# Generated by roxygen2: do not edit by hand

export(GRanges2GRangesList)
export(GRangesList2GRanges)
export(calculateShift)
export(distanceTx)
export(extractRegions)
export(getPermSpaceByFeatures)
export(getPermSpaceByTxID)
export(getPermSpaceByType)
export(getStopCodon)
export(getTransInfo)
export(overlapCountsTx)
export(overlapCountsTxIA)
export(overlapWidthTx)
export(permTestTx)
export(permTestTxIA)
export(permTestTxIA_customPick)
export(permTestTx_customAll)
export(permTestTx_customPick)
export(plotPermResults)
export(plotShiftedZScoreTx)
export(randomizeFeaturesTx)
export(randomizeFeaturesTxIA)
export(randomizeTransByOrder)
export(randomizeTx)
export(shiftTx)
export(shiftedZScoreTx)
import(TxDb.Hsapiens.UCSC.hg19.knownGene)
importFrom(GenomeInfoDb,seqnames)
importFrom(GenomicFeatures,cdsBy)
importFrom(GenomicFeatures,exonsBy)
importFrom(GenomicFeatures,fiveUTRsByTranscript)
importFrom(GenomicFeatures,mapToTranscripts)
importFrom(GenomicFeatures,threeUTRsByTranscript)
importFrom(GenomicFeatures,transcriptsBy)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,end)
importFrom(GenomicRanges,makeGRangesListFromFeatureFragments)
importFrom(GenomicRanges,mcols)
importFrom(GenomicRanges,ranges)
importFrom(GenomicRanges,start)
importFrom(GenomicRanges,strand)
importFrom(GenomicRanges,width)
importFrom(IRanges,IRanges)
importFrom(IRanges,IntegerList)
importFrom(IRanges,LogicalList)
importFrom(IRanges,countOverlaps)
importFrom(IRanges,distanceToNearest)
importFrom(IRanges,findOverlaps)
importFrom(IRanges,shift)
importFrom(S4Vectors,Rle)
importFrom(ggplot2,aes)
importFrom(ggplot2,annotate)
importFrom(ggplot2,arrow)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_line)
importFrom(ggplot2,element_text)
importFrom(ggplot2,geom_histogram)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_polygon)
importFrom(ggplot2,geom_segment)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,labs)
importFrom(ggplot2,stat_function)
importFrom(ggplot2,theme)
importFrom(ggplot2,unit)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(ggplot2,ylim)
importFrom(graphics,hist)
importFrom(methods,is)
importFrom(regioneR,overlapRegions)
importFrom(stats,dnorm)
importFrom(stats,pnorm)
importFrom(stats,qnorm)
importFrom(stats,runif)
importFrom(stats,sd)
