├── .gitignore ├── LICENSE ├── README.md ├── __init__.py ├── docs └── logo_1_transparent.png ├── formatted_data_links └── README.md ├── helper_for_preprocessing_and_analysis ├── README.md ├── example_head_10lines_data_K562_5kb_regression.txt ├── extract_hicpro_matrix.pl ├── functions_for_HiC.R ├── functions_for_deepC.R ├── match_query_table.pl ├── prepare_query_table.pl ├── reference_manual_deepC_R_utility.pdf ├── wrapper_plot_deepc_predictions.R └── wrapper_preprocess_hic_data.R ├── legacy_version_tf1.8 ├── README.md ├── deepCregr.py ├── deepCregr_utility.py ├── run_deploy_shape_combination_deepCregr.py ├── run_deploy_shape_deepCregr.py ├── run_get_saliency.py └── run_training_deepCregr.py ├── models └── README.md ├── tensorflow1_version ├── README.md ├── deepCregr.py ├── deepCregr_utility.py ├── run_deploy_shape_combination_deepCregr.py ├── run_deploy_shape_deepCregr.py ├── run_get_saliency.py └── run_training_deepCregr.py ├── tensorflow2.0_compatibility_version ├── README.md ├── deepCregr.py ├── deepCregr_utility.py ├── run_deploy_shape_combination_deepCregr.py ├── run_deploy_shape_deepCregr.py ├── run_get_saliency.py └── run_training_deepCregr.py ├── tensorflow2.1plus_compatibility_version ├── README.md ├── deepCregr.py ├── deepCregr_utility.py ├── run_deploy_shape_combination_deepCregr.py ├── run_deploy_shape_deepCregr.py ├── run_get_saliency.py └── run_training_deepCregr.py └── tutorials ├── README.md ├── example_region_short.bed ├── example_script_deepc_predict.sh ├── example_script_deepc_train.sh ├── example_variant.bed ├── hg19_chrom_sizes.txt ├── test_predict_out └── class_predictions_predict_provided_1_chr17_71000000_71999999.txt ├── test_variant_out └── class_predictions_predict_variant_provided_1_chr17_71706322_71706671.txt ├── tutorial_format_HiC_data_for_deepC.Rmd ├── tutorial_format_HiC_data_for_deepC.html ├── tutorial_predict_and_plot.Rmd ├── tutorial_predict_and_plot.html └── tutorial_train_a_model.md /.gitignore: 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