# RNA-Seq Utilities

## Documentation for package ‘bcbioRNASeq’ version 0.1.5

- DESCRIPTION file.

## Help Pages

bcbioRNASeq-package | bcbioRNASeq
alphaSummary | Print Summary Statistics of Alpha Level Cutoffs
alphaSummary-method | Print Summary Statistics of Alpha Level Cutoffs
annotable | Ensembl Annotations
annotable-method | Ensembl Annotations
bcbio | bcbioRNASeq Additional Run Data Accessor
bcbio-method | bcbioRNASeq Additional Run Data Accessor
bcbio<--method | bcbioRNASeq Additional Run Data Accessor
bcbioRNASeq | bcbioRNASeq Object Class
bcbioRNASeq-class | bcbioRNASeq Object Class
coerce | Coerce Object
coerce-bcbioRNASeq-SummarizedExperiment | Coerce Object
colData | Column Data
colData<--method | Column Data
counts | Count Matrix Accessors
counts-method | Count Matrix Accessors
design | Design Formula Accessor
design-method | Design Formula Accessor
design<--method | Design Formula Accessor
flatFiles | Get Flat Files from S4 Object
flatFiles-method | Get Flat Files from S4 Object
gene2symbol | Gene to Symbol Mappings
gene2symbol-method | Gene to Symbol Mappings
interestingGroups | Interesting Groups
interestingGroups-method | Interesting Groups
interestingGroups<--method | Interesting Groups
loadRNASeq | Load bcbio RNA-Seq Data
meltLog10 | Melt Count Matrix to Long Format and log10 Transform
meltLog10-method | Melt Count Matrix to Long Format and log10 Transform
metrics | Sample Metrics
metrics-method | Sample Metrics
plot53Bias | Plot 5'->3' Bias
plot53Bias-method | Plot 5'->3' Bias
plotCorrelationHeatmap | Plot Correlation Heatmap
plotCorrelationHeatmap-method | Plot Correlation Heatmap
plotCountDensity | Plot Count Density
plotCountDensity-method | Plot Count Density
plotCountsPerGene | Plot Counts Per Gene
plotCountsPerGene-method | Plot Counts Per Gene
plotDEGHeatmap | Differentially Expressed Gene Heatmap
plotDEGHeatmap-method | Differentially Expressed Gene Heatmap
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 Markers
plotGenderMarkers-method | Plot Sexually Dimorphic Gender Markers
plotGene | Plot Individual Genes
plotGene-method | Plot Individual Genes
plotGeneSaturation | Plot Gene Detection Saturation
plotGeneSaturation-method | Plot Gene Detection Saturation
plotGenesDetected | Plot Genes Detected
plotGenesDetected-method | Plot Genes Detected
plotHeatmap | Plot Heatmap
plotHeatmap-method | Plot Heatmap
plotIntronicMappingRate | Plot Intronic Mapping Rate
plotIntronicMappingRate-method | Plot Intronic Mapping Rate
plotMA | Plot Mean Average
plotMA-method | Plot Mean Average
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 | Sample PCA Plot for Transformed Data
plotPCA-method | Sample PCA Plot for Transformed Data
plotPCACovariates | Find Correlation Between Principal Components (PCs) and Covariates
plotPCACovariates-method | Find Correlation Between Principal Components (PCs) and Covariates
plotRRNAMappingRate | Plot Ribosomal RNA (rRNA) Mapping Rate
plotRRNAMappingRate-method | Plot Ribosomal RNA (rRNA) Mapping Rate
plotTotalReads | Plot Total Reads
plotTotalReads-method | Plot Total Reads
plotVolcano | Plot Volcano
plotVolcano-method | Plot Volcano
prepareRNASeqTemplate | Prepare RNA-Seq R Markdown Template
prepareRNASeqTemplate-method | Prepare RNA-Seq R Markdown Template
resultsTables | Differential Expression Results Tables
resultsTables-method | Differential Expression Results Tables
sampleMetadata | Sample Metadata
sampleMetadata-method | Sample Metadata
selectSamples | Select Samples
selectSamples-method | Select Samples
subset | Bracket-Based Subsetting
topTables | Top Tables of Differential Expression Results
topTables-method | Top Tables of Differential Expression Results
tpm | Transcripts Per Million (TPM)
tpm-method | Transcripts Per Million (TPM)
upgrade-bcbioRNASeq | Coerce Object
[-method | Bracket-Based Subsetting