SeqGSEA-package	SeqGSEA-package
calES	calES
calES.perm	calES.perm
convertEnsembl2Symbol	convertEnsembl2Symbol
convertSymbol2Ensembl	convertSymbol2Ensembl
counts	counts-methods
counts,ReadCountSet-method	counts-methods
counts-methods	counts-methods
counts<-,ReadCountSet,matrix-method	counts-methods
DENBStat4GSEA	DENBStat4GSEA
DENBStatPermut4GSEA	DENBStatPermut4GSEA
DENBTest	DENBTest
DEpermutePval	DEpermutePval
DEscore	DEscore
DEscore.perm	DEscore
DSpermute4GSEA	DSpermute4GSEA
DSpermutePval	DSpermutePval
DSresultExonTable	DSresultExonTable
DSresultGeneTable	DSresultGeneTable
DSscore	DEscore
DSscore.perm	DEscore
estiExonNBstat	estiExonNBstat
estiGeneNBstat	estiGeneNBstat
exonID	exonID
exonID<-	exonID
exonTestability	exonTestability
geneID	geneID
geneID<-	geneID
geneList	geneList
genePermuteScore	genePermuteScore
geneScore	geneScore
geneSetDescs	geneSetDescs
geneSetNames	geneSetNames
geneSetSize	geneSetSize
geneTestability	geneTestability
genpermuteMat	genpermuteMat
getGeneCount	getGeneCount
GSEAresultTable	GSEAresultTable
GSEnrichAnalyze	GSEnrichAnalyze
GS_example	GS_example
label	label
loadExonCountData	loadExonCountData
loadGenesets	loadGenesets
newGeneSets	newGeneSets
newReadCountSet	newReadCountSet
normES	normES
normFactor	normFactor
plotES	plotES
plotGeneScore	plotGeneScore
plotSig	plotSig
plotSigGeneSet	plotSigGeneSet
rankCombine	rankCombine
RCS_example	RCS_example
ReadCountSet	ReadCountSet-class
ReadCountSet-class	ReadCountSet-class
runDESeq	runDESeq
runSeqGSEA	runSeqGSEA
scoreNormalization	scoreNormalization
SeqGeneSet	SeqGeneSet-class
SeqGeneSet-class	SeqGeneSet-class
SeqGSEA	SeqGSEA-package
show,SeqGeneSet-method	SeqGeneSet-class
signifES	signifES
size	size
subsetByGenes	subsetByGenes
topDEGenes	topDEGenes
topDSExons	topDSExons
topDSGenes	topDSGenes
topGeneSets	topGeneSets
writeScores	writeScores
writeSigGeneSet	writeSigGeneSet
[,SeqGeneSet,numeric-method	SeqGeneSet-class
