buildAllPlots	buildAllPlots
buildAllPlotsForGene	buildAllPlotsForGene
defaultColorList	defaultColorList
estimateEffectSizes	estimateEffectSizes
estimateJunctionSeqDispersions	estimateJunctionSeqDispersions
estimateJunctionSeqSizeFactors	estimateJunctionSeqSizeFactors
fitJunctionSeqDispersionFunction	fitJunctionSeqDispersionFunction
JUNCTIONSEQ.DEFAULT.COLOR.LIST	defaultColorList
junctionSeqColors	defaultColorList
JunctionSeqCountSet	JunctionSeqCountSet-class
JunctionSeqCountSet-class	JunctionSeqCountSet-class
plotDispEsts	plotDispEsts
plotJunctionSeqResultsForGene	plotJunctionSeqResultsForGene
plotMA	plotMA
readAnnotationData	readAnnotationData
readJunctionSeqCounts	readJunctionSeqCounts
runJunctionSeqAnalyses	runJunctionSeqAnalyses
setJunctionSeqCompiledSourcePackage	setJunctionSeqCompiledSourcePackage
testForDiffUsage	testForDiffUsage
writeCompleteResults	writeCompleteResults
writeExprBedTrack	writeBedTrack
writeSigBedTrack	writeBedTrack
writeSizeFactors	estimateJunctionSeqSizeFactors
