Reference

S4 classes
bcbioRNASeq-class	bcbio RNA-Seq data set
bcbioRNASeq()	bcbio RNA-Seq data set
coerce	Methods for coercing an object to a class
`[`(<bcbioRNASeq>,<ANY>,<ANY>,<ANY>)	Extract or replace parts of an object
show(<bcbioRNASeq>)	Show an object
updateObject(<bcbioRNASeq>)	Update an object to its current class definition
Counts
counts(<bcbioRNASeq>)	Counts
relativeLogExpression()	Relative log expression
slotAlignedCounts()	Slot aligned counts into object
tmm()	Trimmed mean of M-values
Plots
plot5Prime3PrimeBias()	Plot 5' to 3' bias
plotCorrelationHeatmap(<bcbioRNASeq>)	Correlation heatmap
plotCounts()	Plot counts
plotCountsPerBiotype() plotCountsPerBroadClass()	Plot counts per biotype
plotCountsPerFeature() plotCountDensity()	Plot counts per feature
plotDispEsts()	Plot dispersion estimates
plotExonicMappingRate()	Plot exonic mapping rate
plotGenderMarkers()	Plot sexually dimorphic gender marker genes
plotGeneSaturation()	Plot gene detection saturation
plotIntronicMappingRate()	Plot intronic mapping rate
plotMappedReads()	Plot mapped reads
plotMappingRate()	Plot mapping rate
plotMeanSD()	Plot row standard deviations vs. row means
plotPCA()	Principal component analysis plot
plotPCACovariates()	Find correlation between principal components (PCs) and covariates
plotPseudoVsAlignedCounts()	Compare pseudoaligned counts to aligned counts.
plotQC()	Quality control
plotRRNAMappingRate()	Plot ribosomal RNA (rRNA) mapping rate
plotTotalReads()	Plot total reads
Example data
bcb	bcbio RNA-seq example data set
Reexports
reexports	Objects exported from other packages