API for hbc/bcbioRnaseq
RNA-Seq Utilities

Global functions
[,bcbioRNASeq,ANY,ANY,ANY-method Man page
\%>\% Man page
addIsDECol Source code
aggregateReplicates Man page
aggregateReplicates,bcbioRNASeq-method Man page
alphaSummary Man page Man page
alphaSummary,DESeqDataSet-method Man page
alphaSummary,bcbioRNASeq-method Man page
as Man page
bcb_small Man page
bcbio,bcbioRNASeq-method Man page
bcbio<-,bcbioRNASeq-method Man page
bcbioRNASeq Man page Source code
bcbioRNASeq-class Man page
bcbioRNASeq-package Man page
coerce Man page
coerce-bcbioRNASeq-DESeqDataSet Man page
contrastName Man page Man page
contrastName,DESeqResults-method Man page
counts Man page
counts,bcbioRNASeq-method Man page
dataHasVariation Source code
dds_small Man page
degList Source code
deprecated Man page
design,bcbioRNASeq-method Man page
design<-,bcbioRNASeq,formula-method Man page
download Man page Source code
extract Man page
genderMarkers Man page
genePoint Source code
general Man page
ggplot Man page
glimpse Man page
loadRNASeq Man page Source code
loadRNASeqRun Man page Source code
markdownResultsTables Source code
meltCounts Source code
meltLog10 Man page Source code
meltLog2Counts Source code
metrics Man page
metrics,bcbioRNASeq-method Man page
new.bcbioRNASeq Source code
nonzeroGenes Source code
plot53Bias Man page Source code
plot5Prime3PrimeBias Man page Man page
plot5Prime3PrimeBias,bcbioRNASeq-method Man page
plotCorrelationHeatmap Man page
plotCorrelationHeatmap,DESeqTransform-method Man page
plotCorrelationHeatmap,bcbioRNASeq-method Man page
plotCountDensity Man page Man page
plotCountDensity,bcbioRNASeq-method Man page
plotCountsPerGene Man page Man page
plotCountsPerGene,bcbioRNASeq-method Man page
plotDEGHeatmap Man page Man page
plotDEGHeatmap,DESeqResults,DESeqDataSet-method Man page
plotDEGHeatmap,DESeqResults,SummarizedExperiment-method Man page
plotDEGHeatmap,DESeqResults,bcbioRNASeq-method Man page
plotDEGPCA Man page Man page
plotDEGPCA,DESeqResults,DESeqDataSet-method Man page
plotDEGPCA,DESeqResults,SummarizedExperiment-method Man page
plotDEGPCA,DESeqResults,bcbioRNASeq-method Man page
plotDispEsts Man page
plotDispEsts,bcbioRNASeq-method Man page
plotDispersion Man page Source code
plotExonicMappingRate Man page Man page
plotExonicMappingRate,bcbioRNASeq-method Man page
plotGenderMarkers Man page Man page
plotGenderMarkers,DESeqDataSet-method Man page
plotGenderMarkers,DESeqTransform-method Man page
plotGenderMarkers,SummarizedExperiment-method Man page
plotGenderMarkers,bcbioRNASeq-method Man page
plotGene Man page
plotGene,DESeqDataSet-method Man page
plotGene,DESeqTransform-method Man page
plotGene,SummarizedExperiment-method Man page
plotGene,bcbioRNASeq-method Man page
plotGeneDetectionSaturation Man page Source code
plotGeneFacet Source code
plotGeneHeatmap Man page Source code
plotGeneList Source code
plotGeneSaturation Man page Man page
plotGeneSaturation,bcbioRNASeq-method Man page
plotGeneWide Source code
plotGenesDetected Man page Man page
plotGenesDetected,bcbioRNASeq-method Man page
plotIntronicMappingRate Man page Man page
plotIntronicMappingRate,bcbioRNASeq-method Man page
plotMappedReads Man page Man page
plotMappedReads,bcbioRNASeq-method Man page
plotMappingRate Man page Man page
plotMappingRate,bcbioRNASeq-method Man page
plotMeanAverage Man page Man page
plotMeanAverage,DESeqResults-method Man page
plotMeanSD Man page Man page Source code
plotMeanSD,DESeqDataSet-method Man page
plotMeanSD,bcbioRNASeq-method Man page
plotPCA Man page
plotPCA,SummarizedExperiment-method Man page
plotPCA,bcbioRNASeq-method Man page
plotPCACovariates Man page Man page
plotPCACovariates,bcbioRNASeq-method Man page
plotRRNAMappingRate Man page Man page
plotRRNAMappingRate,bcbioRNASeq-method Man page
plotTotalReads Man page Man page
plotTotalReads,bcbioRNASeq-method Man page
plotVolcano Man page Man page
plotVolcano,DESeqResults-method Man page
prepareRNASeqTemplate Man page Source code
reexports Man page Man page Man page Man page Man page Man page Man page Man page Man page
regenerateDESeqDataSet Source code
regenerateTximportList Source code
res_small Man page
resultsTables Man page Man page
resultsTables,DESeqResults,DESeqDataSet-method Man page
resultsTables,DESeqResults,missingOrNULL-method Man page
rld_small Man page
scale_color_hue Man page
scale_color_manual Man page
scale_colour_hue Man page
scale_colour_manual Man page
scale_fill_hue Man page
scale_fill_manual Man page
show Man page
show,bcbioRNASeq-method Man page
subsetTop Source code
tmm Man page Man page
tmm,DESeqDataSet-method Man page
tmm,bcbioRNASeq-method Man page
tmm,matrix-method Man page
topTables Man page Man page
topTables,DESeqResults-method Man page
topTables,list-method Man page
tpm Man page Man page
tpm,bcbioRNASeq-method Man page
txi Man page Source code
tximport Source code
updateObject Man page
updateObject,bcbioRNASeq-method Man page
hbc/bcbioRnaseq documentation built on June 26, 2018, 7:17 a.m.