API for hbc/bcbioRnaseq
bcbio RNA-Seq

Global functions
.dataHasVariation Source code
.ddsMsg Source code
.featureCounts Source code
.isGeneLevel Source code
.isTranscriptLevel Source code
.isTximportReturn Source code
.normalizedPlotArgs Source code
.normalizedSE Source code
.requireDESeqAnalysis Source code
.showHeader Source code
.tximport Source code
[,bcbioRNASeq,ANY,ANY,ANY-method Man page
alphaSummary Man page Source code
bcb Man page
bcbioRNASeq Man page Source code
bcbioRNASeq-class Man page
bcbioRNASeqTestsURL Man page
coerce Man page
coerce,bcbioRNASeq,DESeqDataSet-method Man page
coerce,bcbioRNASeq,DESeqTransform-method Man page
coerce,bcbioRNASeq,DGEList-method Man page
contrastName Man page Source code
counts Man page
counts,bcbioRNASeq-method Man page
counts<- Man page
defunct Man page
deprecated Man page
extract Man page
loadRNASeq Man page Source code
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
plotDEGPCA Man page Source code
plotDispEsts Man page
plotDispEsts,bcbioRNASeq-method Man page
plotExonicMappingRate Man page
plotExonicMappingRate,bcbioRNASeq-method Man page
plotFeaturesDetected Man page
plotGenderMarkers Man page
plotGenderMarkers,bcbioRNASeq-method Man page
plotGeneSaturation Man page
plotGeneSaturation,bcbioRNASeq-method Man page
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
plotMeanSD,bcbioRNASeq-method Man page
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
plotQC,bcbioRNASeq-method Man page
plotQuantileHeatmap Man page
plotRRNAMappingRate Man page
plotRRNAMappingRate,bcbioRNASeq-method Man page
plotTotalReads Man page
plotTotalReads,bcbioRNASeq-method Man page
plotVolcano Man page Source code
prepareRNASeqTemplate Man page Source code
reexports Man page
relativeLogExpression Man page
relativeLogExpression,SummarizedExperiment-method Man page
relativeLogExpression,matrix-method Man page
resultsTables Man page Source code
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
hbc/bcbioRnaseq documentation built on Nov. 20, 2019, 10:21 p.m.