alphaSummary	alphaSummary
alphaSummary,DESeqAnalysis-method	alphaSummary
alphaSummary,DESeqDataSet-method	alphaSummary
alphaThreshold	alphaThreshold
alphaThreshold,DESeqAnalysis-method	alphaThreshold
alphaThreshold,DESeqAnalysisList-method	alphaThreshold
alphaThreshold,DESeqResults-method	alphaThreshold
alphaThreshold,DESeqResultsList-method	alphaThreshold
alphaThreshold<-	alphaThreshold
alphaThreshold<-,DESeqAnalysis,NULL-method	alphaThreshold
alphaThreshold<-,DESeqAnalysis,numeric-method	alphaThreshold
alphaThreshold<-,DESeqAnalysisList,NULL-method	alphaThreshold
alphaThreshold<-,DESeqAnalysisList,numeric-method	alphaThreshold
alphaThreshold<-,DESeqResults,numeric-method	alphaThreshold
alphaThreshold<-,DESeqResultsList,NULL-method	alphaThreshold
alphaThreshold<-,DESeqResultsList,numeric-method	alphaThreshold
apeglmResults	apeglmResults
apeglmResults,DESeqDataSet-method	apeglmResults
as.DESeqDataSet	coerce
as.DESeqDataSet,DESeqAnalysis-method	coerce
as.DESeqTransform	coerce
as.DESeqTransform,DESeqAnalysis-method	coerce
base	base
baseMeanThreshold	baseMeanThreshold
baseMeanThreshold,DESeqAnalysis-method	baseMeanThreshold
baseMeanThreshold,DESeqAnalysisList-method	baseMeanThreshold
baseMeanThreshold,DESeqResults-method	baseMeanThreshold
baseMeanThreshold,DESeqResultsList-method	baseMeanThreshold
baseMeanThreshold<-	baseMeanThreshold
baseMeanThreshold<-,DESeqAnalysis,NULL-method	baseMeanThreshold
baseMeanThreshold<-,DESeqAnalysis,numeric-method	baseMeanThreshold
baseMeanThreshold<-,DESeqAnalysisList,NULL-method	baseMeanThreshold
baseMeanThreshold<-,DESeqAnalysisList,numeric-method	baseMeanThreshold
baseMeanThreshold<-,DESeqResults,NULL-method	baseMeanThreshold
baseMeanThreshold<-,DESeqResults,numeric-method	baseMeanThreshold
baseMeanThreshold<-,DESeqResultsList,NULL-method	baseMeanThreshold
baseMeanThreshold<-,DESeqResultsList,numeric-method	baseMeanThreshold
coerce	coerce
coerce,DESeqAnalysis,DESeqDataSet-method	coerce
coerce,DESeqAnalysis,DESeqResultsList-method	coerce
coerce,DESeqAnalysis,DESeqTransform-method	coerce
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
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
degIntersection,DESeqAnalysisList-method	degIntersection
degIntersection,DESeqResultsList-method	degIntersection
degPerContrast	degPerContrast
degPerContrast,DESeqAnalysis-method	degPerContrast
deseq	deseq
DESeqAnalysis	DESeqAnalysis
DESeqAnalysis-class	DESeqAnalysis-class
DESeqAnalysisList	DESeqAnalysisList
DESeqAnalysisList,list-method	DESeqAnalysisList
DESeqAnalysisList,missing-method	DESeqAnalysisList
DESeqAnalysisList,SimpleList-method	DESeqAnalysisList
DESeqAnalysisList-class	DESeqAnalysisList-class
deseqMinimal	deseqMinimal
DESeqResultsList	DESeqResultsList
DESeqResultsList,DESeqAnalysis-method	DESeqResultsList
DESeqResultsList,DESeqAnalysisList-method	DESeqResultsList
DESeqResultsList,list-method	DESeqResultsList
DESeqResultsList,missing-method	DESeqResultsList
DESeqResultsList,SimpleList-method	DESeqResultsList
DESeqResultsList-class	DESeqResultsList-class
dim,DESeqAnalysis-method	base
dimnames,DESeqAnalysis-method	base
export	export
export,DESeqAnalysis,character-method	export
export,DESeqDataSet,character-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,DESeqAnalysisList-method	lfcShrink
lfcShrink,DESeqDataSet-method	lfcShrink
lfcShrink<-	lfcShrink
lfcShrink<-,DESeqAnalysis,logical-method	lfcShrink
lfcShrink<-,DESeqAnalysisList,logical-method	lfcShrink
lfcShrinkType	lfcShrinkType
lfcShrinkType,DESeqAnalysis-method	lfcShrinkType
lfcShrinkType,DESeqAnalysisList-method	lfcShrinkType
lfcShrinkType,DESeqResults-method	lfcShrinkType
lfcShrinkType,DESeqResultsList-method	lfcShrinkType
lfcThreshold	lfcThreshold
lfcThreshold,DESeqAnalysis-method	lfcThreshold
lfcThreshold,DESeqAnalysisList-method	lfcThreshold
lfcThreshold,DESeqResults-method	lfcThreshold
lfcThreshold,DESeqResultsList-method	lfcThreshold
lfcThreshold<-	lfcThreshold
lfcThreshold<-,DESeqAnalysis,NULL-method	lfcThreshold
lfcThreshold<-,DESeqAnalysis,numeric-method	lfcThreshold
lfcThreshold<-,DESeqAnalysisList,NULL-method	lfcThreshold
lfcThreshold<-,DESeqAnalysisList,numeric-method	lfcThreshold
lfcThreshold<-,DESeqResults,numeric-method	lfcThreshold
lfcThreshold<-,DESeqResultsList,numeric-method	lfcThreshold
markdownTables	markdownTables
markdownTables,DESeqAnalysis-method	markdownTables
markdownTables,DESeqResults-method	markdownTables
markdownTables,DFrameList-method	markdownTables
names,DESeqAnalysis-method	base
params	params
plotBaseMean	plotBaseMean
plotBaseMean,DESeqAnalysis-method	plotBaseMean
plotBaseMean,DESeqDataSet-method	plotBaseMean
plotBaseMean,DESeqResults-method	plotBaseMean
plotContrastScatter	plotContrastScatter
plotContrastScatter,DESeqAnalysis-method	plotContrastScatter
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
plotLfc	plotLfc
plotLfc,DESeqAnalysis-method	plotLfc
plotMa	plotMa
plotMa,DESeqAnalysis-method	plotMa
plotMa,DESeqResults-method	plotMa
plotPca	plotPca
plotPca,DESeqAnalysis-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,DESeqAnalysisList-method	resultsNames
resultsNames,DESeqDataSet-method	resultsNames
resultsNames,DESeqResultsList-method	resultsNames
resultsNames<-	resultsNames
resultsNames<-,DESeqAnalysis,character-method	resultsNames
resultsNames<-,DESeqResultsList,character-method	resultsNames
resultsTables	resultsTables
resultsTables,DESeqAnalysis-method	resultsTables
resultsTables,DESeqResults-method	resultsTables
rownames,DESeqAnalysis-method	base
sampleData	sampleData
sampleData,DESeqAnalysis-method	sampleData
sanitizeTximportIdentifiers	sanitizeTximportIdentifiers
show	show
show,DESeqAnalysis-method	show
transformType	transformType
transformType,DESeqAnalysis-method	transformType
transformType,DESeqAnalysisList-method	transformType
transformType,DESeqTransform-method	transformType
updateObject	updateObject
updateObject,DESeqAnalysis-method	updateObject
[,DESeqAnalysis,ANY,ANY,ANY-method	extract
