Files in saezlab/decoupleR
decoupleR: Ensemble of computational methods to infer biological activities from omics data
.Rbuildignore
.bumpversion.cfg
.github/ISSUE_TEMPLATE/issue_template.md
.github/workflows/check-bioc.yml
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md
R/decoupleR-consensus.R
R/decoupleR-decouple.R
R/decoupleR-package.R
R/decoupleR-pre.R
R/statistic-aucell.R
R/statistic-fgsea.R
R/statistic-gsva.R
R/statistic-mdt.R
R/statistic-mlm.R
R/statistic-ora.R
R/statistic-udt.R
R/statistic-ulm.R
R/statistic-viper.R
R/statistic-wmean.R
R/statistic-wsum.R
R/statistic-zscore.R
R/utils-dataset-converters.R
R/utils-decoupler-formats.R
R/utils-omnipath.R
R/utils-pipe.R
R/utils-profiles.R
R/utils-randomize-matrix.R
R/utils-tidy-eval.R
README.Rmd
README.md
_pkgdown.yml
codecov.yml
inst/CITATION
inst/extdata/bk_data.rds
inst/extdata/sc_data.rds
inst/figures/graphical_abstract.png
inst/figures/logo.svg
inst/figures/net_plot.png
inst/testdata/README.md
inst/testdata/generate_expected_output.R
inst/testdata/inputs/mat.rds
inst/testdata/inputs/net.rds
inst/testdata/outputs/aucell/output-aucell.rds
inst/testdata/outputs/decouple/output-decouple.rds
inst/testdata/outputs/fgsea/output-fgsea.rds
inst/testdata/outputs/gsva/output-gsva.rds
inst/testdata/outputs/mdt/output-mdt.rds
inst/testdata/outputs/mlm/output-mlm.rds
inst/testdata/outputs/ora/output-ora.rds
inst/testdata/outputs/udt/output-udt.rds
inst/testdata/outputs/ulm/output-ulm.rds
inst/testdata/outputs/viper/output-viper.rds
inst/testdata/outputs/wmean/output-wmean.rds
inst/testdata/outputs/wsum/output-wsum.rds
man/check_corr.Rd
man/convert_f_defaults.Rd
man/decouple.Rd
man/decoupleR-package.Rd
man/dot-decoupler_mat_format.Rd
man/dot-decoupler_network_format.Rd
man/dot-fit_preprocessing.Rd
man/extract_sets.Rd
man/figures/logo.svg
man/filt_minsize.Rd
man/get_collectri.Rd
man/get_dorothea.Rd
man/get_ksn_omnipath.Rd
man/get_profile_of.Rd
man/get_progeny.Rd
man/get_resource.Rd
man/get_toy_data.Rd
man/intersect_regulons.Rd
man/pipe.Rd
man/pivot_wider_profile.Rd
man/randomize_matrix.Rd
man/rename_net.Rd
man/run_aucell.Rd
man/run_consensus.Rd
man/run_fgsea.Rd
man/run_gsva.Rd
man/run_mdt.Rd
man/run_mlm.Rd
man/run_ora.Rd
man/run_udt.Rd
man/run_ulm.Rd
man/run_viper.Rd
man/run_wmean.Rd
man/run_wsum.Rd
man/show_methods.Rd
man/show_resources.Rd
man/tidyeval.Rd
pkgdown/extra.css
pkgdown/favicon/apple-touch-icon-120x120.png
pkgdown/favicon/apple-touch-icon-152x152.png
pkgdown/favicon/apple-touch-icon-180x180.png
pkgdown/favicon/apple-touch-icon-60x60.png
pkgdown/favicon/apple-touch-icon-76x76.png
pkgdown/favicon/apple-touch-icon.png
pkgdown/favicon/favicon-16x16.png
pkgdown/favicon/favicon-32x32.png
pkgdown/favicon/favicon.ico
tests/testthat.R
tests/testthat/test-decoupleR-decouple.R
tests/testthat/test-decoupleR-pre.R
tests/testthat/test-omnipath.R
tests/testthat/test-statistic-aucell.R
tests/testthat/test-statistic-fgsea.R
tests/testthat/test-statistic-gsva.R
tests/testthat/test-statistic-mdt.R
tests/testthat/test-statistic-mlm.R
tests/testthat/test-statistic-ora.R
tests/testthat/test-statistic-udt.R
tests/testthat/test-statistic-ulm.R
tests/testthat/test-statistic-viper.R
tests/testthat/test-statistic-wmean.R
tests/testthat/test-statistic-wsum.R
tests/testthat/test-statistic-zscore.R
tests/testthat/test-utils-dataset-converters.R
tests/testthat/test-utils-profiles.R
vignettes/.gitignore
vignettes/decoupleR.Rmd
vignettes/pw_bk.Rmd
vignettes/pw_sc.Rmd
vignettes/tf_bk.Rmd
vignettes/tf_sc.Rmd
