API for hbc/bcbioRNASeq
Bcbio RNA-Seq

Global functions
.assertHasValidCFA	Source code
.assertIsNotFastMode	Source code
.dataHasVariation	Source code
.featureCounts	Source code
.isFastMode	Source code
.isFastPipeline	Source code
.isGeneLevel	Source code
.isTranscriptLevel	Source code
.normalizedPlotArgs	Source code
.normalizedSE	Source code
.tximport	Source code
[,bcbioRNASeq,ANY,ANY,ANY-method	Man page
alphaSummary	Man page
as.DESeqDataSet	Man page
as.DESeqDataSet,bcbioRNASeq-method	Man page
as.DESeqTransform	Man page
as.DESeqTransform,bcbioRNASeq-method	Man page
as.DGEList	Man page
as.DGEList,bcbioRNASeq-method	Man page
bcb	Man page
bcbioRNASeq	Man page Source code
bcbioRNASeq-class	Man page
bcbioRNASeq-package	Man page
bcbioRnaSeqTestsUrl	Man page Man page
camel	Man page Source code
coerce	Man page
coerce,bcbioRNASeq,DESeqDataSet-method	Man page
coerce,bcbioRNASeq,DESeqTransform-method	Man page
coerce,bcbioRNASeq,DGEList-method	Man page
counts	Man page
counts,bcbioRNASeq-method	Man page
counts<-	Man page
deprecated	Man page
extract	Man page
loadRemoteData	Man page
plot5Prime3PrimeBias	Man page
plot5Prime3PrimeBias,bcbioRNASeq-method	Man page
plotCorrelationHeatmap	Man page
plotCorrelationHeatmap,bcbioRNASeq-method	Man page
plotCountDensity	Man page Source code
plotCounts	Man page
plotCounts,bcbioRNASeq-method	Man page
plotCountsPerBiotype	Man page
plotCountsPerBiotype,bcbioRNASeq-method	Man page
plotCountsPerBroadClass	Man page
plotCountsPerBroadClass,bcbioRNASeq-method	Man page
plotCountsPerFeature	Man page
plotCountsPerFeature,bcbioRNASeq-method	Man page
plotCountsPerGene	Man page Source code
plotDEGHeatmap	Man page Source code
plotDegHeatmap	Man page
plotDegHeatmap,missing-method	Man page
plotDispEsts	Man page
plotDispEsts,bcbioRNASeq-method	Man page
plotExonicMappingRate	Man page
plotExonicMappingRate,bcbioRNASeq-method	Man page
plotFeatureSaturation	Man page
plotFeatureSaturation,bcbioRNASeq-method	Man page
plotFeaturesDetected	Man page
plotGenderMarkers	Man page
plotGenderMarkers,bcbioRNASeq-method	Man page
plotGeneSaturation	Man page Source code
plotGenesDetected	Man page Source code
plotHeatmap	Man page
plotIntronicMappingRate	Man page
plotIntronicMappingRate,bcbioRNASeq-method	Man page
plotMA	Man page Source code
plotMappedReads	Man page
plotMappedReads,bcbioRNASeq-method	Man page
plotMappingRate	Man page
plotMappingRate,bcbioRNASeq-method	Man page
plotMeanAverage	Man page Source code
plotMeanSD	Man page Source code
plotMeanSd	Man page
plotMeanSd,bcbioRNASeq-method	Man page
plotPCA	Man page Source code
plotPCACovariates	Man page Source code
plotPca	Man page
plotPca,bcbioRNASeq-method	Man page
plotPcaCovariates	Man page
plotPcaCovariates,bcbioRNASeq-method	Man page
plotPseudoVsAlignedCounts	Man page
plotPseudoVsAlignedCounts,bcbioRNASeq-method	Man page
plotQC	Man page Source code
plotQc	Man page
plotQc,bcbioRNASeq-method	Man page
plotQuantileHeatmap	Man page
plotRRNAMappingRate	Man page Source code
plotRrnaMappingRate	Man page
plotRrnaMappingRate,bcbioRNASeq-method	Man page
plotTotalReads	Man page
plotTotalReads,bcbioRNASeq-method	Man page
prepareRNASeqTemplate	Man page Source code
reexports	Man page
relativeLogExpression	Man page
relativeLogExpression,SummarizedExperiment-method	Man page
relativeLogExpression,matrix-method	Man page
saveData	Man page
show	Man page
show,bcbioRNASeq-method	Man page
slotAlignedCounts	Man page
slotAlignedCounts,bcbioRNASeq-method	Man page
tmm	Man page
tmm,SummarizedExperiment-method	Man page
tmm,matrix-method	Man page
topTables	Man page Source code
updateObject	Man page
updateObject,bcbioRNASeq-method	Man page
writeCounts	Man page Source code