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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export(EMclust)
export(SaaRclust)
export(clusters2ranges)
export(collapseBins)
export(countDirectionalReads)
export(countProb)
export(counts2ranges)
export(estimateTheta)
export(exportClusteredReads)
export(exportGenomicLocations)
export(filterInput)
export(findAntiparallelClusters)
export(findClusterPartners)
export(findClusterPartners_simple)
export(findSplitedClusters)
export(flipCounts)
export(gammaFunction)
export(getClusterIdentityPerChr)
export(getClusterIdentityPerChrPerDir)
export(getQualMeasure)
export(getRepresentativeAlignments)
export(hardClust)
export(hardClustAccuracy)
export(importBams)
export(importData)
export(kahansum)
export(mergeClusters)
export(plotClustAccuracy)
export(plotHeatmap)
export(plotQualMeasure)
export(plotReadAlignments)
export(plotReadMappingDist)
export(plotThetaEstimates)
export(randomTheta)
export(readBamFileAsGRanges)
export(runSaaRclust)
export(thetaRescale)
importFrom(GenomicAlignments,first)
importFrom(GenomicAlignments,last)
importFrom(GenomicAlignments,readGAlignmentPairs)
importFrom(GenomicAlignments,readGAlignments)
importFrom(Rsamtools,ScanBamParam)
importFrom(Rsamtools,indexBam)
importFrom(Rsamtools,scanBamFlag)
importFrom(Rsamtools,scanBamHeader)
importFrom(data.table,data.table)
importFrom(data.table,fread)
importFrom(data.table,tstrsplit)
importFrom(dplyr,group_by)
importFrom(dplyr,summarise)
importFrom(igraph,V)
importFrom(igraph,clusters)
importFrom(igraph,graph)
importFrom(lpSolve,lp.assign)
importFrom(matrixStats,logSumExp)
importFrom(matrixStats,rowLogSumExps)
importFrom(reshape2,melt)
importFrom(tidyr,separate)