# Generated by roxygen2: do not edit by hand

export(addchr)
export(annotateAnchors)
export(annotateAnchors.bed)
export(annotateAnchors.bigwig)
export(annotateLoops)
export(annotateLoops.dge)
export(bedToGRanges)
export(calcLDSizeFactors)
export(callCCDs)
export(computeBoundaryScores)
export(featureTest)
export(filterLoops)
export(filterSpanningLoops)
export(getHumanGenes)
export(getHumanTSS)
export(getMouseGenes)
export(getMouseTSS)
export(interchromosomal)
export(intrachromosomal)
export(keepCTCFloops)
export(keepEPloops)
export(loopAssoc)
export(loopDistancePlot)
export(loopGenes)
export(loopMetrics)
export(loopPlot)
export(loopWidth)
export(loopsMake)
export(loopsMake.mango)
export(loopsSubset)
export(mangoCorrection)
export(manyLoopPlots)
export(mergeAnchors)
export(numAnchors)
export(numLoops)
export(padGRanges)
export(pcaPlot)
export(plotTopLoops)
export(quickAssoc)
export(quickAssocVoom)
export(removeRegion)
export(removeSelfLoops)
export(rmchr)
export(slidingWindowTest)
export(splitSamples)
export(subsetLoops)
export(subsetRegion)
export(subsetRegionAB)
export(topLoops)
export(updateLDGroups)
exportClasses(loops)
exportMethods("sampleNames<-")
exportMethods(sampleNames)
exportMethods(summary)
exportMethods(union)
import(GenomicRanges)
import(Sushi)
import(biomaRt)
import(edgeR)
import(foreach)
import(ggplot2)
import(grDevices)
import(limma)
import(locfit)
import(methods)
import(plyr)
import(readr)
import(reshape2)
import(statmod)
import(utils)
importFrom(GenomeInfoDb,"seqlevels<-")
importFrom(GenomeInfoDb,seqlevels)
importFrom(GenomeInfoDb,sortSeqlevels)
importFrom(IRanges,IRanges)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,subjectHits)
importFrom(data.table,as.data.table)
importFrom(dplyr,full_join)
importFrom(dplyr,group_by)
importFrom(grDevices,recordPlot)
importFrom(graphics,mtext)
importFrom(graphics,par)
importFrom(matrixStats,colMedians)
importFrom(pbapply,pbsapply)
importFrom(rtracklayer,import.bw)
importFrom(stats,aggregate)
importFrom(stats,complete.cases)
importFrom(stats,model.matrix)
importFrom(stats,na.omit)
importFrom(stats,p.adjust)
importFrom(stats,pbinom)
importFrom(stats,prcomp)
importFrom(stats,predict)
importFrom(stats,quantile)
importFrom(stats,setNames)
importFrom(stats,smooth.spline)
importFrom(tools,file_path_sans_ext)
importFrom(utils,read.table)
importFrom(utils,stack)
importMethodsFrom(Biobase,"sampleNames<-")
importMethodsFrom(Biobase,sampleNames)
