# Generated by roxygen2: do not edit by hand

export(DEXSeqIdsToGeneIds)
export(UTR2UTR53)
export(addBroadTypes)
export(addIntronInTranscript)
export(alternativeIntronUsage)
export(annotateGeneModel)
export(attrChangeAltSpliced)
export(exonsToTranscripts)
export(filterGtfOverlap)
export(filterWhippetEvents)
export(findDEXexonType)
export(findExonContainingTranscripts)
export(findIntronContainingTranscripts)
export(findJunctionPairs)
export(formatWhippetEvents)
export(getOrfs)
export(getUOrfs)
export(leafcutterTranscriptChangeSummary)
export(makeGeneModel)
export(maxLocation)
export(orfDiff)
export(orfSimilarity)
export(overlapTypes)
export(readWhippetDIFFfiles)
export(readWhippetDataSet)
export(readWhippetJNCfiles)
export(readWhippetPSIfiles)
export(removeDuplicateTranscripts)
export(removeSameExon)
export(removeVersion)
export(reorderExonNumbers)
export(replaceJunction)
export(skipExonInTranscript)
export(summariseExonTypes)
export(transcriptChangeSummary)
export(whippetTranscriptChangeSummary)
exportClasses(whippetDataSet)
exportMethods(coordinates)
exportMethods(diffSplicingResults)
exportMethods(junctions)
exportMethods(readCounts)
import(Biostrings)
import(GenomicRanges)
import(methods)
import(plyr)
import(stringdist)
import(stringr)
import(BSgenome.Mmusculus.UCSC.mm10)
import(Gviz)
importFrom(IRanges,IRanges)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,Rle)
importFrom(data.table,fread)
importFrom(plyr,arrange)
importFrom(plyr,desc)
importFrom(rtracklayer,import)
importFrom(stats,aggregate)
importFrom(stats,median)
importFrom(stringr,str_split)
importFrom(utils,adist)
importFrom(utils,installed.packages)
importFrom(utils,setTxtProgressBar)
importFrom(utils,txtProgressBar)
importFrom(utils,write.table)
