addORFfromGTF	addORFfromGTF
analyzeAlternativeSplicing	analyzeAlternativSplicing
analyzeCPAT	analyzeCPAT
analyzeCPC2	analyzeCPC2
analyzeDeepLoc2	analyzeDeepLoc2
analyzeDeepTMHMM	analyzeDeepTMHMM
analyzeIntronRetention	analyzeAlternativSplicing
analyzeIUPred2A	analyzeIUPred2A
analyzeNetSurfP3	analyzeNetSurfP3
analyzeNovelIsoformORF	analyzeNovelIsoformORF
analyzeORF	analyzeORF
analyzePFAM	analyzePFAM
analyzeSignalP	analyzeSignalP
analyzeSwitchConsequences	analyzeSwitchConsequences
createSwitchAnalyzeRlist	switchAnalyzeRlist
exampleSwitchList	testData
exampleSwitchListAnalyzed	testData
exampleSwitchListIntermediary	testData
exportToPairedGSEA	exportToPairedGSEA
extractConsequenceEnrichment	extractConsequenceEnrichment
extractConsequenceEnrichmentComparison	extractConsequenceEnrichmentComparison
extractConsequenceGenomeWide	extractGenomeWideAnalysis
extractConsequenceSummary	extractConsequenceSummary
extractGeneExpression	extractGeneExpression
extractGenomeWideAnalysis	extractGenomeWideAnalysis
extractSequence	extractSequence
extractSplicingEnrichment	extractSplicingEnrichment
extractSplicingEnrichmentComparison	extractSplicingEnrichmentComparison
extractSplicingGenomeWide	extractGenomeWideSplicingAnalysis
extractSplicingSummary	extractSplicingSummary
extractSubCellShifts	extractSubCellShifts
extractSwitchOverlap	extractSwitchOverlap
extractSwitchSummary	extractSwitchSummary
extractTopSwitches	extractTopSwitches
importCufflinksFiles	importCufflinksGalaxyData
importGTF	importGTF
importIsoformExpression	importIsoformExpression
importPairedGSEA	importPairedGSEA
importRdata	importRdata
importSalmonData	importSalmonData
isoformSwitchAnalysisCombined	isoformSwitchAnalysisCombined
isoformSwitchAnalysisPart1	isoformSwitchAnalysisPart1
isoformSwitchAnalysisPart2	isoformSwitchAnalysisPart2
isoformSwitchTestDEXSeq	IsoformSwitchTestDEXSeq
isoformSwitchTestSatuRn	IsoformSwitchTestSatuRn
isoformToGeneExp	isoformToGeneExp
isoformToIsoformFraction	isoformToIsoformFraction
preFilter	preFilter
prepareSalmonFileDataFrame	prepareSalmonFilesDataFrame
subsetSwitchAnalyzeRlist	subsetSwitchAnalyzeRlist
switchAnalyzeRlist	switchAnalyzeRlist
switchAnalyzeRlist-class	switchAnalyzeRlist
switchPlot	switchPlot
switchPlotGeneExp	expressionAnalysisPlots
switchPlotIsoExp	expressionAnalysisPlots
switchPlotIsoUsage	expressionAnalysisPlots
switchPlotTopSwitches	switchPlotTopSwitches
switchPlotTranscript	switchPlotTranscript
