc-chainantirepeat 482 doc dev Varies; XX Get rid of chains that are primarily the results of repeats and degenerate DNA.
ucsc-chainbridge 377 varies; XX 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 482 doc dev Varies; XX Filter chain files. Output goes to standard out.
ucsc-chainmergesort 482 doc dev Varies; XX Combine sorted files into larger sorted file.
ucsc-chainnet 482 doc dev Varies; XX Make alignment nets out of chains.
ucsc-chainprenet 482 doc dev Varies; XX 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 482 doc dev Varies; XX Sort chains. By default sorts by score.
ucsc-chainsplit 482 doc dev Varies; XX Split chains up by target or query sequence.
ucsc-chainstitchid 482 doc dev Varies; XX Join chain fragments with the same chain ID into a single chain per ID.
ucsc-chainswap 482 doc dev Varies; XX Swap target and query in chain.
ucsc-chaintoaxt 482 doc dev Varies; XX Convert from chain to axt file.
ucsc-chaintopsl 482 doc dev Varies; XX Convert chain file to psl format.
ucsc-chaintopslbasic 482 doc dev Varies; XX Basic conversion chain file to psl format.
ucsc-checkagpandfa 482 doc dev Varies; XX Takes a .agp file and .fa file and ensures that they are in synch.
ucsc-checkcoveragegaps 482 doc dev Varies; XX Check for biggest gap in coverage for a list of tracks.
ucsc-checkhgfindspec 482 doc dev Varies; XX Test and describe search specs in hgFindSpec tables.
ucsc-checktablecoords 482 doc dev Varies; XX Check invariants on genomic coords in table(s).
ucsc-chopfalines 482 doc dev Varies; XX Read in FA file with long lines and rewrite it with shorter lines.
ucsc-chromgraphfrombin 482 doc dev Varies; XX Convert chromGraph binary to ascii format.
ucsc-chromgraphtobin 482 doc dev Varies; XX Make binary version of chromGraph.
ucsc-clustergenes 377 varies; XX Cluster genes from genePred tracks
ucsc-coltransform 482 doc dev Varies; XX Add and/or multiply column by constant.
ucsc-countchars 482 doc dev Varies; XX Count the number of occurrences of a particular char.
ucsc-crtreeindexbed 482 doc dev Varies; XX Create an index for a bed file.
ucsc-crtreesearchbed 482 doc dev Varies; XX Search a crTree indexed bed file and print all items that overlap query.
ucsc-dbsnoop 482 doc dev Varies; XX Produce an overview of a database.
ucsc-dbtrash 482 doc dev Varies; XX Drop tables from a database older than specified N hours.
ucsc-endsinlf 377 varies; XX Check that last letter in files is end of line
ucsc-estorient 482 doc dev Varies; XX Read ESTs from a database and determine orientation based on...
ucsc-expmatrixtobarchartbed 469 doc dev varies; XX Generate a barChart bed6+5 file from a matrix, meta data, and coordinates.
ucsc-faalign 482 doc dev Varies; XX Align two fasta files.
ucsc-facmp 482 doc dev Varies; XX Compare two .fa files.
ucsc-facount 482 doc dev Varies; XX Count base statistics and CpGs in FA files.
ucsc-fafilter 482 doc dev Varies; XX Filter fa records, selecting ones that match the specified conditions.
ucsc-fafiltern 482 doc dev Varies; XX Get rid of sequences with too many N's.
ucsc-fafrag 482 doc dev Varies; XX Extract a piece of DNA from a .fa file.
ucsc-fanoise 482 doc dev Varies; XX Add noise to .fa file.
ucsc-faonerecord 482 doc dev Varies; XX Extract a single record from a .FA file.
ucsc-fapolyasizes 482 doc dev Varies; XX Get poly A sizes.
ucsc-farandomize 482 doc dev Varies; XX Program to create random fasta records.
ucsc-farc 482 doc dev Varies; XX Reverse complement a FA file.
ucsc-fasize 482 doc dev Varies; XX Print total base count in fa files.
ucsc-fasomerecords 482 doc dev Varies; XX Extract multiple fa records.
ucsc-fasplit 482 doc dev Varies; XX Split an fa file into several files.
ucsc-fastqstatsandsubsample 482 doc dev Varies; XX Go through a fastq file doing sanity checks and collecting stats.
ucsc-fastqtofa 482 doc dev Varies; XX Convert from fastq to fasta format.
ucsc-fatofastq 482 doc dev Varies; XX Convert fa to fastq format, just faking quality values.
ucsc-fatotab 482 doc dev Varies; XX Convert fa file to tab separated file.
ucsc-fatotwobit 482 doc dev Varies; XX Convert DNA from fasta to 2bit format.
ucsc-fatovcf 482 doc dev Varies; XX Extract VCF from a multi-sequence FASTA alignment.
ucsc-fatrans 482 doc dev Varies; XX Translate DNA .fa file to peptide.
ucsc-featurebits 482 doc dev Varies; XX Correlate tables via bitmap projections.
ucsc-fetchchromsizes 482 doc dev Varies; XX Used to fetch chrom.sizes information from UCSC for the given <db>.
ucsc-findmotif 482 doc dev Varies; XX Find specified motif in sequence.
ucsc-gaptolift 482 doc dev Varies; XX Create lift file from gap table(s).
