bcbioRNASeq-package	bcbioRNASeq-package
aggregateReplicates	aggregateReplicates
aggregateReplicates,bcbioRNASeq-method	aggregateReplicates
alphaSummary	alphaSummary
alphaSummary,DESeqDataSet-method	alphaSummary
as	coerce
bcbioRNASeq	bcbioRNASeq
bcbioRNASeq-class	bcbioRNASeq
bcb_small	bcb_small
coerce	coerce
coerce,bcbioRNASeq,DESeqDataSet-method	coerce
contrastName	contrastName
contrastName,DESeqResults-method	contrastName
counts	counts
counts,bcbioRNASeq-method	counts
dds_small	dds_small
deprecated	deprecated
design,bcbioRNASeq-method	deprecated
design<-,bcbioRNASeq,formula-method	deprecated
download	deprecated
extract	extract
gender_markers	gender_markers
general	general
loadRNASeq	bcbioRNASeq
loadRNASeqRun	deprecated
meltLog10	deprecated
metrics	metrics
metrics,bcbioRNASeq-method	metrics
plot53Bias	deprecated
plot5Prime3PrimeBias	plot5Prime3PrimeBias
plot5Prime3PrimeBias,bcbioRNASeq-method	plot5Prime3PrimeBias
plotCorrelationHeatmap	plotCorrelationHeatmap
plotCorrelationHeatmap,bcbioRNASeq-method	plotCorrelationHeatmap
plotCorrelationHeatmap,DESeqTransform-method	plotCorrelationHeatmap
plotCountDensity	plotCountDensity
plotCountDensity,bcbioRNASeq-method	plotCountDensity
plotCountsPerGene	plotCountsPerGene
plotCountsPerGene,bcbioRNASeq-method	plotCountsPerGene
plotDEGHeatmap	plotDEGHeatmap
plotDEGHeatmap,DESeqResults,bcbioRNASeq-method	plotDEGHeatmap
plotDEGHeatmap,DESeqResults,DESeqDataSet-method	plotDEGHeatmap
plotDEGHeatmap,DESeqResults,DESeqTransform-method	plotDEGHeatmap
plotDEGHeatmap,DESeqResults,SummarizedExperiment-method	plotDEGHeatmap
plotDEGPCA	plotDEGPCA
plotDEGPCA,DESeqResults,bcbioRNASeq-method	plotDEGPCA
plotDEGPCA,DESeqResults,DESeqDataSet-method	plotDEGPCA
plotDEGPCA,DESeqResults,DESeqTransform-method	plotDEGPCA
plotDEGPCA,DESeqResults,SummarizedExperiment-method	plotDEGPCA
plotDispersion	deprecated
plotDispEsts	plotDispEsts
plotDispEsts,bcbioRNASeq-method	plotDispEsts
plotExonicMappingRate	plotExonicMappingRate
plotExonicMappingRate,bcbioRNASeq-method	plotExonicMappingRate
plotGenderMarkers	plotGenderMarkers
plotGenderMarkers,bcbioRNASeq-method	plotGenderMarkers
plotGenderMarkers,DESeqDataSet-method	plotGenderMarkers
plotGenderMarkers,DESeqTransform-method	plotGenderMarkers
plotGenderMarkers,SummarizedExperiment-method	plotGenderMarkers
plotGene	plotGene
plotGene,bcbioRNASeq-method	plotGene
plotGene,DESeqDataSet-method	plotGene
plotGene,DESeqTransform-method	plotGene
plotGene,SummarizedExperiment-method	plotGene
plotGeneDetectionSaturation	deprecated
plotGeneHeatmap	deprecated
plotGeneSaturation	plotGeneSaturation
plotGeneSaturation,bcbioRNASeq-method	plotGeneSaturation
plotGenesDetected	plotGenesDetected
plotGenesDetected,bcbioRNASeq-method	plotGenesDetected
plotIntronicMappingRate	plotIntronicMappingRate
plotIntronicMappingRate,bcbioRNASeq-method	plotIntronicMappingRate
plotMA	plotMA
plotMA,DESeqResults-method	plotMA
plotMappedReads	plotMappedReads
plotMappedReads,bcbioRNASeq-method	plotMappedReads
plotMappingRate	plotMappingRate
plotMappingRate,bcbioRNASeq-method	plotMappingRate
plotMeanAverage	plotMA
plotMeanSD	plotMeanSD
plotMeanSD,bcbioRNASeq-method	plotMeanSD
plotMeanSD,DESeqDataSet-method	plotMeanSD
plotPCA	plotPCA
plotPCA,bcbioRNASeq-method	plotPCA
plotPCA,SummarizedExperiment-method	plotPCA
plotPCACovariates	plotPCACovariates
plotPCACovariates,bcbioRNASeq-method	plotPCACovariates
plotRRNAMappingRate	plotRRNAMappingRate
plotRRNAMappingRate,bcbioRNASeq-method	plotRRNAMappingRate
plotTotalReads	plotTotalReads
plotTotalReads,bcbioRNASeq-method	plotTotalReads
plotVolcano	plotVolcano
plotVolcano,DESeqResults-method	plotVolcano
prepareRNASeqTemplate	prepareRNASeqTemplate
resultsTables	resultsTables
resultsTables,DESeqResults,DESeqDataSet-method	resultsTables
resultsTables,DESeqResults,missingOrNULL-method	resultsTables
res_small	res_small
sampleData	sampleData
sampleData,bcbioRNASeq-method	sampleData
sampleData<-	sampleData
sampleData<-,bcbioRNASeq,DataFrame-method	sampleData
show	show
show,bcbioRNASeq-method	show
tmm	tmm
tmm,bcbioRNASeq-method	tmm
tmm,DESeqDataSet-method	tmm
tmm,matrix-method	tmm
topTables	topTables
topTables,DESeqResults-method	topTables
topTables,list-method	topTables
tpm	tpm
tpm,bcbioRNASeq-method	tpm
txi	deprecated
updateObject	updateObject
updateObject,bcbioRNASeq-method	updateObject
[,bcbioRNASeq,ANY,ANY,ANY-method	extract
