# Generated by roxygen2: do not edit by hand

export(BamBigwig_to_chipProfile)
export(annotateRanges)
export(as_profileplyr)
export(clusterRanges)
export(convertToEnrichedHeatmapMat)
export(export_deepToolsMat)
export(generateEnrichedHeatmap)
export(generateProfilePlot)
export(groupBy)
export(import_deepToolsMat)
export(orderBy)
export(params)
export(pwmToCoverage)
export(sampleData)
export(summarize)
exportClasses(ChIPprofile)
exportClasses(profileplyr)
exportMethods("sampleData<-")
exportMethods(annotateRanges)
exportMethods(annotateRanges_great)
exportMethods(c)
exportMethods(clusterRanges)
exportMethods(convertToEnrichedHeatmapMat)
exportMethods(export_deepToolsMat)
exportMethods(groupBy)
exportMethods(orderBy)
exportMethods(sampleData)
exportMethods(summarize)
import(BiocGenerics, except = Position)
import(ChIPseeker)
import(GenomicFeatures)
import(GenomicRanges)
import(IRanges)
import(SummarizedExperiment)
import(TxDb.Hsapiens.UCSC.hg19.knownGene)
import(TxDb.Hsapiens.UCSC.hg38.knownGene)
import(TxDb.Mmusculus.UCSC.mm10.knownGene)
import(TxDb.Mmusculus.UCSC.mm9.knownGene)
import(circlize)
import(grid)
import(org.Hs.eg.db)
import(org.Mm.eg.db)
import(rGREAT)
import(tiff)
importClassesFrom(GenomicRanges,GenomicRanges_OR_GRangesList)
importClassesFrom(S4Vectors,DataFrame)
importClassesFrom(S4Vectors,character_OR_NULL)
importClassesFrom(methods,ANY)
importClassesFrom(methods,character)
importClassesFrom(methods,list)
importClassesFrom(methods,missing)
importFrom(BiocParallel,MulticoreParam)
importFrom(BiocParallel,SerialParam)
importFrom(BiocParallel,bplapply)
importFrom(BiocParallel,multicoreWorkers)
importFrom(Biostrings,matchPWM)
importFrom(Biostrings,reverseComplement)
importFrom(ComplexHeatmap,Heatmap)
importFrom(ComplexHeatmap,HeatmapAnnotation)
importFrom(ComplexHeatmap,anno_mark)
importFrom(ComplexHeatmap,anno_summary)
importFrom(ComplexHeatmap,rowAnnotation)
importFrom(EnrichedHeatmap,EnrichedHeatmap)
importFrom(EnrichedHeatmap,anno_enriched)
importFrom(GenomeInfoDb,Seqinfo)
importFrom(GenomeInfoDb,seqlengths)
importFrom(GenomeInfoDb,seqlevels)
importFrom(GenomeInfoDb,seqlevelsInUse)
importFrom(GenomicAlignments,qwidth)
importFrom(GenomicAlignments,readGAlignments)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,GRangesList)
importFrom(IRanges,IRanges)
importFrom(R.utils,gzip)
importFrom(Rsamtools,BamFile)
importFrom(Rsamtools,ScanBamParam)
importFrom(Rsamtools,index)
importFrom(Rsamtools,indexBam)
importFrom(Rsamtools,scanBamFlag)
importFrom(Rsamtools,scanBamHeader)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,Rle)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,subjectHits)
importFrom(circlize,colorRamp2)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,select)
importFrom(dplyr,vars)
importFrom(ggplot2,aes)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_rect)
importFrom(ggplot2,element_text)
importFrom(ggplot2,expand_limits)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(grDevices,hcl)
importFrom(grid,gpar)
importFrom(grid,unit)
importFrom(magrittr,"%>%")
importFrom(methods,as)
importFrom(methods,is)
importFrom(methods,new)
importFrom(pheatmap,pheatmap)
importFrom(rGREAT,submitGreatJob)
importFrom(rjson,fromJSON)
importFrom(rjson,toJSON)
importFrom(rlang,.data)
importFrom(rtracklayer,import)
importFrom(rtracklayer,import.bed)
importFrom(rtracklayer,import.bw)
importFrom(stats,cutree)
importFrom(stats,spline)
importFrom(tidyr,gather)
importFrom(tidyr,pivot_longer)
importFrom(tidyr,separate)
importFrom(tidyr,unnest)
importFrom(txdbmaker,makeTxDbFromGFF)
importFrom(utils,combn)
importFrom(utils,read.delim)
importFrom(utils,write.table)
importMethodsFrom(ComplexHeatmap,draw)
importMethodsFrom(GenomicFeatures,as.list)
importMethodsFrom(GenomicRanges,as.data.frame)
importMethodsFrom(GenomicRanges,as.factor)
importMethodsFrom(GenomicRanges,duplicated)
importMethodsFrom(GenomicRanges,end)
importMethodsFrom(GenomicRanges,findOverlaps)
importMethodsFrom(GenomicRanges,match)
importMethodsFrom(GenomicRanges,order)
importMethodsFrom(GenomicRanges,score)
importMethodsFrom(GenomicRanges,seqnames)
importMethodsFrom(GenomicRanges,start)
importMethodsFrom(GenomicRanges,strand)
importMethodsFrom(IRanges,"colnames<-")
importMethodsFrom(IRanges,"rownames<-")
importMethodsFrom(IRanges,as.matrix)
importMethodsFrom(IRanges,cbind)
importMethodsFrom(IRanges,colnames)
importMethodsFrom(IRanges,diff)
importMethodsFrom(IRanges,gsub)
importMethodsFrom(IRanges,lapply)
importMethodsFrom(IRanges,ncol)
importMethodsFrom(IRanges,nrow)
importMethodsFrom(IRanges,paste)
importMethodsFrom(IRanges,quantile)
importMethodsFrom(IRanges,rbind)
importMethodsFrom(IRanges,rownames)
importMethodsFrom(IRanges,subsetByOverlaps)
importMethodsFrom(IRanges,table)
importMethodsFrom(IRanges,unique)
importMethodsFrom(IRanges,which)
importMethodsFrom(S4Vectors,"%in%")
importMethodsFrom(S4Vectors,"mcols<-")
importMethodsFrom(S4Vectors,"metadata<-")
importMethodsFrom(S4Vectors,Reduce)
importMethodsFrom(S4Vectors,do.call)
importMethodsFrom(S4Vectors,expand.grid)
importMethodsFrom(S4Vectors,grep)
importMethodsFrom(S4Vectors,grepl)
importMethodsFrom(S4Vectors,head)
importMethodsFrom(S4Vectors,levels)
importMethodsFrom(S4Vectors,mcols)
importMethodsFrom(S4Vectors,metadata)
importMethodsFrom(S4Vectors,subset)
importMethodsFrom(S4Vectors,t)
importMethodsFrom(S4Vectors,tail)
