# Generated by roxygen2: do not edit by hand

export(aggregateByNdimBins)
export(applyNFsGRanges)
export(binNdimensions)
export(densityInNdimBins)
export(genebodies)
export(getCountsByPositions)
export(getCountsByRegions)
export(getDESeqDataSet)
export(getDESeqResults)
export(getMaxPositionsBySignal)
export(getPausingIndices)
export(getSpikeInCounts)
export(getSpikeInNFs)
export(getSpikeInReads)
export(getStrandedCoverage)
export(import_bam)
export(import_bam_ATACseq)
export(import_bam_PROcap)
export(import_bam_PROseq)
export(import_bedGraph)
export(import_bigWig)
export(intersectByGene)
export(isBRG)
export(makeGRangesBRG)
export(mergeGRangesData)
export(mergeReplicates)
export(metaSubsample)
export(metaSubsampleMatrix)
export(reduceByGene)
export(removeSpikeInReads)
export(spikeInNormGRanges)
export(subsampleBySpikeIn)
export(subsampleGRanges)
export(subsetRegionsBySignal)
export(tidyChromosomes)
import(GenomicAlignments)
import(GenomicRanges)
import(Rsamtools)
import(S4Vectors)
import(rtracklayer)
importFrom(DESeq2,"sizeFactors<-")
importFrom(DESeq2,DESeq)
importFrom(DESeq2,DESeqDataSet)
importFrom(DESeq2,results)
importFrom(DESeq2,sizeFactors)
importFrom(GenomeInfoDb,"genome<-")
importFrom(GenomeInfoDb,dropSeqlevels)
importFrom(GenomeInfoDb,keepSeqlevels)
importFrom(GenomeInfoDb,seqlengths)
importFrom(GenomeInfoDb,seqlevels)
importFrom(GenomeInfoDb,sortSeqlevels)
importFrom(GenomeInfoDb,standardChromosomes)
importFrom(GenomicRanges,"mcols<-")
importFrom(GenomicRanges,"ranges<-")
importFrom(GenomicRanges,"score<-")
importFrom(GenomicRanges,"strand<-")
importFrom(GenomicRanges,GPos)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,countOverlaps)
importFrom(GenomicRanges,disjoin)
importFrom(GenomicRanges,duplicated)
importFrom(GenomicRanges,end)
importFrom(GenomicRanges,findOverlaps)
importFrom(GenomicRanges,gaps)
importFrom(GenomicRanges,isDisjoint)
importFrom(GenomicRanges,mcols)
importFrom(GenomicRanges,promoters)
importFrom(GenomicRanges,reduce)
importFrom(GenomicRanges,resize)
importFrom(GenomicRanges,score)
importFrom(GenomicRanges,seqinfo)
importFrom(GenomicRanges,seqnames)
importFrom(GenomicRanges,shift)
importFrom(GenomicRanges,sort)
importFrom(GenomicRanges,split)
importFrom(GenomicRanges,start)
importFrom(GenomicRanges,strand)
importFrom(GenomicRanges,width)
importFrom(IRanges,IRanges)
importFrom(IRanges,findOverlapPairs)
importFrom(IRanges,pintersect)
importFrom(IRanges,subsetByOverlaps)
importFrom(S4Vectors,from)
importFrom(S4Vectors,pc)
importFrom(S4Vectors,to)
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(methods,as)
importFrom(methods,is)
importFrom(parallel,mcMap)
importFrom(parallel,mclapply)
importFrom(parallel,mcmapply)
importFrom(stats,median)
importFrom(stats,quantile)
importFrom(utils,data)
