Man pages for grst/immunedeconv
Methods for immune cell deconvolution

annotate_cell_typeAnnotate unified cell_type names
available_datasetsAvailable methods and datasets.
cell_type_mapTable mapping the cell types from methods/datasets to a...
cell_type_mappingFunctions for mapping cell types between deconvolution...
cell_type_treeAvailable cell types in the controlled vocabulary organized...
check_cancer_typesprocess batch table and check cancer types.
deconvolutePerform an immune cell deconvolution on a dataset.
deconvolute_quantiseq.defaultUse quanTIseq to deconvolute a gene expression matrix.
deconvolute_timerDeconvolute using the TIMER technique
deconvolution_methodsList of supported immune deconvolution methods
eset_to_matrixConvert a 'Biobase::ExpressionSet' to a gene-expression...
example_gene_expression_matrixexample gene expression dataset
find_childrenrecursively traverse the cell type tree to resolve the...
GetFractions.AbbasConstrained regression method implemented in Abbas et al.,...
immune_deconvolution_methodsCollection of immune cell deconvolution methods.
make_bulk_esetMake a random expression set from a single-cell dataset
make_random_bulkMake a random bulk sample from a single-cell dataset
map_cell_typesUse a tree-hierarchy to map cell types among different...
map_result_to_celltypesMap a result table as generated by 'deconvolute' to a...
quantiseq_helperHelper functions for quanTIseq
scale_to_millionScale sample to TPM
set_cibersort_binarySet Path to CIBERSORT R script ('CIBERSORT.R')
set_cibersort_matSet Path to CIBERSORT matrix file ('LM22.txt')
single_cell_simulationFunctions for generating simulated bulk samples from a single...
summarise_childrensum up the fraction of all child nodes to a single value....
timerSource code for the TIMER deconvolution method.
timer_available_cancersTIMER signatures are cancer specific. This is the list of...
xCell.dataData object from xCell.
grst/immunedeconv documentation built on Nov. 11, 2018, 11:05 p.m.