alphaSummary	alphaSummary
alphaSummary,DESeqAnalysis-method	alphaSummary
alphaSummary,DESeqDataSet-method	alphaSummary
alphaThreshold	alphaThreshold
alphaThreshold,DESeqAnalysis-method	alphaThreshold
alphaThreshold,DESeqResults-method	alphaThreshold
alphaThreshold<-	alphaThreshold
alphaThreshold<-,DESeqAnalysis,NULL-method	alphaThreshold
alphaThreshold<-,DESeqAnalysis,numeric-method	alphaThreshold
apeglmContrast	deprecated
apeglmResults	apeglmResults
apeglmResults,DESeqDataSet-method	apeglmResults
as	as
base	base
baseMeanThreshold	baseMeanThreshold
baseMeanThreshold,DESeqAnalysis-method	baseMeanThreshold
baseMeanThreshold,DESeqResults-method	baseMeanThreshold
baseMeanThreshold<-	baseMeanThreshold
baseMeanThreshold<-,Annotated,NULL-method	baseMeanThreshold
baseMeanThreshold<-,DESeqAnalysis,numeric-method	baseMeanThreshold
coerce	as
coerce,DESeqAnalysis,DESeqDataSet-method	as
coerce,DESeqAnalysis,DESeqResults-method	as
coerce,DESeqAnalysis,DESeqTransform-method	as
colnames,DESeqAnalysis-method	base
combine	combine
combine,DESeqAnalysis,DESeqAnalysis-method	combine
contrastName	contrastName
contrastName,DESeqAnalysis-method	contrastName
contrastName,DESeqResults-method	contrastName
contrastName<-	contrastName
contrastName<-,DESeqResults,character-method	contrastName
contrastNames	resultsNames
contrastNames,DESeqAnalysis-method	resultsNames
contrastNames,DESeqDataSet-method	resultsNames
contrastNames<-	resultsNames
contrastNames<-,DESeqAnalysis,character-method	resultsNames
contrastSamples	contrastSamples
contrastSamples,DESeqAnalysis-method	contrastSamples
correlation	correlation
correlation,DESeqAnalysis,missingOrNULL-method	correlation
correlation,DESeqResults,DESeqResults-method	correlation
deg	deg
deg,DESeqAnalysis-method	deg
deg,DESeqResults-method	deg
degIntersection	degIntersection
degIntersection,DESeqAnalysis-method	degIntersection
degPerContrast	degPerContrast
degPerContrast,DESeqAnalysis-method	degPerContrast
deprecated	deprecated
deseq	deseq
DESeqAnalysis	DESeqAnalysis
DESeqAnalysis-class	DESeqAnalysis-class
DESeqAnalysisList	DESeqAnalysisList
DESeqAnalysisList-class	DESeqAnalysisList-class
dim,DESeqAnalysis-method	base
dimnames,DESeqAnalysis-method	base
export	export
export,DESeqAnalysis-method	export
export,DESeqDataSet-method	export
extract	extract
importPairwiseContrasts	importPairwiseContrasts
interestingGroups	interestingGroups
interestingGroups,DESeqAnalysis-method	interestingGroups
interestingGroups<-	interestingGroups
interestingGroups<-,DESeqAnalysis,character-method	interestingGroups
interestingGroups<-,DESeqAnalysis,NULL-method	interestingGroups
lfcShrink	lfcShrink
lfcShrink,DESeqAnalysis-method	lfcShrink
lfcShrink,DESeqDataSet-method	lfcShrink
lfcShrink<-	lfcShrink
lfcShrink<-,DESeqAnalysis,logical-method	lfcShrink
lfcShrinkType	lfcShrinkType
lfcShrinkType,DESeqAnalysis-method	lfcShrinkType
lfcShrinkType,DESeqResults-method	lfcShrinkType
lfcThreshold	lfcThreshold
