# Generated by roxygen2: do not edit by hand

export(curate_clusters)
export(form_combined_panel)
export(generate_all_plots)
export(generate_html_report)
export(handle_tc_from_cage)
export(iqw_tpm_plots)
export(order_clusters_iqw)
export(per_cluster_annotations)
export(per_cluster_go_term_enrichments)
export(per_cluster_seqlogos)
export(per_cluster_strand_dist)
export(plot_motif_heatmaps)
export(plot_motif_heatmaps2)
export(seqs_acgt_image)
export(write_seqArchR_cluster_track_bed)
importFrom(BiocParallel,MulticoreParam)
importFrom(BiocParallel,SerialParam)
importFrom(BiocParallel,SnowParam)
importFrom(BiocParallel,bplapply)
importFrom(BiocParallel,ipclock)
importFrom(BiocParallel,ipcremove)
importFrom(BiocParallel,ipcunlock)
importFrom(BiocParallel,multicoreWorkers)
importFrom(Biostrings,width)
importFrom(GenomicRanges,promoters)
importFrom(GenomicRanges,trim)
importFrom(IRanges,IRanges)
importFrom(S4Vectors,mcols)
importFrom(Seqinfo,"seqinfo<-")
importFrom(Seqinfo,"seqlevels<-")
importFrom(Seqinfo,seqinfo)
importFrom(Seqinfo,seqlevels)
importFrom(cli,cli_alert_info)
importFrom(cli,cli_alert_warning)
importFrom(cli,cli_h1)
importFrom(clusterProfiler,dotplot)
importFrom(clusterProfiler,enrichGO)
importFrom(cowplot,plot_grid)
importFrom(ggimage,as.ggplot)
importFrom(ggplot2,aes)
importFrom(ggplot2,dup_axis)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_line)
importFrom(ggplot2,element_text)
importFrom(ggplot2,expansion)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,geom_boxplot)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,guide_legend)
importFrom(ggplot2,margin)
importFrom(ggplot2,position_fill)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_x_log10)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,scale_y_discrete)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,theme_classic)
importFrom(ggplot2,theme_void)
importFrom(ggplot2,unit)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(grDevices,png)
importFrom(graphics,barplot)
importFrom(magick,image_read)
importFrom(methods,is)
importFrom(seqArchR,collate_clusters)
importFrom(seqArchR,collate_seqArchR_result)
importFrom(seqArchR,get_seqs_clust_list)
importFrom(seqArchR,plot_arch_for_clusters)
importFrom(seqArchR,plot_ggseqlogo_of_seqs)
importFrom(seqArchR,seqs_str)
importFrom(seqArchR,viz_seqs_acgt_mat)
importFrom(seqPattern,plotPatternDensityMap)
importFrom(stats,cutree)
importFrom(stats,median)
importFrom(stats,reorder)
importFrom(utils,read.delim)
importFrom(utils,write.table)
