Package: GSVA 2.7.3

Robert Castelo

GSVA: Gene Set Variation Analysis for Microarray and RNA-Seq Data

Gene Set Variation Analysis (GSVA) is a non-parametric, unsupervised method for estimating variation of gene set enrichment through the samples of a expression data set. GSVA performs a change in coordinate systems, transforming the data from a gene by sample matrix to a gene-set by sample matrix, thereby allowing the evaluation of pathway enrichment for each sample. This new matrix of GSVA enrichment scores facilitates applying standard analytical methods like functional enrichment, survival analysis, clustering, CNV-pathway analysis or cross-tissue pathway analysis, in a pathway-centric manner.

Authors:Robert Castelo [aut, cre], Justin Guinney [aut], Alexey Sergushichev [ctb], Pablo Sebastian Rodriguez [ctb], Axel Klenk [ctb], Chan Zuckerberg Initiative [fnd], Spanish Ministry of Science, Innovation and Universities [fnd]

GSVA_2.7.3.tar.gz
GSVA_2.7.3.zip(r-4.7)GSVA_2.7.3.zip(r-4.6)GSVA_2.7.3.zip(r-4.5)
GSVA_2.7.3.tgz(r-4.6-x86_64)GSVA_2.7.3.tgz(r-4.6-arm64)GSVA_2.7.3.tgz(r-4.5-x86_64)GSVA_2.7.3.tgz(r-4.5-arm64)
GSVA_2.7.3.tar.gz(r-4.7-arm64)GSVA_2.7.3.tar.gz(r-4.7-x86_64)GSVA_2.7.3.tar.gz(r-4.6-arm64)GSVA_2.7.3.tar.gz(r-4.6-x86_64)
GSVA_2.7.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
GSVA/json (API)
NEWS

# Install 'GSVA' in R:
install.packages('GSVA', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/rcastelo/gsva/issues

On BioConductor:GSVA-2.7.2(bioc 3.24)GSVA-2.6.2(bioc 3.23)

functionalgenomicsmicroarrayrnaseqpathwaysgenesetenrichmentgene-set-enrichmentgenomicspathway-enrichment-analysis

15.53 score 242 stars 21 packages 3.2k scripts 15k downloads 893 mentions 27 exports 95 dependencies

Last updated from:3644b54d30. Checks:1 ERROR, 13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR322
linux-devel-arm64OK498
linux-devel-x86_64OK622
source / vignettesOK555
linux-release-arm64OK482
linux-release-x86_64OK580
macos-release-arm64OK373
macos-release-x86_64OK594
macos-oldrel-arm64OK343
macos-oldrel-x86_64OK613
windows-develOK551
windows-releaseOK474
windows-oldrelOK526
wasm-releaseOK272

Exports:computeGeneSetsOverlapdeduplicateGeneSetsdetailsfilterGeneSetsgeneIdsToGeneSetCollectiongeneSetsgeneSets<-geneSetSizesgsvagsvaAnnotationgsvaAnnotation<-gsvaColRanksgsvaColScoresgsvaEnrichmentgsvaParamgsvaRanksgsvaRowNormgsvaScoresguessGeneIdTypeigsvaloadHDF5GSVAranksplageParamreadGMTsaveHDF5GSVAranksspatCorssgseaParamzscoreParam

Dependencies:abindannotateAnnotationDbiaskpassassortheadbeachmatBHBiobaseBiocFileCacheBiocGenericsbiocmakeBiocParallelBiocSingularBiostringsbitbit64blobcachemclicodetoolscpp11crayoncurlDBIdbplyrDelayedArrayDelayedMatrixStatsdir.expirydplyrfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomicRangesgluegraphGSEABaseh5mreadHDF5Arrayhttrhttr2IRangesirlbajsonliteKEGGRESTlambda.rlatticelifecyclemagickmagrittrMatrixMatrixGenericsmatrixStatsmemoisememusemimeopensslpillarpkgconfigpngpurrrR6rappdirsRcpprhdf5rhdf5filtersRhdf5librjsonrlangRSQLitersvdS4ArraysS4VectorsScaledMatrixSeqinfoSingleCellExperimentsnowSparseArraysparseMatrixStatsSpatialExperimentstringistringrSummarizedExperimentsystibbletidyrtidyselectutf8vctrswithrXMLxtableXVector

GSVA: gene set variation analysis

Robert Castelo, Axel Klenk, Justin Guinney

Rendered fromGSVA.Rmdusingknitr::rmarkdownon May 26 2026.