lfcThreshold,DESeqAnalysis-method	lfcThreshold
lfcThreshold,DESeqResults-method	lfcThreshold
lfcThreshold<-	lfcThreshold
lfcThreshold<-,DESeqAnalysis,NULL-method	lfcThreshold
lfcThreshold<-,DESeqAnalysis,numeric-method	lfcThreshold
markdown	markdown
markdown,DESeqAnalysis-method	markdown
matchMetadataToFiles	matchMetadataToFiles
names,DESeqAnalysis-method	base
params	params
plotBaseMean	plotBaseMean
plotBaseMean,DESeqAnalysis-method	plotBaseMean
plotBaseMean,DESeqDataSet-method	plotBaseMean
plotBaseMean,DESeqResults-method	plotBaseMean
plotBaseMean,numeric-method	plotBaseMean
plotCorrelationHeatmap	plotHeatmap
plotCorrelationHeatmap,DESeqAnalysis-method	plotHeatmap
plotCounts	plotCounts
plotCounts,DESeqAnalysis-method	plotCounts
plotCounts,DESeqDataSet-method	plotCounts
plotCounts,DESeqTransform-method	plotCounts
plotDEGHeatmap	plotDEGHeatmap
plotDEGHeatmap,DESeqAnalysis-method	plotDEGHeatmap
plotDEGHeatmap,DESeqResults-method	plotDEGHeatmap
plotDEGPCA	plotDEGPCA
plotDEGPCA,DESeqAnalysis-method	plotDEGPCA
plotDEGPCA,DESeqResults-method	plotDEGPCA
plotDEGStackedBar	plotDEGStackedBar
plotDEGStackedBar,DESeqAnalysis-method	plotDEGStackedBar
plotDEGUpset	plotDEGUpset
plotDEGUpset,DESeqAnalysis-method	plotDEGUpset
plotHeatmap	plotHeatmap
plotHeatmap,DESeqAnalysis-method	plotHeatmap
plotMA	plotMA
plotMA,DESeqAnalysis-method	plotMA
plotMA,DESeqResults-method	plotMA
plotMeanAverage	plotMA
plotPCA	plotPCA
plotPCA,DESeqAnalysis-method	plotPCA
plotPCA,DESeqDataSet-method	plotPCA
plotPCA,DESeqTransform-method	plotPCA
plotQuantileHeatmap	plotHeatmap
plotQuantileHeatmap,DESeqAnalysis-method	plotHeatmap
plotVolcano	plotVolcano
plotVolcano,DESeqAnalysis-method	plotVolcano
plotVolcano,DESeqResults-method	plotVolcano
prepareTximportFiles	prepareTximportFiles
results	results
results,DESeqAnalysis-method	results
results,DESeqDataSet-method	results
resultsDiff	resultsDiff
resultsDiff,DESeqAnalysis,missingOrNULL-method	resultsDiff
resultsDiff,DESeqResults,DESeqResults-method	resultsDiff
resultsMatrix	resultsMatrix
resultsMatrix,DESeqAnalysis-method	resultsMatrix
resultsMatrix,DESeqAnalysisList-method	resultsMatrix
resultsNames	resultsNames
resultsNames,DESeqAnalysis-method	resultsNames
resultsNames,DESeqDataSet-method	resultsNames
resultsNames<-	resultsNames
resultsNames<-,DESeqAnalysis,character-method	resultsNames
resultsTables	resultsTables
resultsTables,DESeqAnalysis-method	resultsTables
resultsTables,DESeqResults-method	resultsTables
rownames,DESeqAnalysis-method	base
sampleData	sampleData
sampleData,DESeqAnalysis-method	sampleData
show	show
show,DESeqAnalysis-method	show
topTables	topTables
topTables,DESeqAnalysis-method	topTables
topTables,DESeqResults-method	topTables
topTables,list-method	topTables
transformType	transformType
transformType,DESeqAnalysis-method	transformType
transformType,DESeqTransform-method	transformType
updateObject	updateObject
updateObject,DESeqAnalysis-method	updateObject
[,DESeqAnalysis,ANY,ANY,ANY-method	extract
