Files in ctlab/fgsea
Fast Gene Set Enrichment Analysis
.Rbuildignore
.gitattributes
.github/workflows/R-CMD-check.yaml
.gitignore
DESCRIPTION
LICENCE
NAMESPACE
NEWS
R/RcppExports.R
R/fgsea-package.R
R/fgsea.R
R/fgseaMultilevel.R
R/fgseaORA.R
R/geseca-multilevel.R
R/geseca-plot.R
R/geseca-simple.R
R/geseca-utils.R
R/pathways.R
R/plot.R
R/util.R
README.md
data-raw/exampleExpressionMatrix.R
data-raw/examplePathways.R
data-raw/exampleRanks.R
data/exampleExpressionMatrix.rda
data/examplePathways.rda
data/exampleRanks.rda
fgsea.Rproj
inst/CITATION
inst/exact/exact.cpp
inst/exact/exact_readme.md
inst/exact/runFgsea.R
inst/extdata/GDS289.tsv
inst/extdata/fgsea_res.tsv
inst/extdata/gse14308_expression_matrix.tsv
inst/extdata/mouse.reactome.gmt
inst/extdata/naive.vs.th1.rnk
inst/extdata/pathway.txt
inst/gen_gene_ranks.R
inst/gen_gse14308_expression_matrix.R
inst/gene_reactome_pathways.R
inst/gse19429_gsea.R
inst/run_broad_gsea.R
inst/th1_gsea.R
man/calcGseaStat.Rd
man/calcGseaStatBatchCpp.Rd
man/collapsePathways.Rd
man/collapsePathwaysGeseca.Rd
man/collapsePathwaysORA.Rd
man/exampleExpressionMatrix.Rd
man/examplePathways.Rd
man/exampleRanks.Rd
man/fgsea.Rd
man/fgseaLabel.Rd
man/fgseaMultilevel.Rd
man/fgseaSimple.Rd
man/fgseaSimpleImpl.Rd
man/fora.Rd
man/geseca.Rd
man/gesecaSimple.Rd
man/gmtPathways.Rd
man/mapIdsList.Rd
man/multilevelError.Rd
man/multilevelImpl.Rd
man/plotCoregulationProfile.Rd
man/plotCoregulationProfileReduction.Rd
man/plotCoregulationProfileSpatial.Rd
man/plotEnrichment.Rd
man/plotEnrichmentData.Rd
man/plotGesecaTable.Rd
man/plotGseaTable.Rd
man/reactomePathways.Rd
man/writeGmtPathways.Rd
src/RcppExports.cpp
src/ScoreCalculation.cpp
src/ScoreCalculation.h
src/ScoreRuler.cpp
src/ScoreRuler.h
src/esCalculation.cpp
src/esCalculation.h
src/fastGSEA.cpp
src/fastGSEA.h
src/fgseaMultilevel.cpp
src/fgseaMultilevel.h
src/fgseaMultilevelSupplement.cpp
src/fgseaMultilevelSupplement.h
src/geseca.cpp
src/geseca.h
src/util.cpp
src/util.h
test.R
tests/testthat.R
tests/testthat/test_fora.R
tests/testthat/test_geseca.R
tests/testthat/test_gsea_analysis.R
tests/testthat/test_gsea_multilevel.R
tests/testthat/test_gsea_stat.R
tests/testthat/test_pathways.R
tests/testthat/test_plot.R
vignettes/fgsea-tutorial.Rmd
vignettes/geseca-spatial-top.png
vignettes/geseca-tutorial.Rmd
vignettes/geseca-tutorial.md
vignettes/geseca-vignette-score-toy-example.png
