# Generated by roxygen2: do not edit by hand

export(coord_to_grng)
export(coord_to_lst)
export(depth_hist)
export(filt_samples)
export(gene_cn_heatmaps)
export(get_depth_matrix)
export(get_new_baseline)
export(integrative_heatmap)
export(norm_fun)
export(plot_pileUp_multisample)
export(run_ELViS)
import(BiocGenerics, except=c(mad,sd,combine,Position,normalize,path,image,density,setequal,intersect))
import(GenomicRanges, except=c(subtract,intersect))
import(IRanges, except=c(slice,mad,median,quantile,sd,intersect))
import(data.table, except=c(between,first,last,shift,yearmon,yearqtr))
import(ggplot2)
importFrom(ComplexHeatmap,"%v%")
importFrom(ComplexHeatmap,Heatmap)
importFrom(ComplexHeatmap,HeatmapAnnotation)
importFrom(ComplexHeatmap,column_order)
importFrom(ComplexHeatmap,rowAnnotation)
importFrom(GenomicFeatures,cdsBy)
importFrom(GenomicFeatures,genes)
importFrom(GenomicFeatures,transcriptsBy)
importFrom(circlize,colorRamp2)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,group_split)
importFrom(dplyr,matches)
importFrom(dplyr,mutate)
importFrom(dplyr,n)
importFrom(dplyr,select)
importFrom(dplyr,slice_max)
importFrom(dplyr,slice_min)
importFrom(dplyr,summarise)
importFrom(dplyr,transmute)
importFrom(dplyr,ungroup)
importFrom(glue,glue)
importFrom(grDevices,axisTicks)
importFrom(grDevices,col2rgb)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,palette)
importFrom(grDevices,rainbow)
importFrom(grDevices,rgb)
importFrom(graphics,abline)
importFrom(graphics,axis)
importFrom(graphics,box)
importFrom(graphics,image)
importFrom(graphics,layout)
importFrom(graphics,lines)
importFrom(graphics,mtext)
importFrom(graphics,par)
importFrom(graphics,plot.new)
importFrom(graphics,points)
importFrom(graphics,polygon)
importFrom(graphics,segments)
importFrom(graphics,text)
importFrom(graphics,title)
importFrom(igraph,"E<-")
importFrom(igraph,"V<-")
importFrom(igraph,E)
importFrom(igraph,V)
importFrom(igraph,add_edges)
importFrom(igraph,cliques)
importFrom(igraph,induced_subgraph)
importFrom(igraph,make_empty_graph)
importFrom(magrittr,"%>%")
importFrom(magrittr,set_colnames)
importFrom(magrittr,set_names)
importFrom(magrittr,set_rownames)
importFrom(memoise,memoise)
importFrom(methods,is)
importFrom(parallel,detectCores)
importFrom(parallel,mclapply)
importFrom(patchwork,plot_layout)
importFrom(scales,alpha)
importFrom(scales,hue_pal)
importFrom(scales,log_breaks)
importFrom(scales,muted)
importFrom(scales,trans_new)
importFrom(scales,viridis_pal)
importFrom(segclust2d,segclust)
importFrom(segclust2d,segment)
importFrom(segclust2d,segmentation)
importFrom(stats,as.dendrogram)
importFrom(stats,cutree)
importFrom(stats,density)
importFrom(stats,dist)
importFrom(stats,hclust)
importFrom(stats,mad)
importFrom(stats,median)
importFrom(stats,quantile)
importFrom(stats,sd)
importFrom(stringr,str_extract_all)
importFrom(stringr,str_replace)
importFrom(stringr,str_replace_all)
importFrom(stringr,str_split)
importFrom(stringr,str_to_title)
importFrom(txdbmaker,makeTxDbFromGFF)
importFrom(utils,combn)
importFrom(utils,globalVariables)
importFrom(utils,read.csv)
importFrom(utils,tail)
importFrom(uuid,UUIDgenerate)
importFrom(zoo,rollapply)
importFrom(reticulate,conda_create)
importFrom(reticulate,conda_list)