ucsc-genepredcheck 482 doc dev Varies; XX Validate genePred files or tables.
ucsc-genepredfilter 482 doc dev Varies; XX Filter a genePred file.
ucsc-genepredhisto 482 doc dev Varies; XX Get data for generating histograms from a genePred file.
ucsc-genepredsinglecover 482 doc dev Varies; XX Create single-coverage genePred files.
ucsc-genepredtobed 482 doc dev Varies; XX Convert from genePred to bed format. Does not yet handle genePredExt.
ucsc-genepredtobiggenepred 482 doc dev Varies; XX Converts genePred or genePredExt to bigGenePred input (bed format with...
ucsc-genepredtofakepsl 482 doc dev Varies; XX Create a psl of fake-mRNA aligned to gene-preds from a file or table.
ucsc-genepredtogtf 482 doc dev Varies; XX Convert genePred table or file to gtf.
ucsc-genepredtomafframes 482 doc dev Varies; XX Create mafFrames tables from a genePreds.
ucsc-genepredtoprot 482 doc dev Varies; XX Create protein sequences by translating gene annotations.
ucsc-gensub2 469 doc dev Varies; XX version 12.18
ucsc-getrna 482 doc dev Varies; XX Get mrna for GenBank or RefSeq sequences found in a database.
ucsc-getrnapred 482 doc dev Varies; XX Get virtual RNA for gene predictions.
ucsc-gff3togenepred 482 doc dev Varies; XX Convert a GFF3 file to a genePred file.
ucsc-gff3topsl 482 doc dev Varies; XX Convert a GFF3 CIGAR file to a PSL file.
ucsc-gmtime 482 doc dev Varies; XX Convert unix timestamp to date string.
ucsc-gtftogenepred 482 doc dev Varies; XX Convert a GTF file to a genePred.
ucsc-headrest 482 doc dev Varies; XX Return all *but* the first N lines of a file.
ucsc-hgbbidblink 482 doc dev Varies; XX Add table that just contains a pointer to a bbiFile to database. This program.
ucsc-hgfakeagp 482 doc dev Varies; XX Create fake AGP file by looking at N's.
ucsc-hgfindspec 482 doc dev Varies; XX Create hgFindSpec table from trackDb.ra files.
ucsc-hggcpercent 482 doc dev Varies; XX Calculate GC Percentage in 20kb windows.
ucsc-hggoldgapgl 377 varies; XX Put chromosome .agp and .gl files into browser database.
ucsc-hgloadbed 482 doc dev Varies; XX Load a generic bed file into database.
ucsc-hgloadchain 482 doc dev Varies; XX Load a generic Chain file into database.
ucsc-hgloadmaf 482 doc dev Varies; XX Load a maf file index into the database.
ucsc-hgloadnet 482 doc dev Varies; XX Load a generic net file into database.
ucsc-hgloadout 482 doc dev Varies; XX Load RepeatMasker .out files into database.
ucsc-hgloadoutjoined 482 doc dev Varies; XX Load new style (2014) RepeatMasker .out files into database.
ucsc-hgloadsqltab 482 doc dev Varies; XX Load table into database from SQL and text files.
ucsc-hgloadwiggle 482 doc dev Varies; XX Load a wiggle track definition into database.
ucsc-hgspeciesrna 482 doc dev Varies; XX Create fasta file with RNA from one species.
ucsc-hgsqldump 482 doc dev Varies; XX Execute mysqldump using passwords from .hg.conf.
ucsc-hgtrackdb 482 doc dev Varies; XX Create trackDb table from text files.
ucsc-hgvstovcf 377 varies; XX Convert HGVS terms to VCF tab-separated output
ucsc-htmlcheck 482 doc dev Varies; XX Do a little reading and verification of html file.
ucsc-hubcheck 482 doc dev Varies; XX Check a track data hub for integrity.
ucsc-hubpubliccheck 482 doc dev Varies; XX Checks that the labels in hubPublic match what is in the hub labels.
ucsc-ixixx 482 doc dev Varies; XX Create indices for simple line-oriented file of format.
ucsc-lavtoaxt 482 doc dev Varies; XX Convert blastz lav file to an axt file (which includes sequence).
ucsc-lavtopsl 482 doc dev Varies; XX Convert blastz lav to psl format.
ucsc-ldhggene 482 doc dev Varies; XX Load database with gene predictions from a gff file.
ucsc-liftover 482 doc dev Varies; XX Move annotations from one assembly to another.
ucsc-liftup 482 doc dev Varies; XX Change coordinates of .psl, .agp, .gap, .gl, .out, .align, .gff, .gtf.
ucsc-linestora 482 doc dev Varies; XX Generate .ra format from lines with pipe-separated fields.
ucsc-localtime 482 doc dev Varies; XX Convert unix timestamp to date string.
ucsc-mafaddirows 482 doc dev Varies; XX Add 'i' rows to a maf.
ucsc-mafaddqrows 482 doc dev Varies; XX Add quality data to a maf.
ucsc-mafcoverage 482 doc dev Varies; XX Analyse coverage by maf files - chromosome by.
ucsc-maffetch 482 doc dev Varies; XX Get overlapping records from an MAF using an index table.
ucsc-maffilter 482 doc dev Varies; XX Filter out maf files. Output goes to standard out.
