API for hbc/bcbioRNASeq
RNA-Seq Utilities

Global functions
AllGenerics Man page
[,bcbioRNASeq,ANY,ANY,ANY-method Man page
aggregateReplicates Man page
aggregateReplicates,DESeqDataSet-method Man page
aggregateReplicates,matrix-method Man page
aggregateReplicatesDESeqDataSet Source code
aggregateReplicatesMatrix Source code
alphaSummary Man page Source code
alphaSummary,DESeqDataSet-method Man page
alphaSummary,bcbioRNASeq-method Man page
annotable Man page
annotable,bcbioRNASeq-method Man page
bcb Man page
bcbio Man page
bcbio,bcbioRNADataSet-method Man page
bcbio,bcbioRNASeq-method Man page
bcbio<-,bcbioRNADataSet-method Man page
bcbio<-,bcbioRNASeq-method Man page
bcbioRNADataSet Man page
bcbioRNADataSet-class Man page
bcbioRNASeq Man page
bcbioRNASeq-class Man page
bcbioRNASeq-package Man page
coerce Man page
coerceLegacy Source code
countSubset Source code
counts Man page
counts,bcbioRNASeq-method Man page
createDDS Source code
dds Man page
deprecated Man page
download Man page Source code
flatFiles Man page
flatFiles,bcbioRNASeq-method Man page
genderMarkers Man page
ggplot Man page
inferno Man page
interestingGroups Man page
interestingGroups,bcbioRNASeq-method Man page
interestingGroups<-,bcbioRNASeq,NULL-method Man page
interestingGroups<-,bcbioRNASeq,character-method Man page
joinMelt Source code
loadRNASeq Man page Source code
loadRNASeqRun Man page Source code
mdResultsTables Source code
meltLog10 Man page Source code
meltLog10,DESeqDataSet-method Man page
meltLog10,DESeqTransform-method Man page
meltLog10,bcbioRNASeq-method Man page
metrics Man page
metrics,bcbioRNASeq-method Man page
onLoad Source code
plot53Bias Man page Source code
plot53Bias,bcbioRNASeq-method Man page
plot53Bias,data.frame-method Man page
plotCorrelationHeatmap Man page Source code
plotCorrelationHeatmap,bcbioRNASeq-method Man page
plotCountDensity Man page Source code
plotCountDensity,bcbioRNASeq-method Man page
plotCountDensity,data.frame-method Man page
plotCountsPerGene Man page Source code
plotCountsPerGene,bcbioRNASeq-method Man page
plotCountsPerGene,data.frame-method Man page
plotDEGHeatmap Man page Source code
plotDEGHeatmap,DESeqResults,DESeqDataSet-method Man page
plotDEGHeatmap,DESeqResults,DESeqTransform-method Man page
plotDispEsts Man page
plotDispEsts,bcbioRNASeq-method Man page
plotDispersion Man page Source code
plotExonicMappingRate Man page Source code
plotExonicMappingRate,bcbioRNASeq-method Man page
plotExonicMappingRate,data.frame-method Man page
plotGenderMarkers Man page Source code
plotGenderMarkers,DESeqDataSet-method Man page
plotGenderMarkers,bcbioRNASeq-method Man page
plotGenderMarkers,matrix-method Man page
plotGene Man page Source code
plotGene,bcbioRNASeq-method Man page
plotGeneDetectionSaturation Man page Source code
plotGeneHeatmap Man page Source code
plotGeneSaturation Man page Source code
plotGeneSaturation,bcbioRNASeq,missing-method Man page
plotGeneSaturation,data.frame,matrix-method Man page
plotGenesDetected Man page Source code
plotGenesDetected,bcbioRNASeq,missing-method Man page
plotGenesDetected,data.frame,DESeqDataSet-method Man page
plotGenesDetected,data.frame,matrix-method Man page
plotHeatmap Man page Source code
plotHeatmap,DESeqDataSet-method Man page
plotHeatmap,DESeqTransform-method Man page
plotHeatmap,bcbioRNASeq-method Man page
plotHeatmap,matrix-method Man page
plotIntronicMappingRate Man page Source code
plotIntronicMappingRate,bcbioRNASeq-method Man page
plotIntronicMappingRate,data.frame-method Man page
plotMA Man page Source code
plotMA,DESeqResults-method Man page
plotMA,data.frame-method Man page
plotMappedReads Man page Source code
plotMappedReads,bcbioRNASeq-method Man page
plotMappedReads,data.frame-method Man page
plotMappingRate Man page Source code
plotMappingRate,bcbioRNASeq-method Man page
plotMappingRate,data.frame-method Man page
plotMeanSD Man page Source code
plotMeanSD,DESeqDataSet-method Man page
plotMeanSD,bcbioRNASeq-method Man page
plotPCA Man page Source code
plotPCA,bcbioRNASeq-method Man page
plotPCACovariates Man page Source code
plotPCACovariates,bcbioRNASeq-method Man page
plotRRNAMappingRate Man page Source code
plotRRNAMappingRate,bcbioRNASeq-method Man page
plotRRNAMappingRate,data.frame-method Man page
plotTotalReads Man page Source code
plotTotalReads,bcbioRNASeq-method Man page
plotTotalReads,data.frame-method Man page
plotVolcano Man page Source code
plotVolcano,DESeqResults-method Man page
plotVolcano,data.frame-method Man page
prepareRNASeqTemplate Man page
prepareRNASeqTemplate,missing-method Man page
qcPassLine Source code
qcWarnLine Source code
reexports Man page
res Man page
resContrastName Source code
resultsTables Man page
resultsTables,DESeqResults-method Man page
resultsTablesDESeqResults Source code
rld Man page
sampleDirs Source code
sampleMetadata Man page Source code
sampleMetadata,DESeqDataSet-method Man page
sampleMetadata,DESeqTransform-method Man page
sampleMetadata,bcbioRNASeq-method Man page
scale_color_viridis Man page
scale_fill_viridis Man page
subset Man page Source code
subsetTop Source code
tmm Man page Source code
tmm,DESeqDataSet-method Man page
tmm,bcbioRNASeq-method Man page
tmm,matrix-method Man page
topTables Man page
topTables,list-method Man page
tpm Man page
tpm,bcbioRNASeq-method Man page
tx2gene Source code
txi Man page
txi,bcbioRNASeq-method Man page
tximport Source code
upgrade-bcbioRNASeq Man page
viridis Man page
hbc/bcbioRNASeq documentation built on Nov. 9, 2017, 4:14 p.m.