DESeq2-package	DESeq2-package
coef.DESeqDataSet	coef
collapseReplicates	collapseReplicates
counts,DESeqDataSet-method	counts
counts<-,DESeqDataSet,matrix-method	counts
DESeq	DESeq
DESeq2	DESeq2-package
DESeqDataSet	DESeqDataSet
DESeqDataSet-class	DESeqDataSet
DESeqDataSetFromHTSeqCount	DESeqDataSet
DESeqDataSetFromMatrix	DESeqDataSet
DESeqDataSetFromTximport	DESeqDataSet
DESeqResults	DESeqResults
DESeqResults-class	DESeqResults
DESeqTransform	DESeqTransform
DESeqTransform-class	DESeqTransform
design,DESeqDataSet-method	design
design<-,DESeqDataSet,formula-method	design
design<-,DESeqDataSet,matrix-method	design
dispersionFunction	dispersionFunction
dispersionFunction,DESeqDataSet-method	dispersionFunction
dispersionFunction<-	dispersionFunction
dispersionFunction<-,DESeqDataSet,function-method	dispersionFunction
dispersions	dispersions
dispersions,DESeqDataSet-method	dispersions
dispersions<-	dispersions
dispersions<-,DESeqDataSet,numeric-method	dispersions
estimateBetaPriorVar	estimateBetaPriorVar
estimateDispersions,DESeqDataSet-method	estimateDispersions
estimateDispersionsFit	estimateDispersionsGeneEst
estimateDispersionsGeneEst	estimateDispersionsGeneEst
estimateDispersionsMAP	estimateDispersionsGeneEst
estimateDispersionsPriorVar	estimateDispersionsGeneEst
estimateMLEForBetaPriorVar	estimateBetaPriorVar
estimateSizeFactors,DESeqDataSet-method	estimateSizeFactors
estimateSizeFactorsForMatrix	estimateSizeFactorsForMatrix
fpkm	fpkm
fpm	fpm
getVarianceStabilizedData	varianceStabilizingTransformation
lfcShrink	lfcShrink
makeExampleDESeqDataSet	makeExampleDESeqDataSet
nbinomLRT	nbinomLRT
nbinomWaldTest	nbinomWaldTest
normalizationFactors	normalizationFactors
normalizationFactors,DESeqDataSet-method	normalizationFactors
normalizationFactors<-	normalizationFactors
normalizationFactors<-,DESeqDataSet,matrix-method	normalizationFactors
normalizeGeneLength	normalizeGeneLength
normTransform	normTransform
plotCounts	plotCounts
plotDispEsts	plotDispEsts
plotDispEsts,DESeqDataSet-method	plotDispEsts
plotMA	plotMA
plotMA,DESeqDataSet-method	plotMA
plotMA,DESeqResults-method	plotMA
plotPCA	plotPCA
plotPCA,DESeqTransform-method	plotPCA
plotSparsity	plotSparsity
priorInfo	priorInfo
priorInfo,DESeqResults-method	priorInfo
priorInfo<-	priorInfo
priorInfo<-,DESeqResults,list-method	priorInfo
removeResults	results
replaceOutliers	replaceOutliers
replaceOutliersWithTrimmedMean	replaceOutliers
results	results
resultsNames	results
rlog	rlog
rlogTransformation	rlog
show,DESeqResults-method	show
sizeFactors,DESeqDataSet-method	sizeFactors
sizeFactors<-,DESeqDataSet,numeric-method	sizeFactors
summary,DESeqResults-method	summary
unmix	unmix
varianceStabilizingTransformation	varianceStabilizingTransformation
vst	vst