ucsc-maffrag 482 doc dev Varies; XX Extract maf sequences for a region from database.
ucsc-maffrags 482 doc dev Varies; XX Collect MAFs from regions specified in a 6 column bed file.
ucsc-mafgene 490 doc dev Varies; XX Output protein alignments using maf and genePred.
ucsc-mafmefirst 482 doc dev Varies; XX Move component to top if it is one of the named ones.
ucsc-maforder 482 doc dev Varies; XX Order components within a maf file.
ucsc-mafranges 482 doc dev Varies; XX Extract ranges of target (or query) coverage from maf and.
ucsc-mafsinregion 482 doc dev Varies; XX Extract MAFS in a genomic region.
ucsc-mafspecieslist 482 doc dev Varies; XX Scan maf and output all species used in it.
ucsc-mafspeciessubset 482 doc dev Varies; XX Extract a maf that just has a subset of species.
ucsc-mafsplit 482 doc dev Varies; XX Split multiple alignment files.
ucsc-mafsplitpos 482 doc dev Varies; XX Pick positions to split multiple alignment input files.
ucsc-maftoaxt 482 doc dev Varies; XX Convert from maf to axt format.
ucsc-maftobigmaf 482 doc dev Varies; XX Put ucsc standard maf file into bigMaf format.
ucsc-maftopsl 482 doc dev Varies; XX Convert maf to psl format.
ucsc-maftosnpbed 482 doc dev Varies; XX Finds SNPs in MAF and builds a bed with their functional consequence.
ucsc-maketablelist 482 doc dev Varies; XX Create/recreate tableList tables (cache of SHOW TABLES and DESCRIBE).
ucsc-maskoutfa 482 doc dev Varies; XX Produce a masked .fa file given an unmasked .fa and.
ucsc-matrixclustercolumns 482 doc dev Varies; XX Group the columns of a matrix into clusters, and output a matrix with...
ucsc-matrixmarkettotsv 482 doc dev Varies; XX Convert matrix file from Matrix Market sparse matrix format to...
ucsc-matrixnormalize 482 doc dev Varies; XX Normalize a matrix somehow - make it's columns or rows all sum to...
ucsc-matrixtobarchartbed 482 doc dev Varies; XX Attach a labeled expression matrix to a bed file joining.
ucsc-mktime 482 doc dev Varies; XX Convert date string to unix timestamp.
ucsc-mrnatogene 482 doc dev Varies; XX Convert PSL alignments of mRNAs to gene annotations.
ucsc-netchainsubset 482 doc dev Varies; XX Create chain file with subset of chains that appear in the net.
ucsc-netclass 482 doc dev Varies; XX Add classification info to net.
ucsc-netfilter 482 doc dev Varies; XX Filter out parts of net. What passes.
ucsc-netsplit 482 doc dev Varies; XX Split a genome net file into chromosome net files.
ucsc-netsyntenic 482 doc dev Varies; XX Add synteny info to net.
ucsc-nettoaxt 482 doc dev Varies; XX Convert net (and chain) to axt.
ucsc-nettobed 482 doc dev Varies; XX Convert target coverage of net to a bed file.
ucsc-newprog 482 doc dev Varies; XX Make a new C source skeleton.
ucsc-newpythonprog 482 doc dev Varies; XX Make a skeleton for a new python program.
ucsc-nibfrag 482 doc dev Varies; XX Extract part of a nib file as .fa (all bases/gaps lower case by default).
ucsc-nibsize 482 doc dev Varies; XX Print size of nibs.
ucsc-oligomatch 482 doc dev Varies; XX find perfect matches in sequence.
ucsc-overlapselect 482 doc dev Varies; XX Select records based on overlapping chromosome ranges.
ucsc-para 469 doc dev Varies; XX version 12.18
ucsc-parafetch 482 doc dev Varies; XX Try to fetch url with multiple connections.
ucsc-parahub 469 doc dev Varies; XX parasol hub server version 12.18
ucsc-parahubstop 482 doc dev Varies; XX Shut down paraHub daemon.
ucsc-paranode 482 doc dev Varies; XX Parasol node server.
ucsc-paranodestart 482 doc dev Varies; XX Start up parasol node daemons on a list of machines.
ucsc-paranodestatus 482 doc dev Varies; XX Check status of paraNode on a list of machines.
ucsc-paranodestop 482 doc dev Varies; XX Shut down parasol node daemons on a list of machines.
ucsc-parasol 482 doc dev Varies; XX Parallel job management system for a compute cluster.
ucsc-parasync 482 doc dev Varies; XX Uses paraFetch to recursively mirror url to given path.
ucsc-paratestjob 482 doc dev Varies; XX Version 12.18.
ucsc-positionaltblcheck 482 doc dev Varies; XX Check that positional tables are sorted.
ucsc-pslcat 482 doc dev Varies; XX Concatenate psl files.
ucsc-pslcdnafilter 482 doc dev Varies; XX Filter cDNA alignments in psl format. Filtering criteria are...
ucsc-pslcheck 482 doc dev Varies; XX Validate PSL files.
ucsc-psldropoverlap 482 doc dev Varies; XX Deletes all overlapping self alignments.
ucsc-pslfilter 482 doc dev Varies; XX Filter out psl file.
