Files in grst/immunedeconv
Methods for immune cell deconvolution

.Rbuildignore

.conda/meta.yaml

.gitattributes

.github/.gitignore

.github/ISSUE_TEMPLATE/bug-report.md

.github/ISSUE_TEMPLATE/config.yml

.github/ISSUE_TEMPLATE/feature-request.md

.github/workflows/conda.yml

.github/workflows/pkgdown.yml

.github/workflows/roxygenize.yml

.github/workflows/test-coverage.yml

.github/workflows/test.yml

.gitignore

.pre-commit-config.yaml

.prettierignore

CONTRIBUTING.md

DESCRIPTION

LICENSE

Makefile

NAMESPACE

R/BASE.R R/abis.R R/cell_type_mapping.R R/config.R R/custom_deconvolution_methods.R R/datasets.R R/estimate.R R/immune_deconvolution_methods.R R/mouse_cell_type_mapping.R R/mouse_deconvolution_methods.R R/seqImmuCC_LLSR.R R/single_cell_simulation.R R/timer.R R/zzz.R README.md

_pkgdown.yml

codecov.yml

data/dataset_petitprez.rda

data/dataset_racle.rda

inst/extdata/abis/sigmatrixMicro.txt

inst/extdata/abis/sigmatrixRNAseq.txt

inst/extdata/abis/target.txt

inst/extdata/cell_type_mapping.xlsx

inst/extdata/estimate/estimate_genes.rds

inst/extdata/fantom5_expression_set.rda

inst/extdata/mouse_deconvolution/BASE_cell_compendium.rds

inst/extdata/mouse_deconvolution/cell_correspondance.txt

inst/extdata/mouse_deconvolution/sig_matr_seqImmuCC.txt

inst/extdata/quantiseq/HGNC_genenames_20170418.txt

inst/extdata/quantiseq/TIL10_TCGA_aberrant_immune_genes.txt

inst/extdata/quantiseq/TIL10_mRNA_scaling.txt

inst/extdata/quantiseq/TIL10_rmgenes.txt

inst/extdata/quantiseq/TIL10_signature.txt

inst/extdata/timer/immune_datasets/HPCTimmune.Rdata

inst/extdata/timer/immune_datasets/IRIS-marker-gene.txt

inst/extdata/timer/precalculated/genes_acc.RData

inst/extdata/timer/precalculated/genes_blca.RData

inst/extdata/timer/precalculated/genes_brca.RData

inst/extdata/timer/precalculated/genes_cesc.RData

inst/extdata/timer/precalculated/genes_chol.RData

inst/extdata/timer/precalculated/genes_coad.RData

inst/extdata/timer/precalculated/genes_dlbc.RData

inst/extdata/timer/precalculated/genes_esca.RData

inst/extdata/timer/precalculated/genes_gbm.RData

inst/extdata/timer/precalculated/genes_hnsc.RData

inst/extdata/timer/precalculated/genes_kich.RData

inst/extdata/timer/precalculated/genes_kirc.RData

inst/extdata/timer/precalculated/genes_kirp.RData

inst/extdata/timer/precalculated/genes_lgg.RData

inst/extdata/timer/precalculated/genes_lihc.RData

inst/extdata/timer/precalculated/genes_luad.RData

inst/extdata/timer/precalculated/genes_lusc.RData

inst/extdata/timer/precalculated/genes_meso.RData

inst/extdata/timer/precalculated/genes_ov.RData

inst/extdata/timer/precalculated/genes_paad.RData

inst/extdata/timer/precalculated/genes_pcpg.RData

inst/extdata/timer/precalculated/genes_prad.RData

inst/extdata/timer/precalculated/genes_read.RData

inst/extdata/timer/precalculated/genes_sarc.RData

inst/extdata/timer/precalculated/genes_skcm.RData

inst/extdata/timer/precalculated/genes_stad.RData

inst/extdata/timer/precalculated/genes_tgct.RData

inst/extdata/timer/precalculated/genes_thca.RData

inst/extdata/timer/precalculated/genes_thym.RData

inst/extdata/timer/precalculated/genes_ucec.RData

inst/extdata/timer/precalculated/genes_ucs.RData

inst/extdata/timer/precalculated/genes_uvm.RData

inst/extdata/timer/precalculated/immune.expression.curated.RData

man/figures/immunedeconv_logo.png

man/figures/immunedeconv_logo_sm.png

man/find_children.Rd man/fix_namespace.Rd man/get_all_children.Rd man/get_dcq_cell_types_list.Rd man/immunedeconv.Rd man/make_bulk_eset.Rd man/make_random_bulk.Rd man/map_cell_types.Rd man/map_result_to_celltypes.Rd man/mouse_cell_type_mapping.Rd man/mouse_deconvolution.Rd man/node_by_name.Rd man/reduce_mouse_cell_types.Rd man/scale_to_million.Rd man/seqImmuCC_LLSR.Rd man/set_cibersort_binary.Rd man/set_cibersort_mat.Rd man/single_cell_simulation.Rd man/summarise_children.Rd man/timer.Rd man/timer_available_cancers.Rd man/xCell.data.Rd tests/testthat.R

tests/testthat/.c

tests/testthat/bulk_mat.tsv

tests/testthat/bulk_mat_mouse.tsv

tests/testthat/test_custom_matrices.R tests/testthat/test_deconvolution.R tests/testthat/test_deconvolution_mouse.R tests/testthat/test_mapping.R tests/testthat/test_simulation.R vignettes/detailed_example.Rmd vignettes/detailed_example_mouse.Rmd

vignettes/img/concepts_deconvolution.gif

vignettes/immunedeconv.Rmd

vignettes/references.bib

grst/immunedeconv documentation built on Nov. 10, 2023, 1:33 a.m.

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grst/immunedeconv
Methods for immune cell deconvolution

Files in grst/immunedeconv
Methods for immune cell deconvolution

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grst/immunedeconv Methods for immune cell deconvolution

Files in grst/immunedeconv Methods for immune cell deconvolution

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grst/immunedeconv
Methods for immune cell deconvolution

Files in grst/immunedeconv
Methods for immune cell deconvolution