JunctionSeq: A Utility for Detection of Differential Exon and Splice-Junction Usage in RNA-Seq data

Documentation for package ‘JunctionSeq’ version 1.5.4

buildAllPlots	Create and save a full battery of JunctionSeq expression plots.
buildAllPlotsForGene	Create and save one or more JunctionSeq expression plots.
defaultColorList	JunctionSeq Color Parameters
estimateEffectSizes	Estimate Effect Sizes, parameter estimates, etc.
estimateJunctionSeqDispersions	JunctionSeq Dispersion Estimation
estimateJunctionSeqSizeFactors	Estimate Size Factors
fitJunctionSeqDispersionFunction	Fit Shared Dispersion Function
JUNCTIONSEQ.DEFAULT.COLOR.LIST	JunctionSeq Color Parameters
junctionSeqColors	JunctionSeq Color Parameters
JunctionSeqCountSet	Class '"JunctionSeqCountSet"'
JunctionSeqCountSet-class	Class '"JunctionSeqCountSet"'
plotDispEsts	Plot Fitted and Test-wise Dispersion
plotJunctionSeqResultsForGene	Generate a JunctionSeq expression plot.
plotMA	Generate a MA-Plot
readAnnotationData	Read junctionSeq annotation files produced by QoRTs.
readJunctionSeqCounts	Read junctionSeq count files
runJunctionSeqAnalyses	Run a JunctionSeq analysis.
testForDiffUsage	Test Junctions for Differential Junction Usage
writeCompleteResults	Produce output data files, given annotation files and DEXSeq exonCountSet object and DEXSeq results data.
writeExprBedTrack	Write splice junction browser tracks
writeSigBedTrack	Write splice junction browser tracks
writeSizeFactors	Estimate Size Factors