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

## Documentation for package ‘JunctionSeq’ version 1.8.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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.
setJunctionSeqCompiledSourcePackage | Set the source of the internal compiled C++ binaries.
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