Files in lianos/multiGSEA
A unified interface to a plethora of gene set enrichment analysis methods
.Rbuildignore
.gitattributes
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.github/workflows/pkgdown.yaml
.github/workflows/test-coverage.yaml
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
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
codecov.yml
docs/404.html
docs/LICENSE-text.html
docs/articles/images/icons/callout-border.png
docs/articles/images/icons/caution.png
docs/articles/images/icons/download.png
docs/articles/images/icons/example.png
docs/articles/images/icons/important.png
docs/articles/images/icons/note.png
docs/articles/images/icons/tip.png
docs/articles/images/icons/warning.png
docs/articles/index.html
docs/articles/multiGSEA.html
docs/articles/multiGSEA_files/crosstalk-1.0.0/css/crosstalk.css
docs/articles/multiGSEA_files/crosstalk-1.0.0/js/crosstalk.js
docs/articles/multiGSEA_files/crosstalk-1.0.0/js/crosstalk.js.map
docs/articles/multiGSEA_files/crosstalk-1.0.0/js/crosstalk.min.js
docs/articles/multiGSEA_files/crosstalk-1.0.0/js/crosstalk.min.js.map
docs/articles/multiGSEA_files/figure-html/anno-scores-1.png
docs/articles/multiGSEA_files/figure-html/gheatmap-1.png
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docs/articles/multiGSEA_files/htmlwidgets-1.5.1/htmlwidgets.js
docs/articles/multiGSEA_files/jquery-1.11.3/jquery-AUTHORS.txt
docs/articles/multiGSEA_files/jquery-1.11.3/jquery.js
docs/articles/multiGSEA_files/jquery-1.11.3/jquery.min.js
docs/articles/multiGSEA_files/jquery-1.11.3/jquery.min.map
docs/articles/multiGSEA_files/plotly-binding-4.9.2/plotly.js
docs/articles/multiGSEA_files/plotly-htmlwidgets-css-1.52.2/plotly-htmlwidgets.css
docs/articles/multiGSEA_files/plotly-main-1.52.2/plotly-latest.min.js
docs/articles/multiGSEA_files/typedarray-0.1/typedarray.min.js
docs/articles/mystyles.css
docs/authors.html
docs/docsearch.css
docs/docsearch.js
docs/extra.css
docs/index.html
docs/link.svg
docs/news/index.html
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/GeneSetDb-class.html
docs/reference/MultiGSEAResult-utilities.html
docs/reference/MultiGSEAResult.html
docs/reference/addGeneSetMetadata.html
docs/reference/all.equal.GeneSetDb.html
docs/reference/annotateGeneSetMembership.html
docs/reference/append-GeneSetDb-ANY-method.html
docs/reference/calculateIndividualLogFC.html
docs/reference/collectionMetadata.html
docs/reference/combine-GeneSetDb-GeneSetDb-method.html
docs/reference/combine-MultiGSEAResult-MultiGSEAResult-method.html
docs/reference/conform.html
docs/reference/conversion.html
docs/reference/corplot-1.png
docs/reference/corplot.html
docs/reference/do.fgsea.html
docs/reference/do.goseq.html
docs/reference/eigenWeightedMean.html
docs/reference/examples.html
docs/reference/failWith.html
docs/reference/featureIdMap.html
docs/reference/featureIds.html
docs/reference/figures/README_iplot_boxplot.png
docs/reference/figures/README_iplot_density.png
docs/reference/geneSet.html
docs/reference/geneSetSummaryByGenes.html
docs/reference/geneSets.html
docs/reference/geneSetsStats.html
docs/reference/getHousekeepingGeneSetDb.html
docs/reference/getMSigGeneSetDb.html
docs/reference/getPantherGeneSetDb.html
docs/reference/getReactomeGeneSetDb.html
docs/reference/goseq.html
docs/reference/gsdScore.html
docs/reference/gskey.html
docs/reference/hasGeneSet.html
docs/reference/hasGeneSetCollection.html
docs/reference/incidenceMatrix.html
docs/reference/index.html
docs/reference/iplot.html
docs/reference/is.active.html
docs/reference/logFC.html
docs/reference/mgheatmap.html
docs/reference/mgheatmap2-1.png
docs/reference/mgheatmap2.html
docs/reference/msg.html
docs/reference/multiGSEA.html
docs/reference/multiGSEA_methods.html
docs/reference/ora-1.png
docs/reference/ora-2.png
docs/reference/ora.html
docs/reference/p.matrix.html
docs/reference/pcWeightedMean.html
docs/reference/plot_ora_bias.html
docs/reference/rename_rows.html
docs/reference/results.html
docs/reference/scale_rows.html
docs/reference/scoreSingleSamples-1.png
docs/reference/scoreSingleSamples.html
docs/reference/ssGSEA.normalize.html
docs/reference/sub-GeneSetDb-ANY-ANY-ANY-method.html
docs/reference/subset.GeneSetDb.html
docs/reference/subsetByFeatures.html
docs/reference/summarized.html
docs/reference/validateInputs.html
docs/reference/volcanoPlot.html
docs/reference/volcanoStatsTable.html
docs/reference/zScore.html
docs/reference/ztransformPvalues.html
etc/Q-Gen/q-gen-help.md
etc/Q-Gen/q-gen.R
inst/extdata/gsea-methods.csv
inst/extdata/identifiers/human-entrez-ensembl.csv.gz
inst/extdata/identifiers/mouse-entrez-ensembl.csv.gz
inst/extdata/signatures/housekeeping/qiagen-rt2-pcr-array.csv
inst/extdata/species-info.csv
inst/extdata/testdata/TCGA-BRCA-some.DGEList.rds
inst/extdata/testdata/TCGA-BRCA-some.es.rds
inst/extdata/testdata/create-test-MultiGSEAResult.R
inst/extdata/testdata/custom-sigs.csv
inst/extdata/testdata/dataframe-input.csv
inst/extdata/testdata/genesets-multiGSEA-list-of-lists.rds
inst/extdata/testdata/setup-testdata.R
inst/extdata/testdata/test-MultiGSEAResult.rds
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/figures/README_iplot_boxplot.png
man/figures/README_iplot_density.png
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
multiGSEA.Rproj
multiGSEA.code-workspace
pkgdown/_pkgdown.yml
pkgdown/extra.css
tests/facile-usecases/facile-dge.R
tests/testthat.R
tests/testthat/.gitignore
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/clean.sh
vignettes/images/icons/INFO.txt
vignettes/images/icons/callout-border.png
vignettes/images/icons/callouts/1.png
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vignettes/images/icons/caution.png
vignettes/images/icons/download.png
vignettes/images/icons/example.png
vignettes/images/icons/home.png
vignettes/images/icons/important.png
vignettes/images/icons/next.png
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vignettes/images/icons/prev.png
vignettes/images/icons/tip.png
vignettes/images/icons/up.png
vignettes/images/icons/warning.png
vignettes/multiGSEA.Rmd
vignettes/mystyles.css
