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NAMESPACE
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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export(.ExportBamForGviz)
export(.ExportBigwigForGviz)
export(.ExportFastaForGviz)
export(AdaptedIdeogramTrackWithoutBandsData)
export(AddToModBasePropDistFromFeaturePlot)
export(DrawBarplotBothStrands)
export(DrawContigCumulLength)
export(DrawDistriHistBox)
export(DrawFdrEstList)
export(DrawLogoPosNegAxes)
export(DrawModBaseCountsWithinFeature)
export(DrawModBasePropByFeature)
export(DrawModBasePropDistFromFeature)
export(DrawModLogo)
export(DrawParamPerModBaseCategories)
export(ExportFilesForGViz)
export(ExtractListModPosByModMotif)
export(FiltContig)
export(FiltDeepSignal)
export(FiltFdrBased)
export(FiltPacBio)
export(FiltParam)
export(GetAssemblyReport)
export(GetContigCumulLength)
export(GetDistFromFeaturePos)
export(GetFdrBasedThreshLimit)
export(GetFdrEstListByThresh)
export(GetGRangesWindowSeqandParam)
export(GetGenomeGRanges)
export(GetGposCenterFromGRanges)
export(GetListCountsByDist)
export(GetMeanParamByContig)
export(GetModBaseCountsByFeature)
export(GetModBaseCountsWithinFeature)
export(GetModRatioByContig)
export(GetModReportDeepSignal)
export(GetModReportPacBio)
export(GetSeqPctByContig)
export(ImportBamExtendedAnnotationTrack)
export(ImportDeepSignalModFrequency)
export(ImportPacBioCSV)
export(ImportPacBioGFF)
export(PredictMissingAnnotation)
import(Biostrings)
import(GenomicRanges)
importFrom(BSgenome,getSeq)
importFrom(BSgenome,seqinfo)
importFrom(Biobase,isUnique)
importFrom(BiocGenerics,sort)
importFrom(BiocGenerics,table)
importFrom(BiocGenerics,which)
importFrom(Biostrings,consensusMatrix)
importFrom(GenomeInfoDb,"seqlevels<-")
importFrom(GenomeInfoDb,seqlevels)
importFrom(GenomeInfoDb,seqlevelsInUse)
importFrom(GenomeInfoDb,sortSeqlevels)
importFrom(GenomicRanges,"mcols<-")
importFrom(GenomicRanges,GPos)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,mcols)
importFrom(GenomicRanges,resize)
importFrom(GenomicRanges,seqnames)
importFrom(GenomicRanges,strand)
importFrom(GenomicRanges,width)
importFrom(Gviz,IdeogramTrack)
importFrom(IRanges,IPos)
importFrom(IRanges,IRanges)
importFrom(IRanges,extractList)
importFrom(IRanges,findOverlapPairs)
importFrom(IRanges,subsetByOverlaps)
importFrom(Rsamtools,BamFile)
importFrom(Rsamtools,ScanBamParam)
importFrom(Rsamtools,scanBam)
importFrom(Rsamtools,scanBamFlag)
importFrom(Rsamtools,scanBamHeader)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,Pairs)
importFrom(S4Vectors,countQueryHits)
importFrom(S4Vectors,isEmpty)
importFrom(data.table,":=")
importFrom(data.table,between)
importFrom(data.table,data.table)
importFrom(data.table,fread)
importFrom(data.table,setDF)
importFrom(grDevices,dev.print)
importFrom(grDevices,pdf)
importFrom(grDevices,png)
importFrom(grDevices,rgb)
importFrom(graphics,abline)
importFrom(graphics,axis)
importFrom(graphics,barplot)
importFrom(graphics,boxplot)
importFrom(graphics,grid)
importFrom(graphics,hist)
importFrom(graphics,layout)
importFrom(graphics,legend)
importFrom(graphics,lines)
importFrom(graphics,mtext)
importFrom(graphics,par)
importFrom(graphics,plot)
importFrom(graphics,polygon)
importFrom(graphics,segments)
importFrom(graphics,text)
importFrom(graphics,title)
importFrom(grid,dataViewport)
importFrom(grid,gpar)
importFrom(grid,grid.abline)
importFrom(grid,grid.newpage)
importFrom(grid,grid.polygon)
importFrom(grid,grid.text)
importFrom(grid,grid.xaxis)
importFrom(grid,grid.yaxis)
importFrom(grid,plotViewport)
importFrom(grid,popViewport)
importFrom(grid,pushViewport)
importFrom(grid,unit)
importFrom(methods,as)
importFrom(rtracklayer,export)
importFrom(rtracklayer,export.bw)
importFrom(rtracklayer,export.gff3)
importFrom(rtracklayer,import)
importFrom(seqLogo,ic)
importFrom(seqLogo,makePWM)
importFrom(seqLogo,pwm)
importFrom(stats,aggregate)
importFrom(stats,density)
importFrom(stats,quantile)
importFrom(stats,setNames)
importFrom(utils,write.csv)
importFrom(utils,write.table)