Man pages for sunlightwang/SeqGSEA
Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing

calESCalculate running enrichment scores of gene sets
calES.permCalculate enrichment scores for gene sets in the permutation...
convertEnsembl2SymbolConvert ensembl gene IDs to gene symbols
convertSymbol2EnsemblConvert gene symbols to ensembl gene IDs
counts-methodsAccessors for the 'counts' slot of a ReadCountSet object.
DENBStat4GSEACalculate NB-statistics quantifying differential expression...
DENBStatPermut4GSEACalculate NB-statistics quantifying DE for each gene in the...
DENBTestPerform negative binomial exact test for differential...
DEpermutePvalPermutation for p-values in differential expression analysis
DEscorePre-calculated DE/DS scores
DSpermute4GSEACompute NB-statistics quantifying differential splicing on...
DSpermutePvalPermutation for p-values in differential splicing analysis
DSresultExonTableForm a table for DS analysis results at the Exon level
DSresultGeneTableForm a table for DS analysis results at the gene level
estiExonNBstatCalculate NB-statistics quantifying differential splicing for...
estiGeneNBstatCalculate NB-statistics quantifying differential splicing for...
exonIDAccessor to the exonID slot of ReadCountSet objects
exonTestabilityCheck exon testability
geneIDAccessor to the geneID slot of ReadCountSet objects
geneListGet the gene list in a SeqGeneSet object
genePermuteScoreCalculate gene scores on permutation data sets
geneScoreCalculate gene scores by integrating DE and DS scores
geneSetDescsGet the descriptions of gene sets in a SeqGeneSet object
geneSetNamesGet the names of gene set in a SeqGeneSet object
geneSetSizeGet the numbers of genes in each gene set in a SeqGeneSet...
geneTestabilityCheck gene testability
genpermuteMatGenerate permutation matrix
getGeneCountCalculate read counts of genes from a ReadCountSet object
GSEAresultTableForm a table for GSEA results
GSEnrichAnalyzeMain function of gene set enrichment analysis
GS_exampleSeqGeneSet object example
labelGet the labels of samples in a ReadCountSet object
loadExonCountDataLoad Exon Count Data
loadGenesetsLoad gene sets from files
newGeneSetsInitialize a new SeqGeneSet object
newReadCountSetGenerate a new ReadCountSet object
normESNormalize enrichment scores
normFactorGet normalization factors for normalization DE or DS scores
plotESPlot the distribution of enrichment scores
plotGeneScorePlot gene (DE/DS) scores
plotSigPlot showing SeqGeneSet's p-values/FDRs vs. NESs
plotSigGeneSetPlot gene set details
rankCombineIntegration of differential expression and differential...
RCS_exampleReadCountSet object example
ReadCountSet-classClass '"ReadCountSet"'
runDESeqRun DESeq for differential expression analysis
runSeqGSEAAn all-in function that allows end users to apply SeqGSEA to...
scoreNormalizationNormalization of DE/DS scores
SeqGeneSet-classClass '"SeqGeneSet"'
SeqGSEA-packageSeqGSEA: a Bioconductor package for gene set enrichment...
signifESCalculate significance of ESs
sizeNumber of gene sets in a SeqGeneSet object
subsetByGenesGet a new ReadCountSet with specified gene IDs.
topDEGenesExtract top differentially expressed genes.
topDSExonsExtract top differentially spliced exons
topDSGenesExtract top differentially spliced genes
topGeneSetsExtract top significant gene sets
writeScoresWrite DE/DS scores and gene scores
writeSigGeneSetWrite gene set supporting information
sunlightwang/SeqGSEA documentation built on May 21, 2019, 10:13 a.m.