alphaSummary	deprecated
as.DESeqDataSet	coerce
as.DESeqDataSet,bcbioRNASeq-method	coerce
as.DESeqTransform	coerce
as.DESeqTransform,bcbioRNASeq-method	coerce
as.DGEList	coerce
as.DGEList,bcbioRNASeq-method	coerce
bcb	bcb
bcbioRNASeq	bcbioRNASeq
bcbioRNASeq-class	bcbioRNASeq-class
bcbioRNASeqTestsURL	bcbioRNASeqTestsURL
coerce	coerce
coerce,bcbioRNASeq,DESeqDataSet-method	coerce
coerce,bcbioRNASeq,DESeqTransform-method	coerce
coerce,bcbioRNASeq,DGEList-method	coerce
contrastName	deprecated
counts	counts
counts,bcbioRNASeq-method	counts
counts<-	counts
defunct	defunct
deprecated	deprecated
extract	extract
plot5Prime3PrimeBias	plot5Prime3PrimeBias
plot5Prime3PrimeBias,bcbioRNASeq-method	plot5Prime3PrimeBias
plotCorrelationHeatmap	plotCorrelationHeatmap
plotCorrelationHeatmap,bcbioRNASeq-method	plotCorrelationHeatmap
plotCountDensity	plotCountsPerFeature
plotCounts	plotCounts
plotCounts,bcbioRNASeq-method	plotCounts
plotCountsPerBiotype	plotCountsPerBiotype
plotCountsPerBiotype,bcbioRNASeq-method	plotCountsPerBiotype
plotCountsPerBroadClass	plotCountsPerBiotype
plotCountsPerBroadClass,bcbioRNASeq-method	plotCountsPerBiotype
plotCountsPerFeature	plotCountsPerFeature
plotCountsPerFeature,bcbioRNASeq-method	plotCountsPerFeature
plotCountsPerGene	plotCountsPerFeature
plotDEGHeatmap	deprecated
plotDEGPCA	deprecated
plotDispEsts	plotDispEsts
plotDispEsts,bcbioRNASeq-method	plotDispEsts
plotExonicMappingRate	plotExonicMappingRate
plotExonicMappingRate,bcbioRNASeq-method	plotExonicMappingRate
plotFeaturesDetected	reexports
plotGenderMarkers	plotGenderMarkers
plotGenderMarkers,bcbioRNASeq-method	plotGenderMarkers
plotGeneSaturation	plotGeneSaturation
plotGeneSaturation,bcbioRNASeq-method	plotGeneSaturation
plotGenesDetected	deprecated
plotHeatmap	reexports
plotIntronicMappingRate	plotIntronicMappingRate
plotIntronicMappingRate,bcbioRNASeq-method	plotIntronicMappingRate
plotMA	deprecated
plotMappedReads	plotMappedReads
plotMappedReads,bcbioRNASeq-method	plotMappedReads
plotMappingRate	plotMappingRate
plotMappingRate,bcbioRNASeq-method	plotMappingRate
plotMeanAverage	deprecated
plotMeanSD	plotMeanSD
plotMeanSD,bcbioRNASeq-method	plotMeanSD
plotPCA	plotPCA
plotPCA,bcbioRNASeq-method	plotPCA
plotPCACovariates	plotPCACovariates
plotPCACovariates,bcbioRNASeq-method	plotPCACovariates
plotPseudoVsAlignedCounts	plotPseudoVsAlignedCounts
plotPseudoVsAlignedCounts,bcbioRNASeq-method	plotPseudoVsAlignedCounts
plotQC	plotQC
plotQC,bcbioRNASeq-method	plotQC
plotQuantileHeatmap	reexports
plotRRNAMappingRate	plotRRNAMappingRate
plotRRNAMappingRate,bcbioRNASeq-method	plotRRNAMappingRate
plotTotalReads	plotTotalReads
plotTotalReads,bcbioRNASeq-method	plotTotalReads
plotVolcano	deprecated
prepareRNASeqTemplate	defunct
reexports	reexports
relativeLogExpression	relativeLogExpression
relativeLogExpression,matrix-method	relativeLogExpression
relativeLogExpression,SummarizedExperiment-method	relativeLogExpression
resultsTables	deprecated
show	show
show,bcbioRNASeq-method	show
slotAlignedCounts	slotAlignedCounts
slotAlignedCounts,bcbioRNASeq-method	slotAlignedCounts
tmm	tmm
tmm,matrix-method	tmm
tmm,SummarizedExperiment-method	tmm
topTables	deprecated
updateObject	updateObject
updateObject,bcbioRNASeq-method	updateObject
[,bcbioRNASeq,ANY,ANY,ANY-method	extract
