Files in lianos/sparrow
Take command of set enrichment analyses through a unified interface
.Rbuildignore
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.github/workflows/build-devel-image.yaml
.github/workflows/build-release-image.yaml
.github/workflows/pkgdown.yaml
.github/workflows/test-coverage.yaml
.gitignore
DESCRIPTION
LICENSE
Makefile
NAMESPACE
NEWS.md
R/AllClasses.R
R/AllGenerics.R
R/GeneSetDb-class.R
R/GeneSetDb-methods.R
R/SparrowResult-methods.R
R/aaa.R
R/bioc-accessors.R
R/calculateIndividualLogFC.R
R/convertIdentifiers.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-kegg.R
R/get-msigdb.R
R/get-panther.R
R/get-reactome.R
R/gsea-helpers.R
R/package.R
R/plots-corplot.R
R/plots-interactive.R
R/plots-mgheatmap.R
R/plots-mgheatmap2.R
R/renameCollections.R
R/renameRows.R
R/scale_rows.R
R/scoreSingleSamples.R
R/seas.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
docker/Rprofile.site
docker/devel/Dockerfile
docker/devel/install.R
docker/devel/packages.txt
docker/release/Dockerfile
docker/release/install.R
docker/release/packages.txt
inst/extdata/gsea-methods.csv
inst/extdata/species-info.csv
inst/extdata/testdata/TCGA-BRCA-some.DGEList.rds
inst/extdata/testdata/create-test-SparrowResult.R
inst/extdata/testdata/custom-sigs.csv
inst/extdata/testdata/dataframe-input-short.csv.gz
inst/extdata/testdata/genesets-sparrow-list-of-lists.rds
inst/extdata/testdata/setup-dataframe-input.R
inst/extdata/testdata/setup-testdata.R
inst/extdata/testdata/test-SparrowResult.rds
inst/images/README.md
inst/images/jacksparrow-01.png
inst/scripts/generate-example-data.R
inst/scripts/generate-id-maps.R
inst/scripts/hexSticker.R
man-roxygen/asdt-param.R
man-roxygen/random-seed-param.R
man/GeneSetDb-class.Rd
man/SparrowResult-utilities.Rd
man/SparrowResult.Rd
man/addGeneSetMetadata.Rd
man/all.equal.GeneSetDb.Rd
man/annotateGeneSetMembership.Rd
man/calculateIndividualLogFC.Rd
man/collectionMetadata.Rd
man/combine-GeneSetDb-GeneSetDb-method.Rd
man/combine-SparrowResult-SparrowResult-method.Rd
man/conform.Rd
man/conversion.Rd
man/convertIdentifiers.Rd
man/corplot.Rd
man/eigenWeightedMean.Rd
man/examples.Rd
man/failWith.Rd
man/featureIdMap.Rd
man/featureIds.Rd
man/figures/README_iplot_density.png
man/figures/README_iplot_gsea.png
man/figures/sparrow.png
man/geneSet.Rd
man/geneSetCollectionURLfunction.Rd
man/geneSetSummaryByGenes.Rd
man/geneSets.Rd
man/geneSetsStats.Rd
man/getKeggCollection.Rd
man/getMSigCollection.Rd
man/getPantherCollection.Rd
man/getReactomeCollection.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/logFC.Rd
man/mgheatmap.Rd
man/mgheatmap2.Rd
man/msg.Rd
man/ora.Rd
man/p.matrix.Rd
man/randomGeneSetDb.Rd
man/renameCollections.Rd
man/renameRows.Rd
man/results.Rd
man/scale_rows.Rd
man/scoreSingleSamples.Rd
man/seas.Rd
man/sparrow_methods.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/validateInputs.Rd
man/volcanoPlot.Rd
man/volcanoStatsTable.Rd
man/zScore.Rd
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/setup.R
tests/testthat/test-GeneSetDb-url_function-environment.R
tests/testthat/test-GeneSetDb.R
tests/testthat/test-MultiGSEAResult.R
tests/testthat/test-calculateIndividualLogFC.R
tests/testthat/test-camera.R
tests/testthat/test-convertIdentifiers.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-get-msigdb.R
tests/testthat/test-get-panther.R
tests/testthat/test-goseq.R
tests/testthat/test-iplot.R
tests/testthat/test-logFC.R
tests/testthat/test-ora.R
tests/testthat/test-renameCollections.R
tests/testthat/test-renameRows.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-seas.R
tests/testthat/test-users.R
tests/testthat/test-volcano_plot.R
vignettes/.gitignore
vignettes/WIP/README
vignettes/WIP/adding-new-methods-to-sparrow.Rmd
vignettes/clean.sh
vignettes/images/icons/INFO.txt
vignettes/images/icons/callout-border.png
vignettes/images/icons/callouts/1.png
vignettes/images/icons/callouts/10.png
vignettes/images/icons/callouts/11.png
vignettes/images/icons/callouts/12.png
vignettes/images/icons/callouts/13.png
vignettes/images/icons/callouts/14.png
vignettes/images/icons/callouts/15.png
vignettes/images/icons/callouts/2.png
vignettes/images/icons/callouts/3.png
vignettes/images/icons/callouts/4.png
vignettes/images/icons/callouts/5.png
vignettes/images/icons/callouts/6.png
vignettes/images/icons/callouts/7.png
vignettes/images/icons/callouts/8.png
vignettes/images/icons/callouts/9.png
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
vignettes/images/icons/note.png
vignettes/images/icons/prev.png
vignettes/images/icons/tip.png
vignettes/images/icons/up.png
vignettes/images/icons/warning.png
vignettes/images/sparrow-shiny.png
vignettes/images/static-iplot-wnt-beta-box.png
vignettes/images/static-iplot-wnt-beta-density.png
vignettes/images/static-iplot-wnt-beta-gsea.png
vignettes/mystyles.css
vignettes/sparrow.Rmd
