# Generated by roxygen2: do not edit by hand

export(assignTSSByCage)
export(computeFeatures)
export(coveragePerTiling)
export(defineTrailer)
export(detectRibosomeShifts)
export(disengagementScore)
export(distToCds)
export(distToTSS)
export(entropy)
export(extendLeaders)
export(findMapORFs)
export(findORFs)
export(findORFsFasta)
export(firstEndPerGroup)
export(firstExonPerGroup)
export(firstStartPerGroup)
export(floss)
export(fpkm)
export(fractionLength)
export(fread.bed)
export(getStartStopWindows)
export(groupGRangesBy)
export(initiationScore)
export(insideOutsideORF)
export(isInFrame)
export(isOverlapping)
export(kozakSequenceScore)
export(lastExonEndPerGroup)
export(lastExonPerGroup)
export(lastExonStartPerGroup)
export(longestORFs)
export(makeORFNames)
export(metaWindow)
export(numExonsPerGroup)
export(orfScore)
export(overlapsToCoverage)
export(rankOrder)
export(reassignTSSbyCage)
export(reassignTxDbByCage)
export(reduceKeepAttr)
export(ribosomeReleaseScore)
export(ribosomeStallingScore)
export(seqnamesPerGroup)
export(shiftFootprints)
export(sortPerGroup)
export(startCodons)
export(startDefinition)
export(startSites)
export(stopCodons)
export(stopDefinition)
export(stopSites)
export(strandBool)
export(strandPerGroup)
export(tile1)
export(translationalEff)
export(txNames)
export(txNamesWithLeaders)
export(txSeqsFromFa)
export(uORFSearchSpace)
export(uniqueGroups)
export(uniqueOrder)
export(unlistGrl)
export(widthPerGroup)
import(GenomeInfoDb)
import(GenomicAlignments)
import(GenomicFeatures)
import(GenomicRanges)
import(IRanges)
importFrom(BiocGenerics,Reduce)
importFrom(Biostrings,PWM)
importFrom(GenomicFeatures,pmapFromTranscripts)
importFrom(IRanges,heads)
importFrom(IRanges,tails)
importFrom(Rcpp,sourceCpp)
importFrom(Rsamtools,FaFile)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,Rle)
importFrom(S4Vectors,nrun)
importFrom(S4Vectors,pc)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,runValue)
importFrom(S4Vectors,subjectHits)
importFrom(data.table,":=")
importFrom(data.table,.I)
importFrom(data.table,.N)
importFrom(data.table,.SD)
importFrom(data.table,as.data.table)
importFrom(data.table,chmatch)
importFrom(data.table,data.table)
importFrom(data.table,fread)
importFrom(data.table,rbindlist)
importFrom(data.table,setDF)
importFrom(data.table,setDT)
importFrom(data.table,setkeyv)
importFrom(rtracklayer,import.bed)
importFrom(stats,fft)
importFrom(stats,spec.pgram)
importFrom(tools,file_ext)
useDynLib(ORFik)
