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Gene set enrichment data structures and methods

Bioconductor version: Release (3.19)

This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA).

Author: Martin Morgan [aut], Seth Falcon [aut], Robert Gentleman [aut], Paul Villafuerte [ctb] ('GSEABase' vignette translation from Sweave to Rmarkdown / HTML), Bioconductor Package Maintainer [cre]

Maintainer: Bioconductor Package Maintainer <maintainer at>

Citation (from within R, enter citation("GSEABase")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

An introduction to GSEABase HTML R Script
Reference Manual PDF


biocViews GO, GeneExpression, GeneSetEnrichment, GraphAndNetwork, KEGG, Software
Version 1.66.0
In Bioconductor since BioC 2.1 (R-2.6) (17 years)
License Artistic-2.0
Depends R (>= 2.6.0), BiocGenerics(>= 0.13.8), Biobase(>= 2.17.8), annotate(>= 1.45.3), methods, graph(>= 1.37.2)
Imports AnnotationDbi, XML
System Requirements
See More
Suggests hgu95av2.db, GO.db,, Rgraphviz, ReportingTools, testthat, BiocStyle, knitr, RUnit
Linking To
Depends On Me AGDEX, BicARE, CCPROMISE, Cepo, cpvSNP, npGSEA, PROMISE, splineTimeR, TissueEnrich, GSVAdata, OSCA.basic
Imports Me AUCell, BioCor, canceR, Category, categoryCompare, cellHTS2, cosmosR, dreamlet, EnrichmentBrowser, escape, gep2pep, GlobalAncova, GmicR, GSRI, GSVA, mastR, miRSM, mogsa, oppar, PanomiR, phenoTest, PROMISE, RcisTarget, ReportingTools, scTGIF, signatureSearch, singleCellTK, singscore, slalom, sparrow, TFutils, vissE, zenith, msigdb, SingscoreAMLMutations, clustermole, RVA
Suggests Me BiocSet, gage, globaltest, GOstats, GSAR, MAST, phenoTest, BaseSet
Links To Me
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package GSEABase_1.66.0.tar.gz
Windows Binary
macOS Binary (x86_64) GSEABase_1.66.0.tgz
macOS Binary (arm64) GSEABase_1.66.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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