# RNA-Seq Utilities

## Documentation for package ‘bcbioRNASeq’ version 0.2.9

- DESCRIPTION file.
- Package NEWS.

## Help Pages

bcbioRNASeq-package | bcbioRNASeq
aggregateReplicates | Aggregate Replicates
aggregateReplicates-method | Aggregate Replicates
alphaSummary | Alpha Level Cutoff Summary Statistics
alphaSummary-method | Alpha Level Cutoff Summary Statistics
as | Methods for Coercing an Object to a Class
bcbioRNASeq | 'bcbioRNASeq' Object and Constructor
bcbioRNASeq-class | 'bcbioRNASeq' Object and Constructor
bcb_small | 'bcbioRNASeq' Example
coerce | Methods for Coercing an Object to a Class
coerce-method | Methods for Coercing an Object to a Class
contrastName | Contrast Name
contrastName-method | Contrast Name
counts | Count Matrix Accessors
counts-method | Count Matrix Accessors
dds_small | 'DESeqDataSet' Example
extract | Extract or Replace Parts of an Object
loadRNASeq | 'bcbioRNASeq' Object and Constructor
metrics | Sample Metrics
metrics-method | Sample Metrics
plot5Prime3PrimeBias | Plot 5'->3' Bias
plot5Prime3PrimeBias-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
plotDEGPCA | Plot DEG PCA
plotDEGPCA-method | Plot DEG PCA
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
plotIntronicMappingRate | Plot Intronic Mapping Rate
plotIntronicMappingRate-method | Plot Intronic Mapping Rate
plotMA | MA Plot
plotMA-method | MA Plot
plotMappedReads | Plot Mapped Reads
plotMappedReads-method | Plot Mapped Reads
plotMappingRate | Plot Mapping Rate
plotMappingRate-method | Plot Mapping Rate
plotMeanAverage | MA Plot
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
resultsTables | Differential Expression Results Tables
resultsTables-method | Differential Expression Results Tables
res_small | 'DESeqResults' Example
sampleData | Sample Data
sampleData-method | Sample Data
sampleData<- | Sample Data
sampleData<--method | Sample Data
show | Show an Object
show-method | Show an Object
tmm | *T*rimmed *M*ean of *M*-Values (TMM) Normalization
tmm-method | *T*rimmed *M*ean of *M*-Values (TMM) Normalization
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)
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