├── 0_preproc_dataset ├── 0_onehot_genome.py ├── 0_proc_prom_region_seq.py ├── 1_MAGIC_MCA.py ├── 1_MAGIC_toLabel.py ├── 1_gene_label.ipynb ├── 2_propare_datasets.py └── main.sh ├── 1_benchmark ├── 1_hyperopt_BCE_best_pos.py ├── 1_run_explain_pos.py ├── Basenji_compare.sh ├── Basenji_datasets.py ├── Basset_compare.py ├── Basset_compare.sh ├── Basset_datasets.py ├── DeepSEA_Beluga_compare.py ├── DeepSEA_compare.py ├── Fimo_compare.py ├── Fimo_datasets.py ├── add_orth.py ├── expecto_compare.py ├── expecto_datasets.py ├── expecto_features_Xreduced.py ├── main.sh ├── params.json ├── pretrain_deepsea.py ├── random_feature_datasets.py ├── random_label_datasets.py └── xpresso_compare.py ├── 1_train ├── 0_hyperopt_BCE.py ├── 0_hyperopt_trials.R ├── 0_tensorwatch.ipynb ├── 1_hyperopt_BCE_best.py ├── 1_hyperopt_BCE_best_test.py ├── 1_test_assignment.r ├── 1_test_cluster.r ├── 1_torchMTL.py ├── main.sh ├── metric_CV.py ├── print_losses.py └── utils.py ├── 2_explain ├── 0_cb2meme.py ├── 0_cisbp2meme.py ├── 0_explainer.ipynb ├── 1_run_explain.py ├── 1_run_explain_cv.py ├── 1_run_explain_scRNA.py ├── 2_influence.py ├── 3_filter_annotation.py ├── Influe.filter.py ├── Influe_ETAcorrelation.R ├── Influe_Expr.scatter.R ├── Influe_Expr.tsne.R ├── Influe_Filter_celltype_JSD.ipynb ├── Influence.filter_layer1.clustermap.ipynb ├── calculate_reproduce.py ├── explainer.py ├── filter.annotate.tomtom.py ├── filter.calculate_reproduce.py ├── filter.collect_result.py ├── filter.reductant.py ├── filter.scatter.R ├── filter_annotation.ipynb ├── filter_annotation_famliy.ipynb ├── main.sh ├── motif_length_distribution.r ├── plot.filter.result.R ├── plot.layer_conductance.R ├── plot.motif.R ├── plot.saliancy.R └── visualize.py ├── 3_application ├── callpeak.py ├── download.bw.sh ├── predict_whole_genome.py └── runme.sh ├── 5_predict_whole_genome ├── callpeak.macs.sh ├── callpeak.py ├── download.bw.sh ├── peak_annotation.R ├── peak_overlap.R ├── plot.predict_Null.boxplot.R ├── predict_whole_genome.py ├── pybigwig_bedgraph2bw.py ├── pybigwig_chr8.py └── runme.sh ├── Analysis_plotting ├── 10_Fig2a_heatmap.r ├── 11_Tree_plot.R ├── 1_Pre_sc_processing.R ├── 2_Atlas_tsne.py ├── 3_Atlas_earthworm.R ├── 4_Cell_imputation_MAGIC.py ├── 5_Atlas_sct.R ├── 6_MetaNeighbor.py ├── 7_Jensen_shannon_divergence.py ├── 7_SAMap_analysis.py ├── 8_Sankey.r ├── 8_Tree_plot.R ├── 9_Circos_plot.R └── 9_Jensen_shannon_divergence.py ├── README.md ├── Results ├── Filter_Annotation │ ├── Celegan_Cisbp_tomtom.html │ ├── Ciona_Cisbp_tomtom.html │ ├── Dmel_cisTarget_tomtom.html │ ├── Human_csiTarget_tomtom.html │ ├── Mouse_csiTarget_tomtom.html │ ├── Smed_Cisbp_tomtom.html │ └── Zebrafish_Cisbp_tomtom.html ├── Filters │ ├── Celegan_explain_filter_result.csv │ ├── Ciona_explain_filter_result.csv │ ├── Dmel_explain_filter_result.csv │ ├── EarthWorm_explain_filter_result.csv │ ├── Human_explain_filter_result.csv │ ├── Mouse_explain_filter_result.csv │ ├── Smed_explain_filter_result.csv │ └── Zebrafish_explain_filter_result.csv ├── Influe │ ├── Celegan_Influence │ │ ├── Motif_tf_celltype_influence_JSD.csv │ │ ├── Motif_tf_celltype_influence_JSD_nonDup.csv │ │ ├── combination_positive_influence_bin.clustermap.png │ │ ├── combination_positive_influence_bin_dendrogram.clustermap.png │ │ ├── combination_positive_influence_celltype.clustermap.png │ │ ├── combination_positive_influence_celltype_bin.clustermap.png │ │ ├── combination_positive_influence_celltype_bin_dendrogram.cellanno.csv │ │ ├── combination_positive_influence_celltype_bin_dendrogram.clustermap.png │ │ ├── combination_positive_influence_celltype_dendrogram.cellanno.csv │ │ ├── combination_positive_influence_celltype_dendrogram.clustermap.png │ │ ├── combination_positive_influence_dendrogram.clustermap.pdf │ │ ├── eta.csv │ │ ├── eta_boxplot.pdf │ │ ├── positive_influence.clustermap.png │ │ ├── positive_influence_bin.clustermap.png │ │ ├── positive_influence_bin_dendrogram.cellanno.csv │ │ ├── positive_influence_bin_dendrogram.clustermap.png │ │ ├── positive_influence_celltype.clustermap.png │ │ ├── positive_influence_celltype.csv │ │ ├── positive_influence_celltype_bin.clustermap.png │ │ ├── positive_influence_celltype_bin.csv │ │ ├── positive_influence_celltype_bin_dendrogram.cellanno.csv │ │ ├── positive_influence_celltype_bin_dendrogram.clustermap.png │ │ ├── positive_influence_celltype_dendrogram.cellanno.csv │ │ ├── positive_influence_celltype_dendrogram.clustermap.png │ │ ├── positive_influence_cluster.csv │ │ ├── positive_influence_dendrogram.clustermap.pdf │ │ └── positive_influence_dendrogram.clustermap.png │ ├── Ciona_Influence │ │ ├── combination_positive_influence_bin.clustermap.png │ │ ├── combination_positive_influence_bin_dendrogram.clustermap.png │ │ ├── combination_positive_influence_celltype.clustermap.png │ │ ├── combination_positive_influence_celltype_bin.clustermap.png │ │ ├── combination_positive_influence_celltype_bin_dendrogram.cellanno.csv │ │ ├── combination_positive_influence_celltype_bin_dendrogram.clustermap.png │ │ ├── combination_positive_influence_celltype_dendrogram.cellanno.csv │ │ ├── combination_positive_influence_celltype_dendrogram.clustermap.png │ │ ├── combination_positive_influence_dendrogram.clustermap.pdf │ │ ├── eta.csv │ │ ├── eta_boxplot.pdf │ │ ├── positive_influence.clustermap.png │ │ ├── positive_influence_bin.clustermap.png │ │ ├── positive_influence_bin_dendrogram.cellanno.csv │ │ ├── positive_influence_bin_dendrogram.clustermap.png │ │ ├── positive_influence_celltype.clustermap.png │ │ ├── positive_influence_celltype.csv │ │ ├── positive_influence_celltype_bin.clustermap.png │ │ ├── positive_influence_celltype_bin.csv │ │ ├── positive_influence_celltype_bin_dendrogram.cellanno.csv │ │ ├── positive_influence_celltype_bin_dendrogram.clustermap.png │ │ ├── positive_influence_celltype_dendrogram.cellanno.csv │ │ ├── positive_influence_celltype_dendrogram.clustermap.png │ │ ├── positive_influence_cluster.csv │ │ ├── positive_influence_dendrogram.clustermap.pdf │ │ └── positive_influence_dendrogram.clustermap.png │ ├── Human_Influence │ │ ├── Motif_tf_celltype_influence_JSD.csv │ │ ├── Motif_tf_celltype_influence_JSD_nonDup.csv │ │ ├── combination_positive_influence_bin.clustermap.png │ │ ├── combination_positive_influence_bin_dendrogram.clustermap.png │ │ ├── combination_positive_influence_celltype_bin.clustermap.png │ │ ├── combination_positive_influence_celltype_bin_dendrogram.cellanno.csv │ │ ├── combination_positive_influence_celltype_bin_dendrogram.clustermap.png │ │ ├── combination_positive_influence_celltype_dendrogram.cellanno.csv │ │ ├── combination_positive_influence_dendrogram.clustermap.pdf │ │ ├── eta.csv │ │ ├── eta_boxplot.pdf │ │ ├── positive_influence.clustermap.png │ │ ├── positive_influence_bin.clustermap.png │ │ ├── positive_influence_bin_dendrogram.clustermap.png │ │ ├── positive_influence_celltype.clustermap.png │ │ ├── positive_influence_celltype.csv │ │ ├── positive_influence_celltype_bin.clustermap.png │ │ ├── positive_influence_celltype_bin.csv │ │ ├── positive_influence_celltype_bin_dendrogram.cellanno.csv │ │ ├── positive_influence_celltype_bin_dendrogram.clustermap.png │ │ ├── positive_influence_celltype_dendrogram.cellanno.csv │ │ ├── positive_influence_celltype_dendrogram.clustermap.png │ │ ├── positive_influence_cluster.csv │ │ ├── positive_influence_dendrogram.clustermap.pdf │ │ └── positive_influence_dendrogram.clustermap.png │ ├── Influence_Dmel │ │ ├── Motif_tf_celltype_influence_JSD.csv │ │ ├── Motif_tf_celltype_influence_JSD_nonDup.csv │ │ ├── combination_positive_influence_bin.clustermap.png │ │ ├── combination_positive_influence_bin_dendrogram.clustermap.png │ │ ├── combination_positive_influence_celltype.clustermap.png │ │ ├── combination_positive_influence_celltype_bin.clustermap.png │ │ ├── combination_positive_influence_celltype_bin_dendrogram.cellanno.csv │ │ ├── combination_positive_influence_celltype_bin_dendrogram.clustermap.png │ │ ├── combination_positive_influence_celltype_dendrogram.cellanno.csv │ │ ├── combination_positive_influence_celltype_dendrogram.clustermap.png │ │ ├── combination_positive_influence_cluster.csv │ │ ├── combination_positive_influence_dendrogram.clustermap.pdf │ │ ├── eta_Cellcluster.csv │ │ ├── eta_boxplot_Cellcluster.pdf │ │ ├── positive_influence.clustermap.png │ │ ├── positive_influence_bin.clustermap.png │ │ ├── positive_influence_bin_dendrogram.clustermap.png │ │ ├── positive_influence_celltype.clustermap.png │ │ ├── positive_influence_celltype.csv │ │ ├── positive_influence_celltype_bin.clustermap.png │ │ ├── positive_influence_celltype_bin.csv │ │ ├── positive_influence_celltype_bin_dendrogram.cellanno.csv │ │ ├── positive_influence_celltype_bin_dendrogram.clustermap.png │ │ ├── positive_influence_celltype_dendrogram.cellanno.csv │ │ ├── positive_influence_celltype_dendrogram.clustermap.png │ │ ├── positive_influence_cluster.csv │ │ ├── positive_influence_dendrogram.clustermap.pdf │ │ └── positive_influence_dendrogram.clustermap.png │ ├── Influence_Earthworm │ │ ├── combination_positive_influence_bin.clustermap.png │ │ ├── combination_positive_influence_bin_dendrogram.clustermap.png │ │ ├── combination_positive_influence_celltype.clustermap.png │ │ ├── combination_positive_influence_celltype_bin.clustermap.png │ │ ├── combination_positive_influence_celltype_bin_dendrogram.cellanno.csv │ │ ├── combination_positive_influence_celltype_bin_dendrogram.clustermap.png │ │ ├── combination_positive_influence_celltype_dendrogram.cellanno.csv │ │ ├── combination_positive_influence_celltype_dendrogram.clustermap.png │ │ ├── combination_positive_influence_dendrogram.clustermap.pdf │ │ ├── eta_Cellcluster.csv │ │ ├── eta_boxplot_Cellcluster.pdf │ │ ├── positive_influence.clustermap.png │ │ ├── positive_influence_bin.clustermap.png │ │ ├── positive_influence_bin_dendrogram.cellanno.csv │ │ ├── positive_influence_bin_dendrogram.clustermap.png │ │ ├── positive_influence_celltype.clustermap.png │ │ ├── positive_influence_celltype.csv │ │ ├── positive_influence_celltype_bin.clustermap.png │ │ ├── positive_influence_celltype_bin.csv │ │ ├── positive_influence_celltype_bin_dendrogram.cellanno.csv │ │ ├── positive_influence_celltype_bin_dendrogram.clustermap.png │ │ ├── positive_influence_celltype_dendrogram.cellanno.csv │ │ ├── positive_influence_celltype_dendrogram.clustermap.png │ │ ├── positive_influence_cluster.csv │ │ ├── positive_influence_dendrogram.clustermap.pdf │ │ └── positive_influence_dendrogram.clustermap.png │ ├── Influence_Zebrafish │ │ ├── Motif_tf_celltype_influence_JSD.csv │ │ ├── Motif_tf_celltype_influence_JSD_nonDup.csv │ │ ├── combination_positive_influence_bin.clustermap.png │ │ ├── combination_positive_influence_bin_dendrogram.clustermap.png │ │ ├── combination_positive_influence_celltype.clustermap.png │ │ ├── combination_positive_influence_celltype_bin.clustermap.png │ │ ├── combination_positive_influence_celltype_bin_dendrogram.cellanno.csv │ │ ├── combination_positive_influence_celltype_bin_dendrogram.clustermap.png │ │ ├── combination_positive_influence_celltype_dendrogram.cellanno.csv │ │ ├── combination_positive_influence_celltype_dendrogram.clustermap.png │ │ ├── eta_Cellcluster.csv │ │ ├── eta_boxplot_Cellcluster.pdf │ │ ├── positive_influence.clustermap.png │ │ ├── positive_influence_bin.clustermap.png │ │ ├── positive_influence_bin_dendrogram.clustermap.png │ │ ├── positive_influence_celltype.clustermap.png │ │ ├── positive_influence_celltype.csv │ │ ├── positive_influence_celltype_bin.clustermap.png │ │ ├── positive_influence_celltype_bin.csv │ │ ├── positive_influence_celltype_bin_dendrogram.cellanno.csv │ │ ├── positive_influence_celltype_bin_dendrogram.clustermap.png │ │ ├── positive_influence_celltype_dendrogram.cellanno.csv │ │ ├── positive_influence_celltype_dendrogram.clustermap.png │ │ ├── positive_influence_cluster.csv │ │ ├── positive_influence_dendrogram.clustermap.pdf │ │ └── positive_influence_dendrogram.clustermap.png │ ├── Mouse_Influence │ │ ├── Motif_tf_celltype_influence_JSD.csv │ │ ├── Motif_tf_celltype_influence_JSD_nonDup.csv │ │ ├── combination_positive_influence_bin.clustermap.png │ │ ├── combination_positive_influence_bin_dendrogram.clustermap.png │ │ ├── combination_positive_influence_celltype.clustermap.png │ │ ├── combination_positive_influence_celltype_bin.clustermap.png │ │ ├── combination_positive_influence_celltype_bin_dendrogram.cellanno.csv │ │ ├── combination_positive_influence_celltype_bin_dendrogram.clustermap.png │ │ ├── combination_positive_influence_celltype_dendrogram.cellanno.csv │ │ ├── combination_positive_influence_celltype_dendrogram.clustermap.png │ │ ├── combination_positive_influence_dendrogram.clustermap.pdf │ │ ├── eta.csv │ │ ├── eta_boxplot.pdf │ │ ├── positive_influence.clustermap.png │ │ ├── positive_influence_bin.clustermap.png │ │ ├── positive_influence_bin_dendrogram.clustermap.png │ │ ├── positive_influence_celltype.clustermap.png │ │ ├── positive_influence_celltype.csv │ │ ├── positive_influence_celltype_bin.clustermap.png │ │ ├── positive_influence_celltype_bin.csv │ │ ├── positive_influence_celltype_bin_dendrogram.cellanno.csv │ │ ├── positive_influence_celltype_bin_dendrogram.clustermap.png │ │ ├── positive_influence_celltype_dendrogram.cellanno.csv │ │ ├── positive_influence_celltype_dendrogram.clustermap.png │ │ ├── positive_influence_cluster.csv │ │ ├── positive_influence_dendrogram.clustermap.pdf │ │ └── positive_influence_dendrogram.clustermap.png │ ├── Smed_Influence │ │ ├── combination_positive_influence_bin.clustermap.png │ │ ├── combination_positive_influence_bin_dendrogram.clustermap.png │ │ ├── combination_positive_influence_celltype.clustermap.png │ │ ├── combination_positive_influence_celltype_bin.clustermap.png │ │ ├── combination_positive_influence_celltype_bin_dendrogram.cellanno.csv │ │ ├── combination_positive_influence_celltype_bin_dendrogram.clustermap.png │ │ ├── combination_positive_influence_celltype_dendrogram.cellanno.csv │ │ ├── combination_positive_influence_celltype_dendrogram.clustermap.png │ │ ├── combination_positive_influence_dendrogram.clustermap.pdf │ │ ├── eta.csv │ │ ├── eta_boxplot.pdf │ │ ├── positive_influence.clustermap.png │ │ ├── positive_influence_bin.clustermap.png │ │ ├── positive_influence_bin_dendrogram.clustermap.png │ │ ├── positive_influence_celltype.clustermap.png │ │ ├── positive_influence_celltype.csv │ │ ├── positive_influence_celltype_bin.clustermap.png │ │ ├── positive_influence_celltype_bin.csv │ │ ├── positive_influence_celltype_bin_dendrogram.cellanno.csv │ │ ├── positive_influence_celltype_bin_dendrogram.clustermap.png │ │ ├── positive_influence_celltype_dendrogram.cellanno.csv │ │ ├── positive_influence_celltype_dendrogram.clustermap.png │ │ ├── positive_influence_cluster.csv │ │ ├── positive_influence_dendrogram.clustermap.pdf │ │ └── positive_influence_dendrogram.clustermap.png │ ├── influe_cluster.csv │ └── influe_comb_cluster.csv ├── Metric.csv.tar.gz ├── Species_motif_hit.csv ├── Test_Metrics │ ├── Celegans │ │ ├── test_mode_pr.csv │ │ └── test_mode_roc.csv │ ├── Ciona │ │ ├── test_mode_pr.csv │ │ └── test_mode_roc.csv │ ├── Dmel │ │ ├── test_mode_pr.csv │ │ └── test_mode_roc.csv │ ├── Dmel_bak │ │ ├── test_mode_pr.csv │ │ └── test_mode_roc.csv │ ├── EarthWorm │ │ ├── test_mode_pr.csv │ │ └── test_mode_roc.csv │ ├── Human │ │ ├── test_mode_pr.csv │ │ └── test_mode_roc.csv │ ├── Mouse │ │ ├── test_mode_pr.csv │ │ └── test_mode_roc.csv │ ├── Smed │ │ ├── test_mode_pr.csv │ │ └── test_mode_roc.csv │ └── Zebrafish │ │ ├── test_mode_pr.csv │ │ └── test_mode_roc.csv ├── scATAC_overlap_test │ ├── Dmel.overlap.p.csv │ ├── Human.overlap.p.csv │ ├── Mouse.overlap.p.csv │ 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