Files in lianos/multiGSEA

A unified interface to a plethora of gene set enrichment analysis methods

NEWS.md R/AllClasses.R R/AllGenerics.R R/GeneSetDb-class.R R/GeneSetDb-methods.R R/MultiGSEAResult-methods.R R/aaa.R R/bioc-accessors.R R/calculateIndividualLogFC.R R/do.camera.R R/do.cameraPR.R R/do.fgsea.R R/do.fry.R R/do.geneSetTest.R R/do.goseq.R R/do.logFC.R R/do.ora.R R/do.roast.R R/do.romer.R R/do.svdGeneSetTest.R R/geneSetSummaryByGenes.R R/get-housekeeping.R R/get-msigdb.R R/get-panther.R R/get-reactome.R R/getKeggGeneSetDb.R R/gsea-helpers.R R/multiGSEA.R R/package.R R/plots-corplot.R R/plots-interactive.R R/plots-mgheatmap.R R/plots-mgheatmap2.R R/remap_identifiers.R R/rename_rows.R R/scale_rows.R R/scoreSingleSamples.R R/single-sample-scoring-methods.R R/species.R R/testing-helpers.R R/utilities.R R/validateInputs.R R/volcano_plot.R R/zzz.R README.Rmd README.md etc/Q-Gen/q-gen-help.md etc/Q-Gen/q-gen.R inst/extdata/testdata/create-test-MultiGSEAResult.R inst/extdata/testdata/setup-testdata.R inst/scripts/generate-id-maps.R man-roxygen/asdt-param.R man/GeneSetDb-class.Rd man/MultiGSEAResult-utilities.Rd man/MultiGSEAResult.Rd man/addGeneSetMetadata.Rd man/all.equal.GeneSetDb.Rd man/annotateGeneSetMembership.Rd man/append-GeneSetDb-ANY-method.Rd man/calculateIndividualLogFC.Rd man/collectionMetadata.Rd man/combine-GeneSetDb-GeneSetDb-method.Rd man/combine-MultiGSEAResult-MultiGSEAResult-method.Rd man/conform.Rd man/conversion.Rd man/corplot.Rd man/do.fgsea.Rd man/do.goseq.Rd man/eigenWeightedMean.Rd man/examples.Rd man/failWith.Rd man/featureIdMap.Rd man/featureIds.Rd man/geneSet.Rd man/geneSetSummaryByGenes.Rd man/geneSets.Rd man/geneSetsStats.Rd man/getHousekeepingGeneSetDb.Rd man/getKeggGeneSetDb.Rd man/getMSigGeneSetDb.Rd man/getPantherGeneSetDb.Rd man/getReactomeGeneSetDb.Rd man/goseq.Rd man/gsdScore.Rd man/gskey.Rd man/hasGeneSet.Rd man/hasGeneSetCollection.Rd man/incidenceMatrix.Rd man/iplot.Rd man/is.active.Rd man/load_id_xref.Rd man/logFC.Rd man/mgheatmap.Rd man/mgheatmap2.Rd man/msg.Rd man/multiGSEA.Rd man/multiGSEA_methods.Rd man/ora.Rd man/p.matrix.Rd man/pcWeightedMean.Rd man/plot_ora_bias.Rd man/remap_identifiers.Rd man/rename_rows.Rd man/results.Rd man/scale_rows.Rd man/scoreSingleSamples.Rd man/species_info.Rd man/ssGSEA.normalize.Rd man/sub-GeneSetDb-ANY-ANY-ANY-method.Rd man/subset.GeneSetDb.Rd man/subsetByFeatures.Rd man/summarized.Rd man/validateInputs.Rd man/volcanoPlot.Rd man/volcanoStatsTable.Rd man/zScore.Rd man/ztransformPvalues.Rd tests/facile-usecases/facile-dge.R tests/testthat.R tests/testthat/helper-init-test-env.R tests/testthat/test-GeneSetDb.R tests/testthat/test-MultiGSEAResult.R tests/testthat/test-adversarial-gsea.R tests/testthat/test-calculateIndividualLogFC.R tests/testthat/test-camera.R tests/testthat/test-dataframe-input.R tests/testthat/test-edgeR.R tests/testthat/test-fgsea.R tests/testthat/test-fry.R tests/testthat/test-geneSetSummaryByGenes.R tests/testthat/test-geneSetTest.R tests/testthat/test-geneSetsStats.R tests/testthat/test-getMSigGeneSetDb.R tests/testthat/test-goseq.R tests/testthat/test-iplot.R tests/testthat/test-logFC.R tests/testthat/test-multiGSEA.R tests/testthat/test-ora.R tests/testthat/test-panther.R tests/testthat/test-remap_identifiers.R tests/testthat/test-rename_rows.R tests/testthat/test-roast.R tests/testthat/test-romer.R tests/testthat/test-scale_rows.R tests/testthat/test-scoreSingleSamples.R tests/testthat/test-users.R tests/testthat/test-volcano_plot.R vignettes/multiGSEA.Rmd