buildExonCountSet	buildExonCountSet
class:ExonCountSet	ExonCountSet-class
constructModelFrame	constructModelFrame
countReadsForDEXSeq	countReadsForDEXSeq
countReadsForDEXSeq-deprecated	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
DEXSeq-deprecated	DEXSeq-deprecated
DEXSeqHTML	DEXSeqHTML
doCompleteDEUAnalysis	doCompleteDEUAnalysis
estimateDispersions	estimateDispersions
estimateDispersions,ExonCountSet-method	estimateDispersions
estimateDispersions_BM	estimateDispersions_BM
estimateExonDispersionsForModelFrame_BM	estimateExonDispersionsForModelFrame_BM
estimatelog2FoldChanges	estimatelog2FoldChanges
estimateSizeFactors	estimateSizeFactors
estimateSizeFactors,ExonCountSet-method	estimateSizeFactors
ExonCountSet	ExonCountSet-class
ExonCountSet-class	ExonCountSet-class
exonIDs	exonIDs
exonIDs<-	exonIDs
fitDispersionFunction	fitDispersionFunction
geneCountTable	geneCountTable
geneIDs	geneIDs
geneIDs<-	geneIDs
makeCompleteDEUAnalysis_BM	makeCompleteDEUAnalysis_BM
modelFrameForGene	modelFrameForGene
newExonCountSet	newExonCountSet
perGeneQValue	perGeneQValue
plotDEXSeq	plotDEXSeq
plotDispEsts	plotDispEsts-methods
plotDispEsts,ExonCountSet-method	plotDispEsts-methods
plotDispEsts-methods	plotDispEsts-methods
plotMA	plotMA-methods
plotMA,data.frame-method	plotMA-methods
plotMA,ExonCountSet-method	plotMA-methods
plotMA-methods	plotMA-methods
prepareAnnotationForDEXSeq	prepareAnnotationForDEXSeq-deprecated
prepareAnnotationForDEXSeq-deprecated	prepareAnnotationForDEXSeq-deprecated
read.HTSeqCounts	read.HTSeqCounts
sizeFactors	sizeFactors
sizeFactors,ExonCountSet-method	sizeFactors
sizeFactors<-,ExonCountSet,numeric-method	sizeFactors
subsetByGenes	subsetByGenes
testForDEU	testForDEU
testForDEU_BM	testForDEU_BM
testGeneForDEU_BM	testGeneForDEU
[,ExonCountSet,ANY,ANY-method	ExonCountSet-class
[,ExonCountSet-method	ExonCountSet-class
