All functions
aggregateReplicates	Aggregate Lane-Split Technical Replicates
alphaSummary	Print Summary Statistics of Alpha Level Cutoffs
annotable	Ensembl Annotations
bcbio bcbio<-	bcbioRNASeq Additional Run Data Accessor
bcbioRNASeq-class	bcbioRNASeq
bcbioRNASeq-package	bcbioRNASeq
coerce	Coerce Object
counts	Count Matrix Accessors
flatFiles	Get Flat Files from S4 Object
interestingGroups interestingGroups<-	Interesting Groups
loadRNASeq	Load bcbio RNA-Seq Data
meltLog10	Melt Count Matrix to Long Format and log10 Transform
metrics	Sample Metrics
plot53Bias	Plot 5'->3' Bias
plotCorrelationHeatmap	Plot Correlation Heatmap
plotCountDensity	Plot Count Density
plotCountsPerGene	Plot Counts Per Gene
plotDEGHeatmap	Differentially Expressed Gene Heatmap
plotDispEsts	Plot Dispersion Estimates
plotExonicMappingRate	Plot Exonic Mapping Rate
plotGenderMarkers	Plot Sexually Dimorphic Gender Markers
plotGene	Plot Individual Genes
plotGeneSaturation	Plot Gene Detection Saturation
plotGenesDetected	Plot Genes Detected
plotHeatmap	Heatmap
plotIntronicMappingRate	Plot Intronic Mapping Rate
plotMA	Plot Mean Average
plotMappedReads	Plot Mapped Reads
plotMappingRate	Plot Mapping Rate
plotMeanSD	Plot Row Standard Deviations vs. Row Means
plotPCA	Sample PCA Plot for Transformed Data
plotPCACovariates	Find Correlation Between Principal Components (PCs) and Covariates
plotRRNAMappingRate	Plot Ribosomal RNA (rRNA) Mapping Rate
plotTotalReads	Plot Total Reads
plotVolcano	Plot Volcano
prepareRNASeqTemplate	Prepare RNA-Seq R Markdown Template
resultsTables	Differential Expression Results Tables
sampleMetadata	Sample Metadata
subset	Bracket-Based Subsetting
topTables	Top Tables of Differential Expression Results
tpm	Transcripts Per Million (TPM)