NAMESPACE

# Generated by roxygen2: do not edit by hand

export(AnnotationHeatmap)
export(CountPeakReads)
export(CumulativePlots)
export(DifferentialEnrichment)
export(DrawSummitHeatmaps)
export(FindMotifs)
export(GCbias)
export(SimulatePeaks)
export(SummarizeHeatmaps)
export(SummitHeatmap)
export(calcTracks)
export(plotTracks)
importFrom(BSgenome,getSeq)
importFrom(Biostrings,letterFrequency)
importFrom(Biostrings,writeXStringSet)
importFrom(ComplexHeatmap,Heatmap)
importFrom(ComplexHeatmap,HeatmapAnnotation)
importFrom(ComplexHeatmap,anno_lines)
importFrom(ComplexHeatmap,anno_text)
importFrom(ComplexHeatmap,ht_opt)
importFrom(ComplexHeatmap,max_text_width)
importFrom(GenomicRanges,"end<-")
importFrom(GenomicRanges,"start<-")
importFrom(GenomicRanges,"strand<-")
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,elementMetadata)
importFrom(GenomicRanges,end)
importFrom(GenomicRanges,makeGRangesFromDataFrame)
importFrom(GenomicRanges,promoters)
importFrom(GenomicRanges,resize)
importFrom(GenomicRanges,seqnames)
importFrom(GenomicRanges,slidingWindows)
importFrom(GenomicRanges,start)
importFrom(GenomicRanges,strand)
importFrom(GenomicRanges,terminators)
importFrom(GenomicRanges,width)
importFrom(IRanges,IRanges)
importFrom(IRanges,overlapsAny)
importFrom(IRanges,subsetByOverlaps)
importFrom(QuasR,alignmentStats)
importFrom(QuasR,qAlign)
importFrom(QuasR,qCount)
importFrom(QuasR,qProfile)
importFrom(Rsubread,featureCounts)
importFrom(S4Vectors,mcols)
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,rowRanges)
importFrom(circlize,colorRamp2)
importFrom(cowplot,theme_cowplot)
importFrom(csaw,calculateCPM)
importFrom(csaw,readParam)
importFrom(csaw,windowCounts)
importFrom(data.table,":=")
importFrom(data.table,.N)
importFrom(data.table,data.table)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,mutate)
importFrom(dplyr,pull)
importFrom(dplyr,summarise)
importFrom(dplyr,ungroup)
importFrom(edgeR,DGEList)
importFrom(edgeR,calcNormFactors)
importFrom(ggplot2,aes)
importFrom(ggplot2,annotate)
importFrom(ggplot2,arrow)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_rect)
importFrom(ggplot2,element_text)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_area)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_segment)
importFrom(ggplot2,geom_smooth)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,labs)
importFrom(ggplot2,margin)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_classic)
importFrom(ggplot2,vars)
importFrom(ggplot2,ylab)
importFrom(graphics,lines)
importFrom(graphics,par)
importFrom(graphics,smoothScatter)
importFrom(grid,gpar)
importFrom(grid,grid.lines)
importFrom(grid,grid.points)
importFrom(grid,grid.rect)
importFrom(grid,pushViewport)
importFrom(grid,unit)
importFrom(grid,upViewport)
importFrom(limma,contrasts.fit)
importFrom(limma,eBayes)
importFrom(limma,lmFit)
importFrom(limma,makeContrasts)
importFrom(limma,topTable)
importFrom(limma,voom)
importFrom(parallel,makeCluster)
importFrom(parallel,mclapply)
importFrom(patchwork,plot_layout)
importFrom(patchwork,wrap_plots)
importFrom(plyr,laply)
importFrom(reshape2,melt)
importFrom(rlang,.data)
importFrom(rtracklayer,import.bw)
importFrom(stats,coef)
importFrom(stats,dist)
importFrom(stats,hclust)
importFrom(stats,loess)
importFrom(stats,median)
importFrom(stats,model.matrix)
importFrom(stats,na.omit)
importFrom(stats,predict)
importFrom(stats,qt)
importFrom(stats,sd)
importFrom(tidyr,"%>%")
importFrom(tidyr,pivot_longer)
importFrom(tidyselect,contains)
importFrom(utils,read.table)
importFrom(utils,write.table)
importFrom(viridis,inferno)
importFrom(zoo,rollmean)