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NAMESPACE
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# Generated by roxygen2: do not edit by hand
S3method(flipStrandNames,default)
S3method(flipStrandNames,list)
export(GBreaks)
export(GBreaksToMatrix)
export(GOC)
export(align_scaf_plot_2)
export(as)
export(bp_coverage)
export(bp_heatmap)
export(bp_pair_analysis)
export(bridgeRegions)
export(chain_contigs)
export(cleanGaps)
export(coalesce_contigs)
export(correlation_index)
export(dist2next)
export(feature_coverage)
export(filterColinearRegions)
export(filterDoubleInversions)
export(filterInversions)
export(filterTranslocations)
export(flagAll)
export(flagColinearAlignments)
export(flagDoubleInversions)
export(flagInversions)
export(flagLongShort)
export(flagPairs)
export(flagTranslocations)
export(flipInversions)
export(flipStrandNames)
export(forceSeqLengths)
export(gb2comp)
export(gb2dna_seg)
export(gb2xlim)
export(getRefGenome)
export(get_bps)
export(gr2dna_seg)
export(guessSeqLengths)
export(int_frag)
export(inv2UCSCData)
export(keepLongestPair)
export(leftInversionGaps)
export(load_genomic_breaks)
export(longestMatchesInTarget)
export(makeInversion.chr)
export(makeOxfordPlots)
export(mergeSeqLevels)
export(mergeSeqLevels_to_DF)
export(orderQuerySeqLevels)
export(orderQuerySeqLevels_DF_GR)
export(plotApairOfChrs)
export(scaf_align_plot)
export(scaffoldByFlipAndMerge)
export(showInversions)
export(showTranslocations)
export(splitSeqLevel)
export(strandNames)
export(strand_randomisation_index)
export(swap)
export(synteny_index)
export(tan_bp)
export(wholeGenomeClassification)
export(zipWithNext)
exportClasses(GBreaks)
exportMethods(dist2next)
exportMethods(getSeq)
exportMethods(isSorted)
exportMethods(pairwiseAlignment)
exportMethods(range)
exportMethods(reverse)
exportMethods(subsetByOverlaps)
import(GenomeInfoDb)
import(GenomicRanges)
import(IRanges)
import(ggplot2)
importFrom(BSgenome,getBSgenome)
importFrom(BiocGenerics,`%in%`)
importFrom(BiocParallel,bplapply)
importFrom(Biostrings,getSeq)
importFrom(Biostrings,pairwiseAlignment)
importFrom(CNEr,first)
importFrom(CNEr,second)
importFrom(GenomeInfoDb,seqnames)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,distance)
importFrom(GenomicRanges,end)
importFrom(GenomicRanges,follow)
importFrom(GenomicRanges,precede)
importFrom(GenomicRanges,resize)
importFrom(GenomicRanges,start)
importFrom(IRanges,IRanges)
importFrom(IRanges,reverse)
importFrom(Rcpp,evalCpp)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,Pairs)
importFrom(S4Vectors,Rle)
importFrom(S4Vectors,decode)
importFrom(S4Vectors,endoapply)
importFrom(S4Vectors,isSorted)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,subjectHits)
importFrom(genoPlotR,as.comparison)
importFrom(genoPlotR,dna_seg)
importFrom(genoPlotR,plot_gene_map)
importFrom(graphics,axis)
importFrom(graphics,plot.new)
importFrom(graphics,plot.window)
importFrom(graphics,rect)
importFrom(graphics,title)
importFrom(heatmaps,CoverageHeatmap)
importFrom(heatmaps,PatternHeatmap)
importFrom(methods,as)
importFrom(methods,callNextMethod)
importFrom(methods,new)
importFrom(methods,setAs)
importFrom(methods,setClass)
importFrom(rtracklayer,import.gff3)
importFrom(stats,na.omit)
importFrom(stats,runif)
importFrom(stats,weighted.mean)
importFrom(utils,head)
importFrom(utils,installed.packages)
importFrom(utils,tail)
importFrom(weights,wtd.cor)
importMethodsFrom(Biostrings,getSeq)
importMethodsFrom(Biostrings,pairwiseAlignment)
importMethodsFrom(IRanges,reverse)
importMethodsFrom(S4Vectors,isSorted)
useDynLib(GenomicBreaks, .registration = TRUE)