ucsc-pslhisto 482 doc dev Varies; XX Collect counts on PSL alignments for making histograms. These then be...
ucsc-pslliftsubrangeblat 482 doc dev Varies; XX Lift PSLs from blat subrange alignments.
ucsc-pslmap 482 doc dev Varies; XX Map PSLs alignments to new targets using alignments of the old target...
ucsc-pslmappostchain 482 doc dev Varies; XX Post genomic pslMap (TransMap) chaining. This takes transcripts that...
ucsc-pslmrnacover 482 doc dev Varies; XX Make histogram of coverage percentage of mRNA in psl.
ucsc-pslpairs 482 doc dev Varies; XX Join paired ends in psl alignments.
ucsc-pslpartition 482 doc dev Varies; XX Split PSL files into non-overlapping sets.
ucsc-pslpostarget 482 doc dev Varies; XX flip psl strands so target is positive and implicit
ucsc-pslpretty 482 doc dev Varies; XX Convert PSL to human-readable output.
ucsc-pslprottornacoords 482 doc dev Varies; XX Convert protein alignments to RNA coordinates.
ucsc-pslrc 482 doc dev Varies; XX Reverse-complement psl.
ucsc-pslrecalcmatch 482 doc dev Varies; XX Recalculate match, mismatch, repMatch columns in psl file.
ucsc-pslreps 482 doc dev Varies; XX Analyze repeats and generate genome-wide best alignments from a sorted...
ucsc-pslscore 482 doc dev Varies; XX Calculate web blat score from psl files.
ucsc-pslselect 482 doc dev Varies; XX Select records from a PSL file.
ucsc-pslsomerecords 482 doc dev Varies; XX Extract multiple psl records.
ucsc-pslsort 482 doc dev Varies; XX Merge and sort psCluster .psl output files.
ucsc-pslsortacc 482 doc dev Varies; XX Remove chain-breaking alignments from chains that break nested chains.
ucsc-pslsplicejunctions 482 doc dev Varies; XX Extract splice junctions from a PSL file.
ucsc-pslsplitontarget 482 doc dev Varies; XX Split psl files into one per target.
ucsc-pslstats 482 doc dev Varies; XX Collect statistics from a psl file.
ucsc-pslswap 482 doc dev Varies; XX Swap target and query in psls.
ucsc-psltobed 482 doc dev Varies; XX Transform a psl format file to a bed format file.
ucsc-psltobigpsl 482 doc dev Varies; XX Converts psl to bigPsl input (bed format with extra fields).
ucsc-psltochain 482 doc dev Varies; XX Convert psl records to chain records.
ucsc-psltopslx 482 doc dev Varies; XX Convert from psl to pslx format, which includes sequences.
ucsc-pslxtofa 482 doc dev Varies; XX Convert pslx (with sequence) to fasta file.
ucsc-qacagplift 482 doc dev Varies; XX Use AGP to combine per-scaffold qac into per-chrom qac.
ucsc-qactoqa 482 doc dev Varies; XX Convert from compressed to uncompressed.
ucsc-qactowig 482 doc dev Varies; XX Convert from compressed quality score format to wiggle format.
ucsc-qatoqac 482 doc dev Varies; XX Convert from uncompressed to compressed.
ucsc-randomlines 482 doc dev Varies; XX Pick out random lines from file.
ucsc-rasqlquery 482 doc dev Varies; XX Do a SQL-like query on a RA file.
ucsc-ratolines 482 doc dev Varies; XX Output .ra file stanzas as single lines, with pipe-separated fields.
ucsc-ratotab 482 doc dev Varies; XX Convert ra file to table.
ucsc-rmfadups 482 doc dev Varies; XX Remove duplicate records in FA file.
ucsc-rowstocols 482 doc dev Varies; XX Convert rows to columns and vice versa in a text file.
ucsc-spacedtotab 482 doc dev Varies; XX Convert fixed width space separated fields to tab separated.
ucsc-splitfile 482 doc dev Varies; XX Split up a file.
ucsc-splitfilebycolumn 482 doc dev Varies; XX Split text input into files named by column value.
ucsc-sqltoxml 482 doc dev Varies; XX Dump out all or part of a relational database to XML, guided.
ucsc-stringify 482 doc dev Varies; XX Convert file to C strings.
ucsc-subchar 482 doc dev Varies; XX Substitute one character for another throughout a file.
ucsc-subcolumn 482 doc dev Varies; XX Substitute one column in a tab-separated file.
ucsc-taillines 482 doc dev Varies; XX Add tail to each line of file.
ucsc-tdbquery 482 doc dev Varies; XX Query the trackDb system using SQL syntax.
ucsc-texthistogram 482 doc dev Varies; XX Make a histogram in ascii.
ucsc-ticktodate 482 doc dev Varies; XX Convert seconds since 1970 to time and date.
ucsc-tolower 482 doc dev Varies; XX Convert upper case to lower case in file. Leave other chars alone.
ucsc-toupper 482 doc dev Varies; XX Convert lower case to upper case in file. Leave other chars alone.
ucsc-transmappsltogenepred 482 doc dev Varies; XX Convert PSL alignments of mRNAs to gene annotations.
ucsc-trfbig 482 doc dev Varies; XX Mask tandem repeats on a big sequence file.
