buildExonCountSet	DEXSeq-deprecated
buildExonCountSet-deprecated	DEXSeq-deprecated
constructModelFrame	DEXSeq-deprecated
constructModelFrame-deprecated	DEXSeq-deprecated
countReadsForDEXSeq	DEXSeq-defunct
countReadsForDEXSeq-defunct	DEXSeq-defunct
counts	counts
counts,DEXSeqResults-method	counts
counts,ExonCountSet-method	counts
counts,ExonCountSet-method,deprecated	counts
countTableForGene	DEXSeq-deprecated
countTableForGene-deprecated	DEXSeq-deprecated
design,ExonCountSet	DEXSeq-deprecated
design,ExonCountSet-deprecated	DEXSeq-deprecated
DEUresultTable	DEXSeq-deprecated
DEUresultTable-deprecated	DEXSeq-deprecated
DEXSeq	DEXSeq
DEXSeq-defunct	DEXSeq-defunct
DEXSeq-deprecated	DEXSeq-deprecated
DEXSeqDataSet	DEXSeqDataSet
DEXSeqDataSet-class	DEXSeqDataSet
DEXSeqDataSetFromHTSeq	DEXSeqDataSet
DEXSeqDataSetFromSE	DEXSeqDataSet
DEXSeqHTML	DEXSeqHTML
DEXSeqResults	DEXSeqResults
DEXSeqResults-class	DEXSeqResults
doCompleteDEUAnalysis	DEXSeq-deprecated
doCompleteDEUAnalysis-deprecated	DEXSeq-deprecated
estimateDispersions	estimateDispersions
estimateDispersions,DEXSeqDataSet-method	estimateDispersions
estimateDispersions,ExonCountSet-method	estimateDispersions
estimateDispersions,ExonCountSet-method-deprecated	estimateDispersions
estimateDispersions_BM	DEXSeq-deprecated
estimateDispersions_BM-deprecated	DEXSeq-deprecated
estimateExonDispersion	DEXSeq-deprecated
estimateExonDispersion-deprecated	DEXSeq-deprecated
estimateExonDispersionsForModelFrame_BM	DEXSeq-deprecated
estimateExonDispersionsForModelFrame_BM-deprecated	DEXSeq-deprecated
estimateExonFoldChanges	estimateExonFoldChanges
estimatelog2FoldChanges	DEXSeq-deprecated
estimatelog2FoldChanges-deprecated	DEXSeq-deprecated
estimateSizeFactors	estimateSizeFactors
estimateSizeFactors,DEXSeqDataSet-method	estimateSizeFactors
estimateSizeFactors,ExonCountSet-method	estimateSizeFactors
estimateSizeFactors,ExonCountSet-method,deprecated	estimateSizeFactors
ExonCountSet	class-deprecated
ExonCountSet-class	class-deprecated
exonIDs	accessors
exonIDs<-	accessors
featureCounts	accessors
featureIDs	accessors
featureIDs<-	accessors
findOverlaps	methods-gr
findOverlaps,DEXSeqResults,GenomicRanges-method	methods-gr
findOverlaps-methods	methods-gr
fitDispersionFunction	DEXSeq-deprecated
fitDispersionFunction-deprecated	DEXSeq-deprecated
geneCountTable	DEXSeq-deprecated
geneCountTable-deprecated	DEXSeq-deprecated
geneIDs	accessors
geneIDs<-	accessors
getCountVector	DEXSeq-deprecated
getCountVector-deprecated	DEXSeq-deprecated
groupIDs	accessors
groupIDs<-	accessors
makeCompleteDEUAnalysis_BM	DEXSeq-deprecated
makeCompleteDEUAnalysis_BM-deprecated	DEXSeq-deprecated
modelFrameForGene	DEXSeq-deprecated
modelFrameForGene-deprecated	DEXSeq-deprecated
newExonCountSet	DEXSeq-deprecated
newExonCountSet-deprecated	DEXSeq-deprecated
perGeneQValue	perGeneQValue
plotDEXSeq	plotDEXSeq
plotDispEsts	plotDispEsts
plotDispEsts,DEXSeqDataSet-method	plotDispEsts
plotDispEsts,ExonCountSet-method	methods-deprecated
plotDispEsts,ExonCountSet-method,deprecated	methods-deprecated
plotMA	plotMA
plotMA,DEXSeqDataSet-method	plotMA
plotMA,DEXSeqResults-method	plotMA
plotMA,ExonCountSet	methods-deprecated
plotMA,ExonCountSet-deprecated	methods-deprecated
plotMA,ExonCountSet-method	plotMA
plotMA,ExonCountSet-method,deprecated	plotMA
plotMA-methods	plotMA
prepareAnnotationForDEXSeq	DEXSeq-defunct
prepareAnnotationForDEXSeq-defunct	DEXSeq-defunct
read.HTSeqCounts	DEXSeq-deprecated
read.HTSeqCounts-deprecated	DEXSeq-deprecated
sampleAnnotation	accessors
sizeFactors,ExonCountSet-method	methods-deprecated
sizeFactors,ExonCountSet-method,deprecated	methods-deprecated
subsetByGenes	DEXSeq-deprecated
subsetByGenes-deprecated	DEXSeq-deprecated
subsetByOverlaps	methods-gr
subsetByOverlaps,DEXSeqResults,GenomicRanges-method	methods-gr
subsetByOverlaps-methods	methods-gr
testExonForDEU	DEXSeq-deprecated
testExonForDEU-deprecated	DEXSeq-deprecated
testForDEU	testForDEU
testForDEU_BM	DEXSeq-deprecated
testForDEU_BM-deprecated	DEXSeq-deprecated
testGeneForDEU_BM	DEXSeq-deprecated
testGeneForDEU_BM-deprecated	DEXSeq-deprecated
