# Generated by roxygen2 (4.1.1): do not edit by hand

export("description<-")
export("interactionCounts<-")
export("name<-")
export(GenomicInteractions)
export(anchorOne)
export(anchorTwo)
export(annotateAnchors)
export(annotateInteractions)
export(annotationFeatures)
export(calculateDistances)
export(categoriseInteractions)
export(countsBetweenAnchors)
export(description)
export(export.bed12)
export(export.bedpe)
export(export.chiasig)
export(export.igraph)
export(findOverlaps)
export(get_binom_ligation_threshold)
export(get_self_ligation_threshold)
export(interactionCounts)
export(is.cis)
export(is.dd)
export(is.dt)
export(is.pd)
export(is.pp)
export(is.pt)
export(is.trans)
export(is.tt)
export(isInteractionType)
export(makeGenomicInteractionsFromFile)
export(name)
export(plotCisTrans)
export(plotCounts)
export(plotDists)
export(plotInteractionAnnotations)
export(plotSummaryStats)
export(plotViewpoint)
export(removeDups)
export(resetAnnotations)
export(subsetByFeatures)
export(summariseByFeatures)
export(viewPoint)
exportMethods("$")
exportMethods("$<-")
exportMethods("[")
exportMethods("description<-")
exportMethods("interactionCounts<-")
exportMethods("name<-")
exportMethods("seqinfo<-")
exportMethods(anchorOne)
exportMethods(anchorTwo)
exportMethods(annotateAnchors)
exportMethods(annotateInteractions)
exportMethods(annotationFeatures)
exportMethods(c)
exportMethods(calculateDistances)
exportMethods(countOverlaps)
exportMethods(countsBetweenAnchors)
exportMethods(description)
exportMethods(export.bed12)
exportMethods(export.bedpe)
exportMethods(export.chiasig)
exportMethods(export.igraph)
exportMethods(findOverlaps)
exportMethods(interactionCounts)
exportMethods(is.cis)
exportMethods(is.dd)
exportMethods(is.dt)
exportMethods(is.pd)
exportMethods(is.pp)
exportMethods(is.pt)
exportMethods(is.trans)
exportMethods(is.tt)
exportMethods(isInteractionType)
exportMethods(length)
exportMethods(name)
exportMethods(overlapsAny)
exportMethods(print)
exportMethods(resetAnnotations)
exportMethods(seqinfo)
exportMethods(show)
exportMethods(sort)
exportMethods(subsetByFeatures)
exportMethods(sum)
exportMethods(summariseByFeatures)
exportMethods(trim)
import(BiocGenerics)
import(GenomeInfoDb)
import(GenomicRanges)
import(S4Vectors)
import(ggplot2)
import(methods)
importFrom(IRanges,IRanges)
importFrom(IRanges,trim)
importFrom(Rsamtools,ScanBamParam)
importFrom(Rsamtools,bamFlagAsBitMatrix)
importFrom(Rsamtools,scanBam)
importFrom(Rsamtools,scanBamFlag)
importFrom(data.table,.N)
importFrom(data.table,data.table)
importFrom(data.table,fread)
importFrom(dplyr,"%>%")
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,mutate)
importFrom(dplyr,n)
importFrom(dplyr,select)
importFrom(dplyr,summarise)
importFrom(gridExtra,marrangeGrob)
importFrom(igraph,graph.data.frame)
importFrom(plotrix,ablineclip)
importFrom(rtracklayer,import.bed)
importFrom(stringr,str_split)