ucsc-twobitdup 482 doc dev Varies; XX check to see if a twobit file has any identical sequences in it
ucsc-twobitinfo 482 doc dev Varies; XX Get information about sequences in a .2bit file.
ucsc-twobitmask 482 doc dev Varies; XX Apply masking to a .2bit file, creating a new .2bit file.
ucsc-twobittofa 482 doc dev Varies; XX Convert all or part of .2bit file to fasta.
ucsc-validatefiles 482 doc dev Varies; XX Validates the format of different genomic files.
ucsc-validatemanifest 482 doc dev Varies; XX Validates the ENCODE3 manifest.txt file.
ucsc-websync 469 doc dev varies; XX download from https server, using files.txt on their end to get the...
ucsc-wigcorrelate 482 doc dev Varies; XX Produce a table that correlates all pairs of wigs.
ucsc-wigtobigwig 482 doc dev Varies; XX Convert ascii format wig file (in fixedStep, variableStep).
ucsc-wordline 482 doc dev Varies; XX Chop up words by white space and output them with one.
ucsc-xmlcat 482 doc dev Varies; XX Concatenate xml files together, stuffing all records inside a single outer tag.
ucsc-xmltosql 482 doc dev Varies; XX 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 1.2.1 doc dev BSD-3-Clause XX ULTRA is a tool for finding and annotating tandem repeats within...
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 1.2.10 doc dev MIT XXX An all-in-one software package for processing and demultiplexing fastq files.
umap 1.1.1 GNU X Umap and Bismap: tools for genome and methylome mappability
umi-transfer 1.6.0 MIT XX A tool for transferring Unique Molecular Identifiers (UMIs) from a...
umi_tools 1.1.6 doc dev MIT XX 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 doc dev MIT XX Tools for processing UMI RNA-tag data.
umitools 0.3.4 GPL3 XXX 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
unetcoreograph 2.4.6 dev MIT X UNetCoreograph - Automated segmentation of nuclei in 3D imaging data.
unfazed 1.0.2 MIT X Extended read-backed and allele-balance phasing for de novo variation...
unicore 1.1.1 GNU-3.0-or-later XX Universal and efficient core gene phylogeny with Foldseek and ProstT5
unicycler 0.5.1 doc dev GPL-3.0-or-later XX Hybrid assembly pipeline for bacterial genomes.
unifeb 0.1.1 MIT X unifeb is an non-linear dimension reduction/embedding algorithm for...
unifire 1.0.1 Apache-2.0 X UniFIRE is the official protein annotator from Uniprot. It runs both...
unifrac 1.5.1 doc dev BSD-3-Clause XX Fast phylogenetic diversity calculations.
unifrac-binaries 1.6 doc dev BSD-3-Clause XX Fast phylogenetic diversity calculations
unikmer 0.20.0 MIT XX 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 XX Unimap is a fork of minimap2 optimized for assembly-to-reference alignment.
uniprot 1.3 BSD XXX Retrieve protein sequence identifiers and metadata from http://uniprot.org
uniprot-id-mapper 1.1.4 doc dev MIT X A Python wrapper for the UniProt Mapping RESTful API.
uniqsketch 1.1.0 doc dev MIT XX UniqSketch: sensitive and resource-efficient strain-level detection in...
unitas 1.6.1 Creative XXX 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 XX Determines presence/absence of sequence elements in bacterial sequence data.
unitig-counter 1.1.0 dev 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...
unmicst 2.6.6 MIT X UNMICST - UnMicst Nuclear Segmentation Tool
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 1.13.3 doc dev BSD-3-Clause X UniProt Id Mapping through API
uritemplate 0.6 Apache XX Python implementation of RFC6570, URI Template, and can expand...
urllib3 1.12 MIT XX HTTP library with thread-safe connection pooling, file post, and more.
uropa 4.0.3 doc MIT XXX UROPA (Universal RObust Peak Annotator) is a command line based tool,...
usalign 20241201 doc dev UNKNOWN XX 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 doc GPL-3.0-or-later XX USEARCH is a unique sequence analysis tool which offers search and...
usher 0.6.6 doc dev MIT XX Ultrafast Sample Placement on Existing Trees (UShER).
ushuffle 1.2.2 dev Custom XX 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 XXX Viral Annotation DefineR - classification and annotation of viral...
vafator 2.2.2 doc MIT X VAFator annotates the variants in a VCF file with technical annotations...
valet 1.0 MIT XXX Pipeline for detecting mis-assemblies in metagenomic assemblies
validate-fasta-database 1.0 GPL-3.0 XXX Code for Galaxy tool for quality control on FASTA database
validators 0.14.0 BSD XXX Python Data Validation for Humans.
validictory 1.0.1 BSD XX general purpose python data validator
vamb 5.0.4 doc dev MIT XXX Variational autoencoder for metagenomic binning.
vambcore 0.1.2 dev MIT XX Performant backend functions for the Vamb binning tool.
vamos 2.1.7 dev GPL-2.0-only XX VNTR annotation using efficient motif selection.
vapor 1.0.3 doc GPL-3.0-or-later X VAPOR is a tool for classification of Influenza samples from short read...
var-agg 0.1.1 MIT XX 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 XXX A sensitive variant caller for both single and paired sample variant calling
vardict-java 1.8.3 MIT XXX 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 0.17.3 doc dev MIT X Rust-based tool for the heavy lifting in varfish-server.
