# Gene Set Variation Analysis for Microarray and RNA-Seq Data

## Documentation for package ‘GSVA’ version 2.5.40

- 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
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
gsvaEnrichment | GSVA enrichment data and visualization
gsvaEnrichment-method | GSVA enrichment data and visualization
GsvaExprData | 'GsvaExprData' class
GsvaExprData-class | 'GsvaExprData' class
GsvaGeneSets-class | 'GsvaGeneSets' class
GsvaMethodParam-class | 'GsvaMethodParam' class
gsvaParam | 'gsvaParam' class
gsvaParam-class | 'gsvaParam' class
gsvaRanks | GSVA ranks and scores
gsvaRanks-method | GSVA ranks and scores
gsvaRanksParam-class | 'gsvaParam' class
gsvaScores | GSVA ranks and scores
gsvaScores-method | GSVA ranks and scores
guessGeneIdType | Guess the gene identifier type from a list of character vectors
igsva | Gene Set Variation Analysis
loadHDF5GSVAranks | Save/load GSVA rank values to disk using HDF5 format
plageParam | 'plageParam' class
plageParam-class | 'plageParam' class
readGMT | Import Gene Sets from a GMT File
saveHDF5GSVAranks | Save/load GSVA rank values 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