Package: GSVA 2.1.1
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:
GSVA_2.1.1.tar.gz
GSVA_2.1.1.zip(r-4.5)GSVA_2.1.1.zip(r-4.4)GSVA_2.1.1.zip(r-4.3)
GSVA_2.1.1.tgz(r-4.4-x86_64)GSVA_2.1.1.tgz(r-4.4-arm64)GSVA_2.1.1.tgz(r-4.3-x86_64)GSVA_2.1.1.tgz(r-4.3-arm64)
GSVA_2.1.1.tar.gz(r-4.5-noble)GSVA_2.1.1.tar.gz(r-4.4-noble)
GSVA_2.1.1.tgz(r-4.4-emscripten)GSVA_2.1.1.tgz(r-4.3-emscripten)
GSVA.pdf |GSVA.html✨
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-2.1.0(bioc 3.21)GSVA-2.0.1(bioc 3.20)
functionalgenomicsmicroarrayrnaseqpathwaysgenesetenrichmentgene-set-enrichmentgenomicspathway-enrichment-analysis
Last updated 4 days agofrom:204ab29d20. Checks:OK: 2 WARNING: 4 ERROR: 3. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 09 2024 |
| R-4.5-win-x86_64 | WARNING | Nov 09 2024 |
| R-4.5-linux-x86_64 | WARNING | Nov 09 2024 |
| R-4.4-win-x86_64 | WARNING | Nov 09 2024 |
| R-4.4-mac-x86_64 | WARNING | Nov 09 2024 |
| R-4.4-mac-aarch64 | OK | Nov 09 2024 |
| R-4.3-win-x86_64 | ERROR | Nov 09 2024 |
| R-4.3-mac-x86_64 | ERROR | Nov 09 2024 |
| R-4.3-mac-aarch64 | ERROR | Nov 09 2024 |
Exports:computeGeneSetsOverlapdeduplicateGeneSetsfilterGeneSetsgeneIdsToGeneSetCollectiongeneSetsgeneSets<-geneSetSizesgsvagsvaAnnotationgsvaAnnotation<-gsvaEnrichmentgsvaParamgsvaRanksgsvaScoresguessGeneIdTypeigsvaplageParamreadGMTspatCorssgseaParamzscoreParam
Dependencies:abindannotateAnnotationDbiaskpassassortheadbeachmatBHBiobaseBiocFileCacheBiocGenericsBiocParallelBiocSingularBiostringsbitbit64blobcachemclicodetoolscpp11crayoncurlDBIdbplyrDelayedArrayDelayedMatrixStatsdplyrfansifastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgluegraphGSEABaseHDF5ArrayhttrIRangesirlbajsonliteKEGGRESTlambda.rlatticelifecyclemagickmagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigplogrpngpurrrR6Rcpprhdf5rhdf5filtersRhdf5librjsonrlangRSQLitersvdS4ArraysS4VectorsScaledMatrixSingleCellExperimentsnowSparseArraysparseMatrixStatsSpatialExperimentstringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrswithrXMLxtableXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Compute gene-sets overlap | computeGeneSetsOverlap computeGeneSetsOverlap,GeneSetCollection,character-method computeGeneSetsOverlap,GeneSetCollection,ExpressionSet-method computeGeneSetsOverlap,list,character-method computeGeneSetsOverlap,list,ExpressionSet-method |
| Handling of Duplicated Gene Set Names | deduplicateGeneSets |
| Filter gene sets | filterGeneSets filterGeneSets,GeneSetCollection-method filterGeneSets,list-method |
| Construct a GeneSetCollection object from a list of character vectors | geneIdsToGeneSetCollection |
| Retrieve or Determine Gene Sets | geneSets 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 Analysis | gsva gsva,gsvaParam-method gsva,plageParam-method gsva,ssgseaParam-method gsva,zscoreParam-method |
| Store and Retrieve Annotation Metadata | gsvaAnnotation 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 visualization | gsvaEnrichment gsvaEnrichment,gsvaRanksParam-method |
| 'GsvaExprData' class | GsvaExprData GsvaExprData-class |
| 'GsvaGeneSets' class | GsvaGeneSets-class |
| 'GsvaMethodParam' class | GsvaMethodParam-class |
| 'gsvaParam' class | geneSets<- geneSets<-,gsvaRanksParam,GsvaGeneSets-method gsvaParam gsvaParam-class gsvaRanksParam-class |
| GSVA ranks and scores | gsvaRanks gsvaRanks,gsvaParam-method gsvaScores gsvaScores,gsvaRanksParam-method |
| Guess the gene identifier type from a list of character vectors | guessGeneIdType |
| Gene Set Variation Analysis | igsva |
| 'plageParam' class | plageParam plageParam-class |
| Import Gene Sets from a GMT File | readGMT |
| Compute Spatial Autocorrelation for SpatialExperiment objects | spatCor spatCor,SpatialExperiment-method |
| 'ssgseaParam' class | anyNA,gsvaParam-method anyNA,ssgseaParam-method ssgseaParam ssgseaParam-class |
| 'zscoreParam' class | zscoreParam zscoreParam-class |
