├── .gitignore ├── 01_gex ├── data ├── notebooks │ ├── 01_00_processing │ │ ├── .ipynb_checkpoints │ │ │ ├── 01_00_00_gex_wrangle_for_edger-checkpoint.ipynb │ │ │ ├── 01_00_01_gex_wrangle_for_gls-checkpoint.ipynb │ │ │ ├── 01_00_02_gex_percent_cells_expressed-checkpoint.ipynb │ │ │ ├── aggregate_percent_expressed-Copy1-checkpoint.ipynb │ │ │ ├── aggregate_percent_expressed-checkpoint.ipynb │ │ │ ├── gex_percent_cells_expressed-checkpoint.ipynb │ │ │ └── gex_percent_cells_expressed_old-checkpoint.ipynb │ │ ├── 01_00_00_gex_wrangle_for_edger.ipynb │ │ ├── 01_00_01_gex_wrangle_for_gls.ipynb │ │ ├── 01_00_02_gex_percent_cells_expressed.ipynb │ │ ├── aggregate_percent_expressed-Copy1.ipynb │ │ └── get_exon_phastcons.ipynb │ ├── 01_01_analyzing │ │ ├── .ipynb_checkpoints │ │ │ └── 01_01_02_get_entropy_based_specificity-checkpoint.ipynb │ │ ├── 01_01_00_gex_edger.ipynb │ │ ├── 01_01_01_gex_gls.ipynb │ │ └── 01_01_02_get_entropy_based_specificity.ipynb │ ├── 01_02_aggregating │ │ ├── .ipynb_checkpoints │ │ │ └── aggregate_de_tables-checkpoint.ipynb │ │ ├── aggregate_de_tables.ipynb │ │ ├── aggregate_de_values_fold_change.ipynb │ │ └── aggregate_de_values_for_go_.ipynb │ └── 01_03_plotting │ │ ├── dotplot_cluster.ipynb │ │ ├── geo_enrichr_abc_peaks.ipynb │ │ ├── geo_enrichr_plot.ipynb │ │ ├── get_volcano_plots_for_gex.ipynb │ │ ├── gex_GLS_cartoon.ipynb │ │ └── gex_cons_divergent_plot.ipynb └── scripts │ └── common_funcs.py ├── 02_chromatin_accesibility ├── notebooks │ ├── aggregating │ │ ├── atac_aggregate_de_values.ipynb │ │ └── atac_aggregate_de_values_primate.ipynb │ ├── analyizing │ │ ├── atac_edger_v2.ipynb │ │ ├── atac_gls_per_orgin.ipynb │ │ ├── atac_gls_primate_sequence.ipynb │ │ └── atac_primate_sequence_edger_v2.ipynb │ ├── plotting │ │ ├── atac_cons_divergent_plot_all_comps.ipynb │ │ └── weighted_tf_divergence.ipynb │ └── processing │ │ ├── atac_primate_peaks_wrangle_for_edger.ipynb │ │ ├── atac_primate_peaks_wrangle_for_gls.ipynb │ │ ├── atac_wrangle_for_edger.ipynb │ │ └── atac_wrangle_for_gls.ipynb └── scripts │ ├── common_funcs.py │ ├── iterative_overlap_peak_merging.R │ ├── liftover_reciprocal_github.sh │ ├── macs2.sh │ └── motif_queue_files_distal.py ├── 03_dmr └── notebooks │ ├── analyzing │ ├── annotate_dmr_sets.ipynb │ ├── dmr_TEs_advanced.ipynb │ ├── methylation_gls_per_orgin.ipynb │ ├── methylation_gls_primate_sequence.ipynb │ └── te_annotations_dmr.ipynb │ ├── plotting │ ├── aggregate_dmrs_atac.ipynb │ ├── barplots.ipynb │ ├── dmrs_specificity_and_proximity.ipynb │ └── stacked_barplots.ipynb │ └── processing │ ├── aggregate_dmrs.ipynb │ └── atac_dmr_intersection.ipynb ├── 04_boundary_and_loop └── scripts │ ├── boundary_levels │ ├── level1_mammal_and_primate_only_boundary.sh │ ├── level2_cell_overlap.sh │ ├── level2_mammal.sh │ └── level2_primate_only.sh │ └── loop_levels │ ├── level1_mammal_and_primate_only_loops.sh │ ├── level2_cell_overlap.sh │ ├── level2_mammal.sh │ └── level2_primate_only.sh ├── 05_00_abc └── mappability_analysis │ ├── notebooks │ ├── mapability_final.ipynb │ └── mapability_final_4kb.ipynb │ └── scripts │ ├── get_counts_and_mappability.py │ ├── mappability_norm_abc.py │ ├── mappability_norm_h3k27ac.py │ └── mappability_norm_human_union_peaks.py ├── 05_01_h3k27ac └── notebooks │ ├── analyzing │ └── atac_gls_h3k27ac_dpt.ipynb │ └── processing │ └── dpt_mouse_fc_h3k27ac_pseudobulk.ipynb ├── 06_neural_net ├── 06_00_make_dataset │ ├── 06_00_00_make_jobs.py │ ├── 06_00_01_mouse_multiome.py │ ├── 06_00_02_macaque_multiome.py │ ├── 06_00_03_marmoset_multiome.py │ ├── 06_00_04_human_multiome.py │ ├── 06_00_05_mouse_all_mod.py │ ├── 06_00_06_macaque_both.py │ ├── 06_00_07_marmoset_both.py │ └── 06_00_08_human_all_mod.py ├── 06_01_train_models │ ├── .ipynb_checkpoints │ │ └── run_single_mod-checkpoint.sh │ ├── 06_01_00_train_single_species_models.sh │ └── 06_01_01_train_multi_species_models.sh ├── 06_02_test_models │ ├── aggregate_peaks.sh │ ├── run_single_mod.sh │ ├── 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