vargeno 1.0.3 MIT XX 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 doc dev GPL-3.0-or-later XX 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
varlinker 0.1.0 dev MIT X Parallel threaded variant linker.
varlociraptor 8.9.1 doc dev GPL-3.0-or-later XX Flexible, uncertainty-aware variant calling with parameter free...
varpubs 0.4.1 MIT X Tool for finding PubMed evidence on genetic variants and generating...
varscan 2.4.6 The XXX variant detection in massively parallel sequencing data
vartovcf 1.4.0 doc dev MIT XX Convert variants from VarDict/VarDictJava into VCF v4.2 format.
vartrix 1.1.22 dev MIT XX 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 XX An awk-like VCF parser
vbz-h5py-plugin 1.0.1 dev MPL-2.0 X Oxford Nanopore Technologies VBZ HDF plugin for h5py.
vcf-annotator 0.7 MIT XXX Use the reference GenBank file to add biological annotations to the...
vcf-pg-loader 0.5.4 doc dev MIT X High-performance VCF to PostgreSQL loader with clinical-grade compliance
vcf-reformatter 0.3.0 doc dev MIT XX Fast VCF file parser and reformatter with VEP and SnpEff annotation support
vcf-validator 0.10.2 Apache-2.0 XX 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 0.9.3 MIT X Convert VCF with structural variations to CytoSure format
vcf2db 2020.02.24 MIT XXX Create a gemini-compatible database from a VCF
vcf2genome 0.91 GPLv3 XXX A tool to create a draft genome file out of a GATK VCF file and...
vcf2maf 1.6.22 dev Apache-2.0 XX 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...
vcf2pandas 0.2.0 dev MIT X Package to convert a VCF into a pandas dataframe.
vcf2parquet 0.5.0 MIT XX 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.
vcf_parser 1.6 MIT X Small library for parsing vcf files.
vcfanno 0.3.7 doc dev MIT XX Annotate a VCF with other VCFs/BEDs/tabixed files.
vcfbub 0.1.2 doc dev MIT XX Popping bubbles in vg deconstruct VCFs.
vcfdist 2.6.4 doc GPL-3.0-only XX 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 XXX VCF-kit is a command-line based collection of utilities for performing...
vcflatten 0.5.2 BSD XX A command line tool for flattening VCF files down to simpler TSV files.
vcflib 1.0.14 doc dev MIT XX Command-line tools for manipulating VCF files.
vcfphasesets 0.3 MIT X Get variants as phase sets from a VCF file using pysam.
vcfpy 0.14.2 doc dev MIT XXX 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 XXX This script sorts and (optionally) filters the rows/variants of a VCF...
vcfsim 1.0.27.alpha dev MIT X Script for generating simulated VCF's leveraging a coalescent...
vcftoolbox 1.5.1 MIT XXX Tools for manipulating and parsing vcf files
vcftools 0.1.17 doc dev LGPL-3.0-only XX A set of tools written in Perl and C++ for working with VCF files.
vcfx 1.1.4 doc dev MIT XX VCFX: A Comprehensive VCF Manipulation Toolkit
vclean 0.2.1 dev GPL-3.0-only X vClean: Assessing the contamination of viral genomes
vclust 1.3.1 dev GPL-3.0-or-later XX 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 3.1.6 doc dev 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 XX A library for the analysis of RNA velocity.
velvet 1.2.10 doc dev GPL-2.0-only XX Sequence Assembler for short reads.
velvet-sc 0.7.62 GPL-2.0 XX Efficient de novo assembly of single-cell bacterial genomes from...
vembrane 2.4.0 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 XX verifyBamID verifies identity and purity of sequence data
verifybamid2 2.0.1 MIT XX A robust tool for DNA contamination estimation from sequence reads...
verifyidintensity 0.0.1 GPL3 XX verifyIDintensity detects and estimates sample contamination using...
verkko 2.3 doc dev CC0 XX A hybrid genome assembly pipeline developed for telomere-to-telomere...
verse 0.1.5 GPL-3.0 XX VERSE: a versatile and efficient RNA-Seq read counting tool
versionix 0.99.3 dev BSD-3-Clause X Get version of any tools.
verticall 0.4.3 doc GPL-3.0-or-later X A tool for building recombination-free trees.
veryfasttree 4.0.5 doc dev GPL-3.0-only XX VeryFastTree -- speeding up the estimation of phylogenies for large...
vg 1.70.0 MIT X Variation graph data structures, interchange formats, alignment,...
vgan 3.1.0 GPLv3.0 X Suite of tools for pangenomics built using vg
vgorient 0.1.1 doc dev MIT X Scripts for processing mitochondrial graphs.
vgp-processcuration 1.0 doc dev MIT X ProcessCurated - Toolkit for processing manually curated genome assemblies
vibrant 1.2.1 GPL-3.0 X Virus Identification By iteRative ANnoTation
vidjil-algo 2025.02 doc dev GPL-3.0-or-later XX Vidjil is an open-source platform for the analysis of high-throughput...
viennarna 2.7.1 custom XX 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 0.4.0 dev MIT X Lookup OMIM genes and HPO terms and compute similarities.
