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 Man page Source code
alphaSummary,DESeqDataSet-method Man page
alphaSummary,bcbioRNASeq-method Man page
annotable Man page
annotable,bcbioRNASeq-method 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
coerce-bcbioRNASeq-SummarizedExperiment Man page
coerceLegacy Source code
coerceToSummarizedExperiment Source code
colData Man page
colData<-,bcbioRNASeq,DataFrame-method Man page
counts Man page
counts,bcbioRNASeq-method Man page
deprecated Man page
design Man page
design,bcbioRNASeq-method Man page
design<-,bcbioRNASeq,formula-method Man page
download Man page Source code
flatFiles Man page
flatFiles,bcbioRNASeq-method Man page
genderMarkers Man page
gene2symbol Man page Source code
gene2symbol,bcbioRNASeq-method Man page
ggplot Man page
glimpse 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 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 Man page Source code
plot53Bias,bcbioRNASeq-method Man page
plot53Bias,data.frame-method Man page
plotCorrelationHeatmap Man page Man page Source code
plotCorrelationHeatmap,bcbioRNASeq-method Man page
plotCountDensity Man page Man page Source code
plotCountDensity,bcbioRNASeq-method Man page
plotCountDensity,data.frame-method Man page
plotCountsPerGene Man page Man page Source code
plotCountsPerGene,bcbioRNASeq-method Man page
plotCountsPerGene,data.frame-method Man page
plotDEGHeatmap Man page 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 Man page Source code
plotExonicMappingRate,bcbioRNASeq-method Man page
plotExonicMappingRate,data.frame-method Man page
plotGenderMarkers Man page 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
plotGene,matrix-method Man page
plotGeneDetectionSaturation Man page Source code
plotGeneHeatmap Man page Source code
plotGeneSaturation Man page Man page Source code
plotGeneSaturation,bcbioRNASeq,missing-method Man page
plotGeneSaturation,data.frame,matrix-method Man page
plotGenesDetected Man page 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 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 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 Man page Source code
plotMappedReads,bcbioRNASeq-method Man page
plotMappedReads,data.frame-method Man page
plotMappingRate Man page Man page Source code
plotMappingRate,bcbioRNASeq-method Man page
plotMappingRate,data.frame-method Man page
plotMeanSD Man page 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 Man page Source code
plotPCACovariates,bcbioRNASeq-method Man page
plotRRNAMappingRate Man page Man page Source code
plotRRNAMappingRate,bcbioRNASeq-method Man page
plotRRNAMappingRate,data.frame-method Man page
plotTotalReads Man page Man page Source code
plotTotalReads,bcbioRNASeq-method Man page
plotTotalReads,data.frame-method Man page
plotVolcano Man page Man page Source code
plotVolcano,DESeqResults-method Man page
plotVolcano,data.frame-method Man page
prepareRNASeqTemplate Man page Man page
prepareRNASeqTemplate,missing-method Man page
qcPassLine Source code
qcWarnLine Source code
reexports Man page Man page Man page Man page Man page Man page
resContrastName Source code
resultsTables Man page Man page
resultsTables,DESeqResults-method Man page
resultsTablesDESeqResults Source code
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 Man page Source code
tmm,DESeqDataSet-method Man page
tmm,bcbioRNASeq-method Man page
tmm,matrix-method Man page
topTables Man page Man page
topTables,list-method Man page
tpm Man page Man page
tpm,bcbioRNASeq-method Man page
tx2gene Source code
txi Man page Source code
tximport Source code
upgrade-bcbioRNASeq Man page
viridis Man page
hbc/bcbioRnaseq documentation built on Jan. 23, 2018, 2:56 p.m.