# Generated by roxygen2: do not edit by hand

S3method(print,looplook_karyo)
export(annotate_peaks_and_loops)
export(bedpe_to_gi)
export(consolidate_chromatin_loops)
export(draw_flower_simplified)
export(draw_upset_intersections)
export(looplook_report)
export(plot_peaks_interactions)
export(profile_target_genes)
export(read_simple_bed)
export(reduce_ginteractions)
export(refine_loop_anchors_by_expression)
importFrom(AnnotationDbi,keys)
importFrom(AnnotationDbi,keytypes)
importFrom(GenomeInfoDb,keepSeqlevels)
importFrom(GenomeInfoDb,seqinfo)
importFrom(GenomeInfoDb,seqlengths)
importFrom(GenomeInfoDb,seqlevels)
importFrom(GenomeInfoDb,seqlevelsStyle)
importFrom(GenomicFeatures,exonsBy)
importFrom(GenomicFeatures,genes)
importFrom(GenomicFeatures,promoters)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,GRangesList)
importFrom(GenomicRanges,countOverlaps)
importFrom(GenomicRanges,end)
importFrom(GenomicRanges,findOverlaps)
importFrom(GenomicRanges,makeGRangesFromDataFrame)
importFrom(GenomicRanges,seqnames)
importFrom(GenomicRanges,start)
importFrom(GenomicRanges,tileGenome)
importFrom(IRanges,IRanges)
importFrom(InteractionSet,GInteractions)
importFrom(RColorBrewer,brewer.pal)
importFrom(RColorBrewer,brewer.pal.info)
importFrom(S4Vectors,"mcols<-")
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,subjectHits)
importFrom(UpSetR,fromList)
importFrom(UpSetR,upset)
importFrom(data.table,fread)
importFrom(dplyr,"%>%")
importFrom(dplyr,any_of)
importFrom(dplyr,arrange)
importFrom(dplyr,bind_rows)
importFrom(dplyr,case_when)
importFrom(dplyr,coalesce)
importFrom(dplyr,desc)
importFrom(dplyr,distinct)
importFrom(dplyr,filter)
importFrom(dplyr,full_join)
importFrom(dplyr,group_by)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,pull)
importFrom(dplyr,rename)
importFrom(dplyr,rowwise)
importFrom(dplyr,select)
importFrom(dplyr,summarise)
importFrom(dplyr,ungroup)
importFrom(fields,image.plot)
importFrom(ggforce,geom_bezier)
importFrom(ggforce,geom_circle)
importFrom(ggplot2,aes)
importFrom(ggplot2,annotate)
importFrom(ggplot2,arrow)
importFrom(ggplot2,coord_cartesian)
importFrom(ggplot2,coord_fixed)
importFrom(ggplot2,coord_polar)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_rect)
importFrom(ggplot2,element_text)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,geom_boxplot)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_polygon)
importFrom(ggplot2,geom_rect)
importFrom(ggplot2,geom_segment)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,geom_violin)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggsave)
importFrom(ggplot2,labs)
importFrom(ggplot2,margin)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_fill_brewer)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_classic)
importFrom(ggplot2,theme_minimal)
importFrom(ggplot2,theme_void)
importFrom(ggplot2,unit)
importFrom(ggplot2,xlim)
importFrom(ggrepel,geom_text_repel)
importFrom(grDevices,col2rgb)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,rgb)
importFrom(grid,grid.draw)
importFrom(grid,grid.grabExpr)
importFrom(igraph,add_edges)
importFrom(igraph,components)
importFrom(igraph,make_empty_graph)
importFrom(karyoploteR,getDefaultPlotParams)
importFrom(karyoploteR,kpRect)
importFrom(karyoploteR,plotKaryotype)
importFrom(methods,"slot<-")
importFrom(openxlsx,addWorksheet)
importFrom(openxlsx,createWorkbook)
importFrom(openxlsx,saveWorkbook)
importFrom(openxlsx,writeData)
importFrom(scales,comma)
importFrom(scales,hue_pal)
importFrom(scales,percent)
importFrom(scales,rescale)
importFrom(stats,fisher.test)
importFrom(stats,median)
importFrom(stats,na.omit)
importFrom(stats,p.adjust)
importFrom(stats,quantile)
importFrom(stats,reorder)
importFrom(stats,runif)
importFrom(stats,setNames)
importFrom(stats,t.test)
importFrom(stats,var)
importFrom(stats,wilcox.test)
importFrom(tidyr,pivot_longer)
importFrom(tidyr,separate_rows)
importFrom(utils,capture.output)
importFrom(utils,head)
importFrom(utils,read.table)
importFrom(utils,write.csv)