viloca 1.2.0 doc dev GNU X VILOCA is a tool to analyse short- and long-read sequencing viral...
vinalc 1.4.2 dev Apache-2.0 X VinaLC: MPI-accelerated molecular docking program for virtual screening.
viral-host-hunter 0.2.0 doc dev GPL-3.0-or-later X Decrypting viral dark matter with predictive framework and therapeutic...
viral_consensus 1.0.0 dev GPL-3.0-or-later XX Fast viral consensus genome reconstruction.
viralflye 0.2 BSD-3-Clause X viralFlye is a pipeline to recover high-quality viral genomes from...
viralmsa 1.1.46 GNU X Reference-guided multiple sequence alignment of viral genomes
viralrecall 3.0.2 MIT X Tool to identify giant viruses integrated into eukaryotic 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 XX A de novo transcriptome assembler for coronavirus.
virema 0.6 Custom XXX ViReMa (Viral Recombination Mapper) detects and reports recombination...
vireosnp 0.5.9 doc dev Apache-2.0 X vireoSNP - donor deconvolution for multiplexed scRNA-seq data.
virheat 0.7.6 GPL-3.0-or-later X Visualize microbial evolution at the SNP level by creating a heatmap...
virmet 2.0.0 doc dev MIT XXX A pipeline for viral metagenomics
viroconstrictor 1.6.3 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
virprof 0.9.2 doc GPLv3 X Virus Identification, Quantification and Genome Recovery from RNA-Seq NGS data
virsorter 2.2.4 dev GPL-2.0 XXX 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 3.2.0 Apache-2.0 X VirulenceFinder identifies virulence genes in total or partial...
virulign 1.1.1 doc dev GPL-2.0-only XX VIRULIGN is a tool for codon-correct pairwise alignments, with an...
virusrecom 1.4.0 LGPL-2.1-or-later X An information-theory-based method for recombination detection of viral...
visceral-evaluatesegmentation 2021.03.25 dev Apache-2.0 X EvaluateSegmentation is a tool that compares two volumes (a test...
visitor 0.1.2 MIT XX 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 XXX VISPR is a visualization framework and analysis workflow for...
vitap 1.10 doc GPL-3.0-only X Viral Taxonomic Assignment Pipeline
vitessce-python 3.7.9 doc dev MIT X Jupyter widget facilitating interactive visualization of spatial...
vkmz 1.4.6 MIT X metabolomics formula prediction and van Krevelen diagram generation
vmatch 2.3.1 doc Unknown XX 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 XX Python data validation library
voronota 1.29.4415 doc dev MIT XX Compute Voronoi diagram vertices for macromolecular structures
votuderep 0.6.0 dev MIT X A tool to dereplicate and filter vOTUs
voyager 0.1.4 doc dev LGPL-3.0-only X Rapid and efficient mapping algorithm for long sequencing reads with...
vphaser2 2.0 doc dev Single XX 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-cellpose2 1.0.0 The X Meta-package for VPT with Cellpose 2 plugin
vpt-core 1.2.0 Apache-2.0 X Core components for the Vizgen Post-processing Tool
vpt-plugin-cellpose2 1.0.1 Apache-2.0 X Cellpose2 plugin 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
vqbg 1.0.2 dev MIT X De Novo Reconstruction of Viral Quasispecies from Bubble Graph
vqsr_cnn 0.0.194 MIT XXX 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 XXX Interactive tool for statistical testing, data browsing and interactive...
vsearch 2.30.2 doc dev GPL-3.0-or-later XX 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 3.32 dev GPL-3.0-or-later X Rapidly call, validate, and compare SNPs from FASTQ files in a timely...
vt 2015.11.10 doc MIT XX 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 0.5.1 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 0.2.4.0 GPL-3.0-only X Creates png image file with all [vardict] variants proportions...
w4mclassfilter 0.98.19 MIT XXX Filter Workflow4Metabolomics feature list, optionally imputing NA values.
w4mclstrpeakpics 0.98.1 MIT XX Visualize W4M sample-cluster peaks - Produce a figure to assess the...
wade 1.2.0 doc dev Apache-2.0 X WADE provides a flexible and customizable method to extract specific...
wakhan 0.2.0 dev MIT X A tool to analyze haplotype-specific chromosome-scale somatic copy...
wally 0.7.1 dev BSD-3-Clause XX Visualization of aligned sequencing reads and genomic variants.
watchdog 0.8.3 Apache XX Filesystem events monitoring
watchdog-wms 2.0.8 GNU XXX 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 XXX Command line utilities for interacting with WDL
web.py 0.37 Public XX web.py makes web apps
weblogo 3.7.9 MIT XXX WebLogo3 : Sequence Logos Redrawn
weeder 2.0 GPL3 XX Motif (transcription factor binding sites) discovery in sequences from...
wepp 0.1.5 doc MIT XX Wastewater-Based Epidemiology using Phylogenetic Placements
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 XX Wavefront alignment algorithm library v2.
wfmash 0.24.1 doc dev 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 1.1.0 dev MIT XX 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 0.75 dev BSD-2-Clause X Whole Genome Duplication Identification.
wgfast 1.0.4 GPL XX 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 XXX Toolkit for preparing genomes for submission to NCBI
wgsim 1.0 dev MIT XX 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 2.8 doc dev MIT XX Phase genomic variants using DNA sequencing reads (haplotype assembly).
