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

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Functions
172
Source code
46
Man pages
23
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rcastelo/GSVA: Gene Set Variation Analysis for Microarray and RNA-Seq Data
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API

API for rcastelo/GSVA
Gene Set Variation Analysis for Microarray and RNA-Seq Data

Global functions
.catObj Source code
.check_for_na_values Source code
.check_geneSets_minSize_maxSize_tau Source code
.check_maxDiff_absRanking Source code
.check_rownames Source code
.col_iter Source code
.computeGeneSetsOverlap Source code
.compute_gsva_ranks Source code
.compute_gsva_scores Source code
.ecdfvals_dense_to_dense Source code
.ecdfvals_dense_to_dense_nas Source code
.ecdfvals_sparse_to_dense Source code
.ecdfvals_sparse_to_sparse Source code
.fastRndWalk Source code
.fastRndWalk2 Source code
.fastRndWalkNArm Source code
.filterAndMapGeneSets Source code
.filterAndMapGenesAndGeneSets Source code
.filterGenes Source code
.geneSets Source code
.geneSetsIndices2Names Source code
.gsvaDelayedArray Source code
.gsvaRndWalk Source code
.gsvaRndWalk_nas Source code
.gsvaRndWalk_rankingpos_notau Source code
.gsva_enrichment_data Source code
.gsva_rnd_walk Source code
.gsva_score_genesets Source code
.gsva_score_genesets_Rimp Source code
.guessIfCountData Source code
.isAnnoPkgInstalled Source code
.isAnnoPkgValid Source code
.isCharLength1 Source code
.isCharNonEmpty Source code
.isPackageLoaded Source code
.kcdfvals_sparse_to_dense Source code
.kcdfvals_sparse_to_sparse Source code
.mapGeneSetsToFeatures Source code
.matrix2dgCMatrix Source code
.objPkgClass Source code
.onLoad Source code
.order_rankstat Source code
.order_rankstat_sparse_to_dense Source code
.order_rankstat_sparse_to_sparse Source code
.parse_kcdf_param Source code
.plot_enrichment_base Source code
.plot_enrichment_ggplot Source code
.ranks2stats Source code
.ranks2stats_nas Source code
.rndWalk Source code
.row_iter Source code
.showSome Source code
.sparse2columnList Source code
.sparseColumnApplyAndReplace Source code
.spe_dist_weight_matrix Source code
.stopf Source code
.sufficient_ssize Source code
.warningf Source code
GSVA-pkg-defunct Man page
GSVA-pkg-deprecated Man page
GsvaExprData Man page
GsvaExprData-class Man page
GsvaGeneSets-class Man page
GsvaMethodParam-class Man page
anyNA,gsvaParam-method Man page
anyNA,ssgseaParam-method Man page
combinez Source code
combinezDelayed Source code
compute.gene.cdf Source code
compute.geneset.es Source code
computeGeneSetsOverlap Man page
computeGeneSetsOverlap,GeneSetCollection,ExpressionSet-method Man page
computeGeneSetsOverlap,GeneSetCollection,character-method Man page
computeGeneSetsOverlap,list,ExpressionSet-method Man page
computeGeneSetsOverlap,list,character-method Man page
deduplicateGeneSets Man page Source code
deduplicateGmtLines Source code
filterGeneSets Man page
filterGeneSets,GeneSetCollection-method Man page
filterGeneSets,list-method Man page
geneIdsToGeneSetCollection Man page Source code
geneSetSizes Man page
geneSetSizes,GsvaExprData-method Man page
geneSetSizes,GsvaMethodParam-method Man page
geneSets Man page
geneSets,GsvaExprData-method Man page
geneSets,GsvaMethodParam-method Man page
geneSets,SingleCellExperiment-method Man page
geneSets,SpatialExperiment-method Man page
geneSets,SummarizedExperiment-method Man page
geneSets<- Man page
geneSets<-,gsvaRanksParam,GsvaGeneSets-method Man page
get_NAuse Source code
get_absRanking Source code
get_alpha Source code
get_checkNA Source code
get_didCheckNA Source code
get_kcdf Source code
get_kcdfNoneMinSampleSize Source code
get_maxDiff Source code
get_normalize Source code
get_sparse Source code
get_tau Source code
gsva Man page
gsva,ExpressionSet-method Man page
gsva,SingleCellExperiment-method Man page
gsva,SummarizedExperiment-method Man page
gsva,dgCMatrix-method Man page
gsva,gsvaParam-method Man page
gsva,matrix-method Man page
gsva,missing-method Man page
gsva,plageParam-method Man page
gsva,ssgseaParam-method Man page
gsva,zscoreParam-method Man page
gsva-defunct Man page
gsvaAnnotation Man page
gsvaAnnotation,ExpressionSet-method Man page
gsvaAnnotation,GeneSetCollection-method Man page
gsvaAnnotation,GsvaExprData-method Man page
gsvaAnnotation,SingleCellExperiment-method Man page
gsvaAnnotation,SpatialExperiment-method Man page
gsvaAnnotation,SummarizedExperiment-method Man page
gsvaAnnotation,list-method Man page
gsvaAnnotation<- Man page
gsvaAnnotation<-,ExpressionSet,GeneIdentifierType-method Man page
gsvaAnnotation<-,ExpressionSet,character-method Man page
gsvaAnnotation<-,GsvaExprData,GeneIdentifierType-method Man page
gsvaAnnotation<-,SingleCellExperiment,GeneIdentifierType-method Man page
gsvaAnnotation<-,SpatialExperiment,GeneIdentifierType-method Man page
gsvaAnnotation<-,SummarizedExperiment,GeneIdentifierType-method Man page
gsvaAnnotation<-,list,GeneIdentifierType-method Man page
gsvaEnrichment Man page
gsvaEnrichment,gsvaRanksParam-method Man page
gsvaParam Man page Source code
gsvaParam-class Man page
gsvaRanks Man page
gsvaRanks,gsvaParam-method Man page
gsvaRanksParam-class Man page
gsvaScores Man page
gsvaScores,gsvaRanksParam-method Man page
guessGeneIdType Man page Source code
h5BackendRealization Source code
igsva Man page Source code
ks_test_Rcode Source code
ks_test_m Source code
plage Source code
plageDelayed Source code
plageParam Man page Source code
plageParam-class Man page
rankHDF5 Source code
readGMT Man page
rightsingularsvdvectorgset Source code
rightsvdDelayed Source code
spatCor Man page
spatCor,SpatialExperiment-method Man page
ssgsea Source code
ssgseaDelayed Source code
ssgseaParam Man page Source code
ssgseaParam-class Man page
zorder_rankstat Source code
zscore Source code
zscoreDelayed Source code
zscoreParam Man page Source code
zscoreParam-class Man page
rcastelo/GSVA documentation built on Dec. 17, 2024, 4:51 p.m.

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