# Generated by roxygen2: do not edit by hand

export(DBscore)
export(ESvolcanoplot)
export(TFEA)
export(TFEAresults)
export(calWeights)
export(count5ends)
export(countsNormalization)
export(doTFEA)
export(eventsFilter)
export(expandBindingSites)
export(getBindingSites)
export(getEnrichmentScore)
export(getMotifID)
export(getWeightedBindingScore)
export(importFimoBindingSites)
export(plotES)
export(prepareBindingSites)
export(reduceByPercentage)
exportClasses(TFEAresults)
exportMethods("$")
exportMethods("$<-")
exportMethods("[[")
exportMethods("[[<-")
exportMethods(coerce)
exportMethods(getBindingSites)
exportMethods(getEnrichmentScore)
exportMethods(getMotifID)
exportMethods(show)
importFrom(BiocGenerics,"end<-")
importFrom(BiocGenerics,"start<-")
importFrom(BiocGenerics,`%in%`)
importFrom(BiocGenerics,end)
importFrom(BiocGenerics,start)
importFrom(BiocGenerics,strand)
importFrom(BiocGenerics,width)
importFrom(GenomicAlignments,cigar)
importFrom(GenomicAlignments,cigarNarrow)
importFrom(GenomicAlignments,cigarQNarrow)
importFrom(GenomicAlignments,qwidth)
importFrom(GenomicAlignments,readGAlignments)
importFrom(GenomicAlignments,summarizeOverlaps)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,GRangesList)
importFrom(IRanges,CharacterList)
importFrom(IRanges,IRanges)
importFrom(IRanges,countOverlaps)
importFrom(IRanges,distance)
importFrom(IRanges,findOverlaps)
importFrom(IRanges,pintersect)
importFrom(IRanges,promoters)
importFrom(IRanges,reduce)
importFrom(Matrix,Matrix)
importFrom(Matrix,rowSums)
importFrom(Rsamtools,BamFile)
importFrom(Rsamtools,ScanBamParam)
importFrom(Rsamtools,asMates)
importFrom(S4Vectors,"mcols<-")
importFrom(S4Vectors,SimpleList)
importFrom(S4Vectors,head)
importFrom(S4Vectors,isSingleInteger)
importFrom(S4Vectors,isSingleNumber)
importFrom(S4Vectors,isSingleString)
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,split)
importFrom(S4Vectors,subjectHits)
importFrom(Seqinfo,"seqinfo<-")
importFrom(Seqinfo,Seqinfo)
importFrom(Seqinfo,`seqlevels<-`)
importFrom(Seqinfo,seqinfo)
importFrom(Seqinfo,seqlengths)
importFrom(Seqinfo,seqlevels)
importFrom(Seqinfo,seqnames)
importFrom(SummarizedExperiment,"assays<-")
importFrom(SummarizedExperiment,"rowData<-")
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,rowData)
importFrom(SummarizedExperiment,rowRanges)
importFrom(TFBSTools,ID)
importFrom(TFBSTools,PFMatrixList)
importFrom(TFBSTools,PWMatrixList)
importFrom(dplyr,sample_n)
importFrom(ggplot2,aes_string)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_rug)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggsave)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,theme_classic)
importFrom(ggplot2,unit)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(ggrepel,geom_text_repel)
importFrom(limma,eBayes)
importFrom(limma,lmFit)
importFrom(limma,topTable)
importFrom(methods,"slot<-")
importFrom(methods,as)
importFrom(methods,coerce)
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,prototype)
importFrom(methods,representation)
importFrom(methods,setAs)
importFrom(methods,setClass)
importFrom(methods,setGeneric)
importFrom(methods,setMethod)
importFrom(methods,setReplaceMethod)
importFrom(methods,show)
importFrom(methods,slot)
importFrom(motifmatchr,matchMotifs)
importFrom(pracma,erf)
importFrom(rtracklayer,import)
importFrom(stats,p.adjust)
importFrom(stats,pnorm)
importFrom(stats,sd)
