Gene Set Variation Analysis for Microarray and RNA-Seq Data

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Documentation for package ‘GSVA’ version 2.7.10

• DESCRIPTION file
• User guides, package vignettes and other documentation
• Package NEWS
• Package README

Help Pages

anyNA-method	'gsvaParam' class
anyNA-method	'ssgseaParam' class
computeGeneSetsOverlap	Compute gene-sets overlap
computeGeneSetsOverlap-method	Compute gene-sets overlap
deduplicateGeneSets	Handling of Duplicated Gene Set Names
details-method	'GsvaMethodParam' class
filterGeneSets	Filter gene sets
filterGeneSets-method	Filter gene sets
geneIdsToGeneSetCollection	Construct a GeneSetCollection object from a list of character vectors
geneSets	Retrieve or Determine Gene Sets
geneSets-method	Retrieve or Determine Gene Sets
geneSets<-	'gsvaParam' class
geneSets<--method	'gsvaParam' class
geneSetSizes	Retrieve or Determine Gene Sets
geneSetSizes-method	Retrieve or Determine Gene Sets
gsva	Gene Set Variation Analysis
gsva-method	Gene Set Variation Analysis
gsvaAnnotation	Store and Retrieve Annotation Metadata
gsvaAnnotation-method	Store and Retrieve Annotation Metadata
gsvaAnnotation<-	Store and Retrieve Annotation Metadata
gsvaAnnotation<--method	Store and Retrieve Annotation Metadata
gsvaBatchtoolsSlurmParam	MapReduce parallelization for HPC environments
gsvaColRanks	GSVA ranks and scores
gsvaColScores	GSVA ranks and scores
gsvaEnrichment	GSVA enrichment data and visualization
GsvaExprData	'GsvaExprData' class
GsvaExprData-class	'GsvaExprData' class
GsvaGeneSets-class	'GsvaGeneSets' class
gsvaMap	MapReduce parallelization for HPC environments
GsvaMethodParam-class	'GsvaMethodParam' class
gsvaParam	'gsvaParam' class
gsvaParam-class	'gsvaParam' class
gsvaRanksParam-class	'gsvaParam' class
gsvaReduce	MapReduce parallelization for HPC environments
gsvaRowNorm	GSVA ranks and scores
guessGeneIdType	Guess the gene identifier type from a list of character vectors
igsva	Gene Set Variation Analysis
loadHDF5GSVA	Save/load GSVA output to disk using HDF5 format
plageParam	'plageParam' class
plageParam-class	'plageParam' class
readGMT	Import Gene Sets from a GMT File
saveHDF5GSVA	Save/load GSVA output to disk using HDF5 format
spatCor	Compute Spatial Autocorrelation for SpatialExperiment objects
spatCor-method	Compute Spatial Autocorrelation for SpatialExperiment objects
ssgseaParam	'ssgseaParam' class
ssgseaParam-class	'ssgseaParam' class
zscoreParam	'zscoreParam' class
zscoreParam-class	'zscoreParam' class