Package: sparrow 1.11.0
sparrow: Take command of set enrichment analyses through a unified interface
Provides a unified interface to a variety of GSEA techniques from different bioconductor packages. Results are harmonized into a single object and can be interrogated uniformly for quick exploration and interpretation of results. Interactive exploration of GSEA results is enabled through a shiny app provided by a sparrow.shiny sibling package.
Authors:
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NEWS
# Install 'sparrow' in R: |
install.packages('sparrow', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/lianos/sparrow/issues
On BioConductor:sparrow-1.11.0(bioc 3.20)sparrow-1.10.1(bioc 3.19)
Last updated 2 months agofrom:52fa858161
Exports:addCollectionMetadataaddGeneSetMetadataannotateGeneSetMembershipcalculateIndividualLogFCcollectionMetadatacombineconformconvertIdentifierscorploteigenWeightedMeanencode_gskeyexampleBiocSetexampleDgeResultexampleExpressionSetexampleGeneSetDbexampleGeneSetDFexampleGeneSetsexampleSparrowResultfailWithfeatureIdMapfeatureIdsfeatureIdTypefeatureIdType<-geneSetgeneSetCollectionURLfunctiongeneSetCollectionURLfunction<-geneSetDbGeneSetDbgeneSetsgeneSetsStatsgeneSetSummaryByGenesgeneSetURLgetKeggCollectiongetKeggGeneSetDbgetMSigCollectiongetMSigGeneSetDbgetPantherCollectiongetPantherGeneSetDbgetReactomeCollectiongoseqgsdScorehasGeneSethasGeneSetCollectionincidenceMatrixiplotis.activeis.conformedlogFCmgheatmapmgheatmap2msgnroworap.matrixplot_ora_biasrandomGeneSetDbrenameCollectionsrenameRowsresultresultNamesresultsscale_rowsscoreSingleSamplesseassparrow_methodsspecies_infosplit_gskeysubsetByFeaturestabulateResultsunconformvalidateInputsvolcanoPlotvolcanoStatsTablezScore
Dependencies:abindannotateAnnotationDbiaskpassbabelgenebackportsbase64encBHBiobaseBiocGenericsBiocIOBiocParallelBiocSetBiostringsbitbit64blobbslibcachemcheckmatecirclizecliclueclustercodetoolscolorspaceComplexHeatmapcpp11crayoncrosstalkcurldata.tableDBIDelayedArrayDelayedMatrixStatsdigestdoParalleldplyredgeRevaluatefansifarverfastmapfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGetoptLongggplot2GlobalOptionsgluegraphgridExtraGSEABasegtablehighrhtmltoolshtmlwidgetshttrIRangesirlbaisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeontologyIndexopensslpillarpkgconfigplogrplotlyplyrpngpromisespurrrR6rappdirsRColorBrewerRcpprjsonrlangrmarkdownRSQLiteS4ArraysS4VectorssassscalesshapesnowSparseArraysparseMatrixStatsstatmodstringistringrsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisviridisLitewithrxfunXMLxtableXVectoryamlzlibbioc