Methods for immune cell deconvolution

[Up] [Top]

Documentation for package ‘immunedeconv’ version 2.0.0

Help Pages

immunedeconv-package Collection of immune cell deconvolution methods.
.get_all_children Recursive helper function for get_all_children.
annotate_cell_type Annotate unified cell_type names
available_datasets Available methods and datasets.
cell_type_map Table mapping the cell types from methods/datasets to a single, controlled vocabulary.
cell_type_mapping Functions for mapping cell types between deconvolution methods and datasets.
cell_type_tree Available cell types in the controlled vocabulary organized as a lineage tree.
check_cancer_types process batch table and check cancer types.
dataset_racle Example RNA-seq dataset from the EPIC publication.
deconvolute Perform an immune cell deconvolution on a dataset.
deconvolute_cibersort Deconvolute using CIBERSORT or CIBERSORT abs.
deconvolute_epic Deconvolute using EPIC
deconvolute_mcp_counter Deconvolute using MCP-counter
deconvolute_quantiseq Deconvolute using quanTIseq
deconvolute_quantiseq.default Use quanTIseq to deconvolute a gene expression matrix.
deconvolute_timer Deconvolute using TIMER
deconvolute_xcell Deconvolute using xCell
deconvolution_methods List of supported immune deconvolution methods
eset_to_matrix Convert a 'Biobase::ExpressionSet' to a gene-expression matrix.
find_children Recursive helper function for map_cell_types.
GetFractions.Abbas Constrained regression method implemented in Abbas et al., 2009
get_all_children Get all children of a certain cell type.
immunedeconv Collection of immune cell deconvolution methods.
make_bulk_eset Make a random expression set from a single-cell dataset
make_random_bulk Make a random bulk sample from a single-cell dataset
map_cell_types Use a tree-hierarchy to map cell types among different methods.
map_result_to_celltypes Map a result table as generated by 'deconvolute' to a user-defined list of cell types.
quantiseq_helper Helper functions for quanTIseq
scale_to_million Scale sample to TPM
set_cibersort_binary Set Path to CIBERSORT R script ('CIBERSORT.R')
set_cibersort_mat Set Path to CIBERSORT matrix file ('LM22.txt')
single_cell_simulation Functions for generating simulated bulk samples from a single cell dataset.
summarise_children sum up the fraction of all child nodes to a single value. Take into account which cell types are optional.
timer Source code for the TIMER deconvolution method.
timer_available_cancers TIMER signatures are cancer specific. This is the list of available cancer types.
xCell.data Data object from xCell.