counts	counts
counts,DESeqDataSet-method	counts
counts<-,DESeqDataSet,matrix-method	counts
DESeq	DESeq
DESeqDataSet	DESeqDataSet
DESeqDataSet-class	DESeqDataSet
DESeqDataSetFromHTSeqCount	DESeqDataSet
DESeqDataSetFromMatrix	DESeqDataSet
design	design
design,DESeqDataSet-method	design
design<-,DESeqDataSet,formula-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
estimateDispersions	estimateDispersions
estimateDispersions,DESeqDataSet-method	estimateDispersions
estimateDispersionsFit	estimateDispersionsGeneEst
estimateDispersionsGeneEst	estimateDispersionsGeneEst
estimateDispersionsMAP	estimateDispersionsGeneEst
estimateSizeFactors	estimateSizeFactors
estimateSizeFactors,DESeqDataSet-method	estimateSizeFactors
estimateSizeFactorsForMatrix	estimateSizeFactorsForMatrix
getVarianceStabilizedData	varianceStabilizingTransformation
makeExampleDESeqDataSet	makeExampleDESeqDataSet
nbinomLRT	nbinomLRT
nbinomWaldTest	nbinomWaldTest
normalizationFactors	normalizationFactors
normalizationFactors,DESeqDataSet-method	normalizationFactors
normalizationFactors<-	normalizationFactors
normalizationFactors<-,DESeqDataSet,matrix-method	normalizationFactors
plotDispEsts	plotDispEsts
plotDispEsts,DESeqDataSet-method	plotDispEsts
plotMA	plotMA
plotMA,DESeqDataSet-method	plotMA
plotPCA	plotPCA
removeResults	results
replaceOutliersWithTrimmedMean	replaceOutliersWithTrimmedMean
results	results
resultsNames	results
rlogData	rlogTransformation
rlogTransformation	rlogTransformation
sizeFactors	sizeFactors
sizeFactors,DESeqDataSet-method	sizeFactors
sizeFactors<-,DESeqDataSet,numeric-method	sizeFactors
varianceStabilizingTransformation	varianceStabilizingTransformation