Last update: 2026-02-19
Started: 2021-02-05

GSVA on proteomics data

Robert Castelo, Axel Klenk, Justin Guinney

Rendered fromGSVA_proteomics.Rmdusingknitr::rmarkdownon May 26 2026.

Last update: 2026-05-25
Started: 2026-04-27

GSVA on single-cell RNA-seq data

Robert Castelo, Axel Klenk, Justin Guinney

Rendered fromGSVA_scRNAseq.Rmdusingknitr::rmarkdownon May 26 2026.

Last update: 2026-05-25
Started: 2025-10-27

Readme and manuals

Help Manual

Help pageTopics
Compute gene-sets overlapcomputeGeneSetsOverlap computeGeneSetsOverlap,GeneSetCollection,character-method computeGeneSetsOverlap,list,character-method
Handling of Duplicated Gene Set NamesdeduplicateGeneSets
Filter gene setsfilterGeneSets filterGeneSets,GeneSetCollection-method filterGeneSets,list-method
Construct a GeneSetCollection object from a list of character vectorsgeneIdsToGeneSetCollection
Retrieve or Determine Gene SetsgeneSets geneSets,GsvaExprData-method geneSets,GsvaMethodParam-method geneSets,SingleCellExperiment-method geneSets,SpatialExperiment-method geneSets,SummarizedExperiment-method geneSetSizes geneSetSizes,GsvaExprData-method geneSetSizes,GsvaMethodParam-method
Gene Set Variation Analysisgsva gsva,gsvaParam-method gsva,plageParam-method gsva,ssgseaParam-method gsva,zscoreParam-method
Store and Retrieve Annotation MetadatagsvaAnnotation gsvaAnnotation,ExpressionSet-method gsvaAnnotation,GeneSetCollection-method gsvaAnnotation,GsvaExprData-method gsvaAnnotation,list-method gsvaAnnotation,SingleCellExperiment-method gsvaAnnotation,SpatialExperiment-method gsvaAnnotation,SummarizedExperiment-method gsvaAnnotation<- gsvaAnnotation<-,ExpressionSet,character-method gsvaAnnotation<-,ExpressionSet,GeneIdentifierType-method gsvaAnnotation<-,GsvaExprData,GeneIdentifierType-method gsvaAnnotation<-,list,GeneIdentifierType-method gsvaAnnotation<-,SingleCellExperiment,GeneIdentifierType-method gsvaAnnotation<-,SpatialExperiment,GeneIdentifierType-method gsvaAnnotation<-,SummarizedExperiment,GeneIdentifierType-method
GSVA enrichment data and visualizationgsvaEnrichment gsvaEnrichment,GsvaExprData-method
'GsvaExprData' classGsvaExprData GsvaExprData-class
'GsvaGeneSets' classGsvaGeneSets-class
'GsvaMethodParam' classdetails,GsvaMethodParam-method details,gsvaParam-method details,ssgseaParam-method GsvaMethodParam-class
'gsvaParam' classanyNA,gsvaParam-method geneSets<- geneSets<-,gsvaParam,GsvaGeneSets-method gsvaParam gsvaParam-class gsvaRanksParam-class
GSVA ranks and scoresgsvaColRanks gsvaColRanks,GsvaExprData-method gsvaColScores gsvaColScores,GsvaExprData-method gsvaRowNorm gsvaRowNorm,gsvaParam-method
Guess the gene identifier type from a list of character vectorsguessGeneIdType
Gene Set Variation Analysisigsva
'plageParam' classplageParam plageParam-class
Import Gene Sets from a GMT FilereadGMT
Save/load GSVA rank values to disk using HDF5 formatloadHDF5GSVAranks saveHDF5GSVAranks
Compute Spatial Autocorrelation for SpatialExperiment objectsspatCor spatCor,SpatialExperiment-method
'ssgseaParam' classanyNA,ssgseaParam-method ssgseaParam ssgseaParam-class
'zscoreParam' classzscoreParam zscoreParam-class