bcbio RNA-Seq

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Documentation for package ‘bcbioRNASeq’ version 0.5.4

• DESCRIPTION file.
• Package NEWS.

Help Pages

as.DESeqDataSet	Methods for coercing an object to a class
as.DESeqDataSet-method	Methods for coercing an object to a class
as.DESeqTransform	Methods for coercing an object to a class
as.DESeqTransform-method	Methods for coercing an object to a class
as.DGEList	Methods for coercing an object to a class
as.DGEList-method	Methods for coercing an object to a class
bcb	bcbio RNA-seq example data set
bcbioRNASeq	bcbio RNA-Seq data set
bcbioRNASeq-class	bcbio RNA-Seq data set
coerce	Methods for coercing an object to a class
coerce-method	Methods for coercing an object to a class
counts	Counts
counts-method	Counts
counts<-	Counts
extract	Extract or replace parts of an object
plot5Prime3PrimeBias	Plot 5' to 3' bias
plot5Prime3PrimeBias-method	Plot 5' to 3' bias
plotCorrelationHeatmap	Correlation heatmap
plotCorrelationHeatmap-method	Correlation heatmap
plotCountDensity	Plot counts per feature
plotCounts	Plot counts
plotCounts-method	Plot counts
plotCountsPerBiotype	Plot counts per biotype
plotCountsPerBiotype-method	Plot counts per biotype
plotCountsPerBroadClass	Plot counts per biotype
plotCountsPerBroadClass-method	Plot counts per biotype
plotCountsPerFeature	Plot counts per feature
plotCountsPerFeature-method	Plot counts per feature
plotCountsPerGene	Plot counts per feature
plotDispEsts	Plot dispersion estimates
plotDispEsts-method	Plot dispersion estimates
plotExonicMappingRate	Plot exonic mapping rate
plotExonicMappingRate-method	Plot exonic mapping rate
plotGenderMarkers	Plot sexually dimorphic gender marker genes
plotGenderMarkers-method	Plot sexually dimorphic gender marker genes
plotGeneSaturation	Plot gene detection saturation
plotGeneSaturation-method	Plot gene detection saturation
plotIntronicMappingRate	Plot intronic mapping rate
plotIntronicMappingRate-method	Plot intronic mapping rate
plotMappedReads	Plot mapped reads
plotMappedReads-method	Plot mapped reads
plotMappingRate	Plot mapping rate
plotMappingRate-method	Plot mapping rate
plotMeanSD	Plot row standard deviations vs. row means
plotMeanSD-method	Plot row standard deviations vs. row means
plotPCA	Principal component analysis plot
plotPCA-method	Principal component analysis plot
plotPCACovariates	Find correlation between principal components (PCs) and covariates
plotPCACovariates-method	Find correlation between principal components (PCs) and covariates
plotPseudoVsAlignedCounts	Plot pseudo vs. aligned counts
plotPseudoVsAlignedCounts-method	Plot pseudo vs. aligned counts
plotQC	Quality control
plotQC-method	Quality control
plotRRNAMappingRate	Plot ribosomal RNA (rRNA) mapping rate
plotRRNAMappingRate-method	Plot ribosomal RNA (rRNA) mapping rate
plotTotalReads	Plot total reads
plotTotalReads-method	Plot total reads
relativeLogExpression	Relative log expression
relativeLogExpression-method	Relative log expression
show	Show an object
show-method	Show an object
slotAlignedCounts	Slot aligned counts
slotAlignedCounts-method	Slot aligned counts
tmm	Trimmed mean of M-values
tmm-method	Trimmed mean of M-values
updateObject	Update object
updateObject-method	Update object
[-method	Extract or replace parts of an object