abc_score apa_figures aux_functions call_compartments checkChipEnrichments compute_differential_hic_hub config construct_oe_mat fetching_functions get_focal_contacts get_focal_contacts_with_peak_prominence get_focal_contacts_with_peak_prominence_refine gtf_functions hichip_volcanoes hic_zscore_functions hub_pileup init_bulk_atac init_bulk_RNA initialize init_tss_annotations interchromosomal_hub_plots inter_intra_metadomain_object load_DESeq2_data main_figures_plotting_functions make_figure4 map_to_humans megaloop_functions metadomain_plotting_functions motif_analysis motif_metadata_functions old_make_figures plot_pvals plotting_functions plot_with_coolbox processAdata processIntraDESeq process_loops_from_mustache supp_figures_plotting_functions tad_functions treg_functions volcano_plot

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