bcbioRNASeq-package	bcbioRNASeq-package
AllGenerics	AllGenerics
alphaSummary	alphaSummary
alphaSummary,bcbioRNASeq-method	alphaSummary
alphaSummary,DESeqDataSet-method	alphaSummary
annotable	annotable
annotable,bcbioRNASeq-method	annotable
bcbio	bcbio
bcbio,bcbioRNADataSet-method	bcbio
bcbio,bcbioRNASeq-method	bcbio
bcbio<-,bcbioRNADataSet-method	bcbio
bcbio<-,bcbioRNASeq-method	bcbio
bcbioRNADataSet	bcbioRNADataSet-class
bcbioRNADataSet-class	bcbioRNADataSet-class
bcbioRNASeq	bcbioRNASeq-class
bcbioRNASeq-class	bcbioRNASeq-class
coerce	coerce
coerce-bcbioRNASeq-SummarizedExperiment	coerce
colData	colData
colData<-,bcbioRNASeq,DataFrame-method	colData
counts	counts
counts,bcbioRNASeq-method	counts
deprecated	deprecated
design	design
design,bcbioRNASeq-method	design
design<-,bcbioRNASeq,formula-method	design
download	deprecated
flatFiles	flatFiles
flatFiles,bcbioRNASeq-method	flatFiles
genderMarkers	genderMarkers
gene2symbol	gene2symbol
gene2symbol,bcbioRNASeq-method	gene2symbol
ggplot	reexports
glimpse	reexports
inferno	reexports
interestingGroups	interestingGroups
interestingGroups,bcbioRNASeq-method	interestingGroups
interestingGroups<-,bcbioRNASeq,character-method	interestingGroups
interestingGroups<-,bcbioRNASeq,NULL-method	interestingGroups
loadRNASeq	loadRNASeq
loadRNASeqRun	deprecated
meltLog10	meltLog10
meltLog10,bcbioRNASeq-method	meltLog10
meltLog10,DESeqDataSet-method	meltLog10
meltLog10,DESeqTransform-method	meltLog10
metrics	metrics
metrics,bcbioRNASeq-method	metrics
plot53Bias	plot53Bias
plot53Bias,bcbioRNASeq-method	plot53Bias
plot53Bias,data.frame-method	plot53Bias
plotCorrelationHeatmap	plotCorrelationHeatmap
plotCorrelationHeatmap,bcbioRNASeq-method	plotCorrelationHeatmap
plotCountDensity	plotCountDensity
plotCountDensity,bcbioRNASeq-method	plotCountDensity
plotCountDensity,data.frame-method	plotCountDensity
plotCountsPerGene	plotCountsPerGene
plotCountsPerGene,bcbioRNASeq-method	plotCountsPerGene
plotCountsPerGene,data.frame-method	plotCountsPerGene
plotDEGHeatmap	plotDEGHeatmap
plotDEGHeatmap,DESeqResults,DESeqDataSet-method	plotDEGHeatmap
plotDEGHeatmap,DESeqResults,DESeqTransform-method	plotDEGHeatmap
plotDEGHeatmap,DESeqResults,matrix-method	plotDEGHeatmap
plotDispersion	deprecated
plotDispEsts	plotDispEsts
plotDispEsts,bcbioRNASeq-method	plotDispEsts
plotExonicMappingRate	plotExonicMappingRate
plotExonicMappingRate,bcbioRNASeq-method	plotExonicMappingRate
plotExonicMappingRate,data.frame-method	plotExonicMappingRate
plotGenderMarkers	plotGenderMarkers
plotGenderMarkers,bcbioRNASeq-method	plotGenderMarkers
plotGenderMarkers,DESeqDataSet-method	plotGenderMarkers
plotGenderMarkers,matrix-method	plotGenderMarkers
plotGene	plotGene
plotGene,bcbioRNASeq-method	plotGene
plotGene,DESeqDataSet-method	plotGene
plotGene,DESeqTransform-method	plotGene
plotGene,matrix-method	plotGene
plotGeneDetectionSaturation	deprecated
plotGeneHeatmap	deprecated
plotGeneSaturation	plotGeneSaturation
plotGeneSaturation,bcbioRNASeq,missing-method	plotGeneSaturation
plotGeneSaturation,data.frame,matrix-method	plotGeneSaturation
plotGenesDetected	plotGenesDetected
plotGenesDetected,bcbioRNASeq,missing-method	plotGenesDetected
plotGenesDetected,data.frame,DESeqDataSet-method	plotGenesDetected
plotGenesDetected,data.frame,matrix-method	plotGenesDetected
plotHeatmap	plotHeatmap
plotHeatmap,bcbioRNASeq-method	plotHeatmap
plotHeatmap,DESeqDataSet-method	plotHeatmap
plotHeatmap,DESeqTransform-method	plotHeatmap
plotIntronicMappingRate	plotIntronicMappingRate
plotIntronicMappingRate,bcbioRNASeq-method	plotIntronicMappingRate
plotIntronicMappingRate,data.frame-method	plotIntronicMappingRate
plotMA	plotMA
plotMA,data.frame-method	plotMA
plotMA,DESeqResults-method	plotMA
plotMappedReads	plotMappedReads
plotMappedReads,bcbioRNASeq-method	plotMappedReads
plotMappedReads,data.frame-method	plotMappedReads
plotMappingRate	plotMappingRate
plotMappingRate,bcbioRNASeq-method	plotMappingRate
plotMappingRate,data.frame-method	plotMappingRate
plotMeanSD	plotMeanSD
plotMeanSD,bcbioRNASeq-method	plotMeanSD
plotMeanSD,DESeqDataSet-method	plotMeanSD
plotPCA	plotPCA
plotPCA,bcbioRNASeq-method	plotPCA
plotPCACovariates	plotPCACovariates
plotPCACovariates,bcbioRNASeq-method	plotPCACovariates
plotRRNAMappingRate	plotRRNAMappingRate
plotRRNAMappingRate,bcbioRNASeq-method	plotRRNAMappingRate
plotRRNAMappingRate,data.frame-method	plotRRNAMappingRate
plotTotalReads	plotTotalReads
plotTotalReads,bcbioRNASeq-method	plotTotalReads
plotTotalReads,data.frame-method	plotTotalReads
plotVolcano	plotVolcano
plotVolcano,data.frame-method	plotVolcano
plotVolcano,DESeqResults-method	plotVolcano
prepareRNASeqTemplate	prepareRNASeqTemplate
prepareRNASeqTemplate,missing-method	prepareRNASeqTemplate
reexports	reexports
resultsTables	resultsTables
resultsTables,DESeqResults-method	resultsTables
sampleMetadata	sampleMetadata
sampleMetadata,bcbioRNASeq-method	sampleMetadata
sampleMetadata,DESeqDataSet-method	sampleMetadata
sampleMetadata,DESeqTransform-method	sampleMetadata
scale_color_viridis	reexports
scale_fill_viridis	reexports
selectSamples	selectSamples
selectSamples,bcbioRNASeq-method	selectSamples
subset	subset
tmm	tmm
tmm,bcbioRNASeq-method	tmm
tmm,DESeqDataSet-method	tmm
tmm,matrix-method	tmm
topTables	topTables
topTables,list-method	topTables
tpm	tpm
tpm,bcbioRNASeq-method	tpm
txi	deprecated
upgrade-bcbioRNASeq	coerce
viridis	reexports
[,bcbioRNASeq,ANY,ANY,ANY-method	subset
