buildExonCountSet	buildExonCountSet
countReadsForDEXSeq	countReadsForDEXSeq
counts	counts
counts,ExonCountSet-method	counts
counts<-,ExonCountSet,matrix-method	counts
countTableForGene	countTableForGene
design	design
design,ExonCountSet-method	design
design<-,ExonCountSet-method	design
DEUresultTable	DEUresultTable
DEXSeqHTML	DEXSeqHTML
estimateDispersions	estimateDispersions
estimateDispersions,ExonCountSet-method	estimateDispersions
estimateDispersionsTRT	estimateDispersionsTRT
estimateExonDispersionsForModelFrame	estimateExonDispersionsForModelFrame
estimatelog2FoldChanges	estimatelog2FoldChanges
estimateSizeFactors	estimateSizeFactors
estimateSizeFactors,ExonCountSet-method	estimateSizeFactors
ExonCountSet-class	ExonCountSet-class
exonIDs	exonIDs
exonIDs<-	exonIDs
fitDispersionFunction	fitDispersionFunction
geneCountTable	geneCountTable
geneIDs	geneIDs
geneIDs<-	geneIDs
makeCompleteDEUAnalysis	makeCompleteDEUAnalysis
modelFrameForGene	modelFrameForGene
modelFrameForTRT	modelFrameForTRT
newExonCountSet	newExonCountSet
perGeneQValue	perGeneQValue
plotDEXSeq	plotDEXSeq
prepareAnnotationForDEXSeq	prepareAnnotationForDEXSeq
read.HTSeqCounts	read.HTSeqCounts
sizeFactors	sizeFactors
sizeFactors,ExonCountSet-method	sizeFactors
sizeFactors<-,ExonCountSet,numeric-method	sizeFactors
subsetByGenes	subsetByGenes
testForDEU	testForDEU
testForDEUTRT	testForDEUTRT
testGeneForDEU	testGeneForDEU
