# Generated by roxygen2: do not edit by hand

export(ORFikQC)
export(TOP.Motif.ecdf)
export(assignTSSByCage)
export(bamVarName)
export(computeFeatures)
export(convertToOneBasedRanges)
export(countOverlapsW)
export(countTable)
export(coverageHeatMap)
export(coveragePerTiling)
export(coverageScorings)
export(create.experiment)
export(defineTrailer)
export(detectRibosomeShifts)
export(disengagementScore)
export(distToCds)
export(distToTSS)
export(entropy)
export(export.bed12)
export(extendLeaders)
export(extendTrailers)
export(filterTranscripts)
export(fimport)
export(findFa)
export(findMapORFs)
export(findORFs)
export(findORFsFasta)
export(findUORFs)
export(firstEndPerGroup)
export(firstExonPerGroup)
export(firstStartPerGroup)
export(floss)
export(fpkm)
export(fractionLength)
export(fread.bed)
export(gcContent)
export(groupGRangesBy)
export(import.bedo)
export(initiationScore)
export(insideOutsideORF)
export(isInFrame)
export(isOverlapping)
export(kozakHeatmap)
export(kozakSequenceScore)
export(lastExonEndPerGroup)
export(lastExonPerGroup)
export(lastExonStartPerGroup)
export(loadRegion)
export(loadRegions)
export(loadTxdb)
export(longestORFs)
export(makeORFNames)
export(makeSummarizedExperimentFromBam)
export(metaWindow)
export(numExonsPerGroup)
export(orfScore)
export(outputLibs)
export(pSitePlot)
export(pmapFromTranscriptF)
export(pmapToTranscriptF)
export(rankOrder)
export(read.experiment)
export(readBam)
export(readWidths)
export(reassignTSSbyCage)
export(reassignTxDbByCage)
export(reduceKeepAttr)
export(remove.experiments)
export(ribosomeReleaseScore)
export(ribosomeStallingScore)
export(rnaNormalize)
export(save.experiment)
export(scaledWindowPositions)
export(scoreSummarizedExperiment)
export(seqnamesPerGroup)
export(shiftFootprints)
export(sortPerGroup)
export(startCodons)
export(startDefinition)
export(startRegion)
export(startRegionString)
export(startSites)
export(stopCodons)
export(stopDefinition)
export(stopSites)
export(strandBool)
export(strandPerGroup)
export(subsetToFrame)
export(tile1)
export(transcriptWindow)
export(translationalEff)
export(txNames)
export(txSeqsFromFa)
export(uORFSearchSpace)
export(uniqueGroups)
export(uniqueOrder)
export(unlistGrl)
export(widthPerGroup)
export(windowCoveragePlot)
export(windowPerGroup)
export(windowPerReadLength)
exportClasses(experiment)
exportMethods(show)
import(DESeq2)
import(GenomeInfoDb)
import(GenomicAlignments)
import(GenomicFeatures)
import(GenomicRanges)
import(IRanges)
import(SummarizedExperiment)
import(ggplot2)
importFrom(AnnotationDbi,loadDb)
importFrom(AnnotationDbi,metadata)
importFrom(BiocGenerics,Reduce)
importFrom(BiocGenerics,weights)
importFrom(BiocParallel,bplapply)
importFrom(BiocParallel,bpparam)
importFrom(Biostrings,PWM)
importFrom(Biostrings,alphabetFrequency)
importFrom(GGally,ggpairs)
importFrom(IRanges,heads)
importFrom(IRanges,tails)
importFrom(Rcpp,sourceCpp)
importFrom(Rsamtools,FaFile)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,Rle)
importFrom(S4Vectors,isTRUEorFALSE)
importFrom(S4Vectors,nrun)
importFrom(S4Vectors,pc)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,runValue)
importFrom(S4Vectors,subjectHits)
importFrom(S4Vectors,wmsg)
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,copy)
importFrom(data.table,data.table)
importFrom(data.table,fread)
importFrom(data.table,fwrite)
importFrom(data.table,melt)
importFrom(data.table,rbindlist)
importFrom(data.table,setDF)
importFrom(data.table,setDT)
importFrom(data.table,setkeyv)
importFrom(gridExtra,grid.arrange)
importFrom(methods,as)
importFrom(methods,is)
importFrom(methods,new)
importFrom(rtracklayer,export.bed)
importFrom(rtracklayer,import)
importFrom(rtracklayer,import.bed)
importFrom(rtracklayer,import.wig)
importFrom(stats,fft)
importFrom(stats,spec.pgram)
importFrom(tools,file_ext)
importFrom(tools,file_path_sans_ext)
useDynLib(ORFik)