wheezy.template 3.2.4 doc dev MIT XXX A lightweight template library.
whokaryote 1.1.2 dev AGPL-3.0 X Classify metagenomic contigs as eukaryotic or prokaryotic
wiggletools 1.2.11 doc dev Apache-2.0 XX The WiggleTools package allows genomewide data files to be manipulated...
winnowmap 2.03 doc dev LicenseRef-Publ XX 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 XX The Wise2.4 package is the "revival" release of Wise2
wisecondorx 1.2.9 Attribution-Non XXX 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 XXX Command line utilities for interacting with WDL
workspace 0.3.1 MIT XX Workspace Overmind
ws4py 0.3.2 BSD XX WebSocket library for Python
wtdbg 2.5 doc dev GPL-3.0-or-later X Wtdbg2: A fuzzy Bruijn graph approach to long noisy reads assembly.
wtforms-alchemy 0.16.9 BSD XX Generates WTForms forms from SQLAlchemy models.
wtforms-components 0.10.0 BSD XXX Additional fields, validators and widgets for WTForms.
wtv 0.1.0 doc GPL-3.0-only X A library and CLI for ion selection in mass spectrometry data.
wub 0.5.1 MPL-2.0 XXX Tools and software library developed by the ONT Applications group
x-mapper 1.2.0 MIT X Genomic sequence aligner
xatlas 0.3 BSD-3-Clause XX 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 0.4.0 doc dev Apache-2.0 X Inference of clonal Copy Number Alterations in single cells.
xdg 1.0.5 ISC XX Variables defined by the XDG Base Directory Specification
xengsort 2.1.0 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 XX pythonic way to crate xml/(x)html files
xmltodict 0.9.2 MIT XX Makes working with XML feel like you are working with JSON
xmltramp2 3.1.1 GNU XXX A modern refactoring of the venerable xmltramp application
xopen 0.7.3 MIT XXX 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 XX 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 XX A fast CSV toolkit written in Rust.
xtail 1.1.5 GPL-3 XXX Genome-wide assessment of differential translations with ribosome profiling data
xtandem 15.12.15.2 doc The-Artistic-License XX 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 XXX Python library for terminal color support (including 256-color support
xunit-wrapper 0.12 GNU XXX Wrap python functions with a decorator to handle building XUnit reports.
xxhash 1.0.1 BSD XX Python binding for xxHash
xxmotif 1.6 GPLv3 XX eXhaustive, weight matriX-based motif discovery in nucleotide sequences
xyalign 1.1.5 GPL-3.0 XXX Command line tools and python library to infer ploidy, correct for sex...
yacht 1.3.2 doc dev MIT XXX YACHT is a mathematically rigorous hypothesis test for the presence or...
yacrd 1.0.0 MIT XX Yet Another Chimeric Read Detector, with long-read mapper result as input.
yaggo 1.5.10 GPL-3.0 XXX 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 doc MIT XX YAHMM is a HMM package for Python, implemented in Cython for speed.
yahs 1.2.2 dev MIT XX YaHS, yet another Hi-C scaffolding tool.
yak 0.1 doc dev MIT XX Yet another k-mer analyzer.
yamda 0.1.00e9c9d MIT X A highly scalable GPU-accelerated de novo motif discovery software package
yame 1.0.5 doc dev MIT XX YAME: Yet Another Methylation Extractor.
yamllint 1.2.1 GNU XX A linter for YAML files.
yanagiba 1.0.0 MIT XXX Filter short or low quality Oxford Nanopore reads which have been...
yanc 0.3.3 GNU XXX Yet another nose colorer
yapc 0.1 GPLv3 X Yapc is a (yet another) peak caller for genomic high-throughput sequencing data
yara 1.0.5 BSD XX Yara is an exact tool for aligning DNA sequencing reads to reference genomes.
yasma 1.1.0 GPL-3.0-only X Small RNA annotation suite
yass 1.16 doc dev CeCILL XX YASS is a genomic similarity search tool, for nucleic (DNA/RNA)...
yleaf 3.2.1 doc dev MIT X Yleaf - A tool for Y-chromosome haplogroup prediction
yleaf-pipelines 3.3.0 doc dev MIT X Yleaf-pipelines - A pipeline-optimized version of Yleaf, a tool for...
ymp 0.3.2 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 1.3.11 doc dev MIT X zDB is both a bacterial comparative genomics pipeline and a tool to...
zeroc-ice 3.7.1 GPL XX Ice is a comprehensive RPC framework that helps you network your...
zerone 1.0 dev GPL-3.0-or-later XX 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 XXX Dimensionality reduction for zero-inflated single-cell gene expression analysis
zipstrain 0.2.21 MIT X Fast strain-level metagenomics
zmwfilter 1.0.0 BSD-3-Clause-Clear XX PacBio utility to filter reads on ZMW ID(s)
zol 1.6.17 doc dev BSD-3-Clause XX zol (& fai): large-scale targeted detection and evolutionary...
zorro 2011.12.01 Apache XX ZORRO is a probabilistic masking program that assigns confidence scores...
zpca 0.8.3.post1 Apache X PCA analysis for genes or transcripts.
Updated: 2026-01-03 08:22:41 +0000 - Files: 11790