├── DALL·E 2022-10-05 14.40.17 - Constellation in a shape of groundhog. graphical art.png ├── LICENSE ├── README.md ├── analysis ├── CAGI_analysis.py ├── GIA_addition_experiments.py ├── binary_comparison_run.py ├── evaluate.py ├── paper_run_evaluate.py ├── performance_across_bin_sizes.py ├── robustness_evaluation.py ├── save_model_logits.py ├── smoothening.py ├── test_threshold_experiment.py ├── tomtom_search.py └── umap_embeddings_plot.py ├── crop_gh.png ├── data └── sample_metafile.tsv ├── gopher ├── __init__.py ├── __pycache__ │ ├── custom_fit.cpython-37.pyc │ ├── dinuc_shuffle.cpython-38.pyc │ ├── evaluate.cpython-37.pyc │ ├── evaluate.cpython-38.pyc │ ├── global_importance.cpython-38.pyc │ ├── loss.cpython-37.pyc │ ├── losses.cpython-37.pyc │ ├── metrics.cpython-37.pyc │ ├── metrics.cpython-38.pyc │ ├── modelzoo.cpython-37.pyc │ ├── modelzoo.cpython-38.pyc │ ├── saliency_embed.cpython-38.pyc │ ├── tfr_evaluate.cpython-37.pyc │ ├── util.cpython-37.pyc │ ├── utils.cpython-37.pyc │ ├── utils.cpython-38.pyc │ └── wandb_train.cpython-37.pyc ├── binary_comparison.py ├── custom_fit.py ├── dinuc_shuffle.py ├── filter_viz.py ├── global_importance.py ├── losses.py ├── metrics.py ├── modelzoo.py ├── robustness_test.py ├── saliency_embed.py ├── utils.py ├── variant_effect.py └── wandb_train.py ├── logo.png ├── preprocessing ├── README.md ├── __pycache__ │ └── util.cpython-37.pyc ├── act_bed_construction.py ├── basenji_data.py ├── basenji_data_read.py ├── basenji_data_write.py ├── basset_write_tfr.py ├── bed_generation.py ├── bed_to_tfr.sh ├── binary_dataset_tutorial.ipynb ├── bw_to_tfr.sh ├── dna_io.py ├── genome.py ├── quant_dataset_tutorial.ipynb └── util.py ├── pyproject.toml ├── requirements.txt └── tutorials ├── GIA_occlude_results └── tutorial_outputs │ └── all_threshold_N100 │ └── ATAAA&GGG.csv ├── GIA_results └── tutorial_outputs │ ├── PC-3_replicate_1_.ATAAA. │ └── dinuc_N1000 │ │ └── flanks.csv │ ├── PC-3_replicate_1_.ATAAA._and_GGG. │ └── dinuc_N1000 │ │ ├── 1024_best_distance_interaction.csv │ │ └── 1024_distance.csv │ └── PC-3_replicate_1_GGG. │ └── dinuc_N1000 │ └── flanks.csv ├── VCF_analysis.ipynb ├── binary_evaluation.ipynb ├── cell_line_13_IDR.bed ├── evaluation.ipynb ├── global_importance_analysis.ipynb ├── robustness_test.ipynb ├── tomtom_analysis.ipynb ├── train_model.ipynb ├── umap_and_saliency.ipynb └── write_bw.ipynb /DALL·E 2022-10-05 14.40.17 - Constellation in a shape of groundhog. graphical art.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shtoneyan/gopher/HEAD/DALL·E 2022-10-05 14.40.17 - Constellation in a shape of groundhog. graphical art.png -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shtoneyan/gopher/HEAD/LICENSE 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