# Generated by roxygen2: do not edit by hand

export(Arrange_TFBSs_clusters)
export(BaitCapture)
export(BinMethylation)
export(CallContextMethylation)
export(CollapseStrands)
export(CollapseStrandsSM)
export(CollectCompositeData)
export(CompositeMethylationCorrelation)
export(CompositePlot)
export(ConversionRate)
export(CoverageFilter)
export(Create_MethylationCallingWindows)
export(DetectExperimentType)
export(FilterByConversionRate)
export(FilterContextCytosines)
export(FootprintCharter)
export(GetQuasRprj)
export(GetSingleMolMethMat)
export(MaskSNPs)
export(PlotAvgSMF)
export(PlotFootprints)
export(PlotSM)
export(PlotSingleMoleculeStack)
export(PlotSingleSiteSMF)
export(Plot_FootprintCharter_SM)
export(RollingMean)
export(SingleTFStates)
export(SortReads)
export(SortReadsBySingleTF)
export(SortReadsBySingleTF_MultiSiteWrapper)
export(SortReadsByTFCluster)
export(SortReadsByTFCluster_MultiSiteWrapper)
export(StateQuantification)
export(StateQuantificationBySingleTF)
export(StateQuantificationByTFPair)
export(StateQuantificationPlot)
export(TFPairStates)
export(cbind_fill_sparseMatrix)
export(panel.cor)
export(panel.hist)
export(panel.jet)
export(rbind_fill_sparseMatrix)
import(GenomicRanges)
import(QuasR)
import(ggplot2)
import(graphics)
importFrom(BSgenome,getSeq)
importFrom(BiocGenerics,grep)
importFrom(Biostrings,DNAString)
importFrom(Biostrings,getSeq)
importFrom(Biostrings,seqinfo)
importFrom(Biostrings,vcountPattern)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,elementMetadata)
importFrom(GenomicRanges,end)
importFrom(GenomicRanges,findOverlaps)
importFrom(GenomicRanges,ranges)
importFrom(GenomicRanges,seqnames)
importFrom(GenomicRanges,start)
importFrom(GenomicRanges,strand)
importFrom(GenomicRanges,tileGenome)
importFrom(GenomicRanges,width)
importFrom(IRanges,IRanges)
importFrom(IRanges,cor)
importFrom(IRanges,end)
importFrom(IRanges,findOverlaps)
importFrom(IRanges,isEmpty)
importFrom(IRanges,reduce)
importFrom(IRanges,resize)
importFrom(IRanges,start)
importFrom(IRanges,width)
importFrom(Matrix,colSums)
importFrom(Matrix,rowSums)
importFrom(Matrix,rsparsematrix)
importFrom(Matrix,sparseMatrix)
importFrom(QuasR,qCount)
importFrom(QuasR,qMeth)
importFrom(RColorBrewer,brewer.pal)
importFrom(S4Vectors,elementMetadata)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,subjectHits)
importFrom(Seqinfo,seqlengths)
importFrom(Seqinfo,seqnames)
importFrom(cluster,pam)
importFrom(cluster,silhouette)
importFrom(dplyr,arrange)
importFrom(dplyr,as_tibble)
importFrom(dplyr,desc)
importFrom(dplyr,distinct)
importFrom(dplyr,filter)
importFrom(dplyr,first)
importFrom(dplyr,group_by)
importFrom(dplyr,last)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,right_join)
importFrom(dplyr,rowwise)
importFrom(dplyr,select)
importFrom(dplyr,summarise)
importFrom(dplyr,ungroup)
importFrom(ggpointdensity,geom_pointdensity)
importFrom(grDevices,dev.list)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(magrittr,"%<>%")
importFrom(magrittr,"%>%")
importFrom(magrittr,equals)
importFrom(methods,cbind2)
importFrom(methods,rbind2)
importFrom(miscTools,colMedians)
importFrom(parallel,makeCluster)
importFrom(parallel,mclapply)
importFrom(parallel,stopCluster)
importFrom(parallelDist,parDist)
importFrom(patchwork,plot_layout)
importFrom(plyranges,filter)
importFrom(plyranges,filter_by_non_overlaps)
importFrom(plyranges,find_overlaps)
importFrom(plyranges,group_by)
importFrom(plyranges,mutate)
importFrom(plyranges,reduce_ranges)
importFrom(plyranges,select)
importFrom(plyranges,summarise)
importFrom(rlang,.data)
importFrom(stats,cor.test)
importFrom(stats,dist)
importFrom(stats,hclust)
importFrom(stats,na.omit)
importFrom(stats,symnum)
importFrom(stringr,str_detect)
importFrom(stringr,str_split)
importFrom(tibble,rownames_to_column)
importFrom(tibble,tibble)
importFrom(tidyr,extract)
importFrom(tidyr,gather)
importFrom(tidyr,separate)
importFrom(tidyr,spread)
importFrom(tidyr,unite)
importFrom(tidyr,unnest)
importFrom(utils,head)
importFrom(viridis,scale_color_viridis)
importFrom(viridis,scale_fill_viridis)
