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