All functions

alphaSummary

Print Summary Statistics of Alpha Level Cutoffs

annotable

Ensembl Annotations

assert

Assert Checks

bcbio bcbio<-

bcbioRNASeq Additional Run Data Accessor

bcbioRNASeq-class

bcbioRNASeq Object Class

bcbioRNASeq-package

bcbioRNASeq

coerce

Coerce Object

colData<-

Column Data

counts

Count Matrix Accessors

design design<-

Design Formula Accessor

flatFiles

Get Flat Files from S4 Object

gene2symbol

Gene to Symbol Mappings

interestingGroups interestingGroups<-

Interesting Groups

loadRNASeq

Load bcbio RNA-Seq Data

meltLog10

Melt Count Matrix to Long Format and log10 Transform

metrics

Sample Metrics

plot53Bias plot5x3Bias

Plot 5'->3' Bias

plotCorrelationHeatmap

Plot Correlation Heatmap

plotCountDensity

Plot Count Density

plotCountsPerGene

Plot Counts Per Gene

plotDEGHeatmap

Differentially Expressed Gene Heatmap

plotDEGPCA

Plot DEG PCA

plotDispEsts

Plot Dispersion Estimates

plotExonicMappingRate

Plot Exonic Mapping Rate

plotGenderMarkers

Plot Sexually Dimorphic Gender Markers

plotGene

Plot Individual Genes

plotGeneSaturation

Plot Gene Detection Saturation

plotGenesDetected

Plot Genes Detected

plotHeatmap

Plot Heatmap

plotIntronicMappingRate

Plot Intronic Mapping Rate

plotMA

Plot Mean Average

plotMappedReads

Plot Mapped Reads

plotMappingRate

Plot Mapping Rate

plotMeanSD

Plot Row Standard Deviations vs. Row Means

plotPCA

Sample PCA Plot for Transformed Data

plotPCACovariates

Find Correlation Between Principal Components (PCs) and Covariates

plotRRNAMappingRate

Plot Ribosomal RNA (rRNA) Mapping Rate

plotTotalReads

Plot Total Reads

plotVolcano

Plot Volcano

prepareRNASeqTemplate

Prepare RNA-Seq R Markdown Template

resultsTables

Differential Expression Results Tables

sampleMetadata sampleMetadata<-

Sample Metadata

selectSamples

Select Samples

subset

Bracket-Based Subsetting

topTables

Top Tables of Differential Expression Results

tpm

Transcripts Per Million (TPM)

updateObject

Update Object