# Generated by roxygen2: do not edit by hand

export(TSRchitectUsersGuide)
export(addAnnotationToTSR)
export(addTagCountsToTSR)
export(bedToTSS)
export(cDNAtoBED)
export(createSummarizedExperiment)
export(detTSR)
export(determineTSR)
export(getBamData)
export(getFileNames)
export(getTSRdata)
export(getTSScountData)
export(getTSStagData)
export(getTitle)
export(importAnnotationExternal)
export(importAnnotationHub)
export(inputToTSS)
export(loadTSSobj)
export(makeGRangesFromTSR)
export(mergeSampleData)
export(processTSS)
export(tsrCluster)
export(tssObject)
export(writeTSR)
import(BiocGenerics)
import(GenomicRanges)
importClassesFrom(S4Vectors,Pairs)
importFrom(AnnotationHub,AnnotationHub)
importFrom(AnnotationHub,query)
importFrom(BiocParallel,MulticoreParam)
importFrom(BiocParallel,bplapply)
importFrom(BiocParallel,register)
importFrom(GenomeInfoDb,sortSeqlevels)
importFrom(GenomicAlignments,readGAlignments)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,GRangesList)
importFrom(GenomicRanges,as.data.frame)
importFrom(GenomicRanges,findOverlaps)
importFrom(GenomicRanges,granges)
importFrom(GenomicRanges,makeGRangesFromDataFrame)
importFrom(GenomicRanges,promoters)
importFrom(IRanges,IRanges)
importFrom(Rsamtools,BamViews)
importFrom(Rsamtools,ScanBamParam)
importFrom(Rsamtools,scanBamFlag)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,first)
importFrom(S4Vectors,second)
importFrom(S4Vectors,split)
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(gtools,mixedorder)
importFrom(gtools,mixedsort)
importFrom(methods,new)
importFrom(rtracklayer,export.bed)
importFrom(rtracklayer,import)
importFrom(rtracklayer,import.bed)
importFrom(rtracklayer,import.gff)
importFrom(rtracklayer,import.gff3)
importFrom(utils,write.table)
