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NAMESPACE
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# Generated by roxygen2 (4.1.0): do not edit by hand
export(ampliconAnalysis)
export(ampliconGRanges)
export(annotateRegions)
export(annotateRegionsByInteractions)
export(biasPlots)
export(binarizeFromPeaks)
export(coverageBarplot)
export(coverageRatio)
export(cpgWeights)
export(findDMVs)
export(findDomains)
export(findNDRs)
export(findPMDs)
export(grangesVenn)
export(loadWGBS)
export(lsos)
export(makeTx)
export(methDensityPlot)
export(methHeatmap)
export(methMDS)
export(methRatios)
export(methWindowRatios)
export(methylationBiPlot)
export(methylationPlotRegions)
export(methylationPlotSamples)
export(overlapBoundaries)
export(overlapMeans)
export(overlapPositions)
export(overlapRatios)
export(overlapRegionFlanks)
export(overlapRegions)
export(overlapStats)
export(overlapSums)
export(plotDensities)
export(plotManyUCSC)
export(plotPromoterDMRs)
export(poolGroups)
export(q)
export(regionalAmpliconAnalysis)
export(screenshotUCSC)
export(seqHeatmaps)
export(shuffle)
export(shuffleBed)
export(slidingMethRatios)
export(strip)
export(tabulateCoverage)
export(tissueSpecificDMRs)
export(unstrand)
export(unvalue)
export(weightedMethylation)
importFrom(Biostrings,complement)
importFrom(Biostrings,getSeq)
importFrom(Biostrings,letterFrequency)
importFrom(Biostrings,vmatchPattern)
importFrom(GenomeInfoDb,"seqlengths<-")
importFrom(GenomeInfoDb,seqlengths)
importFrom(GenomeInfoDb,seqlevels)
importFrom(GenomeInfoDb,seqnames)
importFrom(GenomicAlignments,cigar)
importFrom(GenomicAlignments,pileLettersAt)
importFrom(GenomicAlignments,readGAlignments)
importFrom(GenomicRanges,"end<-")
importFrom(GenomicRanges,"start<-")
importFrom(GenomicRanges,"strand<-")
importFrom(GenomicRanges,"values<-")
importFrom(GenomicRanges,"width<-")
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,GRangesList)
importFrom(GenomicRanges,countOverlaps)
importFrom(GenomicRanges,coverage)
importFrom(GenomicRanges,distance)
importFrom(GenomicRanges,distanceToNearest)
importFrom(GenomicRanges,end)
importFrom(GenomicRanges,findOverlaps)
importFrom(GenomicRanges,flank)
importFrom(GenomicRanges,intersect)
importFrom(GenomicRanges,order)
importFrom(GenomicRanges,promoters)
importFrom(GenomicRanges,reduce)
importFrom(GenomicRanges,resize)
importFrom(GenomicRanges,seqnames)
importFrom(GenomicRanges,setdiff)
importFrom(GenomicRanges,split)
importFrom(GenomicRanges,start)
importFrom(GenomicRanges,strand)
importFrom(IRanges,subsetByOverlaps)
importMethodsFrom(GenomicRanges,unlist)
importFrom(GenomicRanges,values)
importFrom(GenomicRanges,width)
importFrom(Gviz,"chromosome<-")
importFrom(Gviz,AnnotationTrack)
importFrom(Gviz,DataTrack)
importFrom(Gviz,GenomeAxisTrack)
importFrom(Gviz,plotTracks)
importFrom(IRanges,"%over%")
importFrom(IRanges,IRanges)
importFrom(IRanges,Views)
importFrom(IRanges,as.data.frame)
importFrom(IRanges,as.matrix)
importFrom(IRanges,cbind)
importFrom(IRanges,elementNROWS)
importFrom(S4Vectors,endoapply)
importFrom(S4Vectors,queryHits)
importFrom(IRanges,ranges)
importFrom(S4Vectors,subjectHits)
importFrom(IRanges,viewMeans)
importFrom(IRanges,viewSums)
importFrom(RColorBrewer,brewer.pal)
importFrom(Repitools,featureScores)
importFrom(Repitools,genomeBlocks)
importFrom(Repitools,tables)
importFrom(Rsamtools,ScanBamParam)
importFrom(Rsamtools,scanBamFlag)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,Rle)
importFrom(S4Vectors,end)
importFrom(S4Vectors,endoapply)
importFrom(S4Vectors,runValue)
importFrom(S4Vectors,start)
importFrom(compiler,cmpfun)
importFrom(data.table,fread)
importFrom(ggplot2,aes)
importFrom(ggplot2,expand_limits)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,xlab)
importFrom(ggplot2,xlim)
importFrom(ggplot2,ylab)
importFrom(ggplot2,ylim)
importFrom(limma,vennCounts)
importFrom(limma,vennDiagram)
importFrom(matrixStats,colMedians)
importFrom(matrixStats,colWeightedMeans)
importFrom(matrixStats,rowSds)
importFrom(matrixStats,rowVars)
importFrom(parallel,mclapply)
importFrom(reshape2,melt)
importFrom(rtracklayer,import.bed)
importFrom(stringr,str_extract)
importFrom(zoo,rollapply)
importFrom(zoo,rollsum)
importMethodsFrom(GenomicRanges,range)