# Generated by roxygen2: do not edit by hand

export(CleanBAMtoBG)
export(CleanBEDtoBG)
export(ExtractTranscriptomeSequence)
export(GenomeMappingToChainFile)
export(assessGrouping)
export(bindingContextDistance)
export(bindingContextDistanceCapR)
export(getChainChrSize)
export(get_outfiles)
export(liftOverToExomicBG)
export(processCapRout)
export(runCapR)
export(runStereogene)
export(runStereogeneOnCapR)
export(symmetryCapR)
export(symmetryContext)
export(visualizeCapRStereogene)
export(visualizeStereogene)
export(write_config)
export(write_fasta)
import(S4Vectors)
import(TxDb.Hsapiens.UCSC.hg19.knownGene)
import(TxDb.Hsapiens.UCSC.hg38.knownGene)
import(rtracklayer)
importFrom(BiocGenerics,strand)
importFrom(BiocGenerics,type)
importFrom(GenomicRanges,countOverlaps)
importFrom(GenomicRanges,makeGRangesFromDataFrame)
importFrom(R.utils,doCall)
importFrom(Rsamtools,ScanBamParam)
importFrom(Rsamtools,filterBam)
importFrom(Rsamtools,idxstatsBam)
importFrom(Rsamtools,indexBam)
importFrom(S4Vectors,FilterRules)
importFrom(S4Vectors,elementMetadata)
importFrom(S4Vectors,elementNROWS)
importFrom(Seqinfo,seqlengths)
importFrom(Seqinfo,seqnames)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,summarize)
importFrom(ggplot2,aes)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,stat_ecdf)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_classic)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(gplots,heatmap.2)
importFrom(gplots,redblue)
importFrom(grDevices,dev.off)
importFrom(grDevices,jpeg)
importFrom(grDevices,pdf)
importFrom(grDevices,rgb)
importFrom(graphics,abline)
importFrom(graphics,arrows)
importFrom(graphics,lines)
importFrom(graphics,par)
importFrom(graphics,plot)
importFrom(magrittr,'%>%')
importFrom(matrixStats,rowSds)
importFrom(methods,as)
importFrom(plyranges,bind_ranges)
importFrom(plyranges,filter)
importFrom(rlang,.data)
importFrom(rtracklayer,import)
importFrom(stats,ks.test)
importFrom(transport,wasserstein1d)
importFrom(utils,read.delim)
importFrom(utils,read.table)
importFrom(utils,write.table)
