# bcbio RNA-Seq

## Documentation for package ‘bcbioRNASeq’ version 0.3.39

- DESCRIPTION file.

## 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 | Compare pseudoaligned counts to aligned counts.
plotPseudoVsAlignedCounts-method | Compare pseudoaligned counts to 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 into object
slotAlignedCounts-method | Slot aligned counts into object
tmm | Trimmed mean of M-values
tmm-method | Trimmed mean of M-values
updateObject | Update an object to its current class definition
updateObject-method | Update an object to its current class definition
[-method | Extract or replace parts of an object