├── .dockerignore ├── .gitignore ├── Dockerfile ├── Jenkinsfile ├── LICENSE ├── MANIFEST.in ├── PULL_REQUEST_TEMPLATE.md ├── README.md ├── RELEASE_NOTES.md ├── config_examples ├── evaluate_test_bed.yml ├── evaluate_test_mat.yml ├── get_predictions.yml ├── in_silico_mutagenesis.yml ├── sample_h5.yml ├── train.yml ├── train_scheduler_early_stopping.yml └── variant_effect_prediction.yml ├── docs ├── Makefile ├── make.bat └── source │ ├── _static │ ├── css │ │ └── selene_docs_theme.css │ └── img │ │ ├── favicon.ico │ │ ├── selene_logo.png │ │ ├── selene_logo.svg │ │ ├── selene_logo_icon.png │ │ ├── selene_logo_icon.svg │ │ ├── selene_overview.png │ │ ├── selene_overview.svg │ │ └── sequence_logo_example.png │ ├── _templates │ └── layout.html │ ├── conf.py │ ├── index.rst │ ├── interpret.rst │ ├── overview │ ├── cli.rst │ ├── faq.rst │ ├── installation.rst │ ├── overview.rst │ └── tutorials.rst │ ├── predict.predict_handlers.rst │ ├── predict.rst │ ├── samplers.file_samplers.rst │ ├── samplers.rst │ ├── selene.rst │ ├── sequences.rst │ ├── targets.rst │ ├── tutorials │ └── index.rst │ └── utils.rst ├── manuscript ├── README.md ├── case1 │ ├── 1_train_and_evaluate │ │ ├── train_and_eval.sh │ │ └── train_and_eval.yml │ ├── 2_in_silico_mutagenesis │ │ ├── in_silico_mutagenesis.yml │ │ └── ism.sh │ ├── 3_visualize_ism_outputs.ipynb │ ├── README.md │ ├── data │ │ ├── README.md │ │ ├── get_test_regions.py │ │ └── process_data.sh │ ├── deepsea.py │ ├── download_data.sh │ └── visualize_ism_outputs │ │ ├── chr8_106051880_106052064_logits.png │ │ ├── chr8_124297519_124297668_logits.png │ │ ├── chr8_125469005_125469262_logits.png │ │ ├── chr8_20344201_20344379_logits.png │ │ ├── chr8_2181863_2182009_logits.png │ │ ├── chr8_23682363_23682839_logits.png │ │ ├── chr8_30500806_30500988_logits.png │ │ ├── chr8_42495351_42495580_logits.png │ │ ├── chr8_60330311_60330580_logits.png │ │ ├── chr8_86033536_86033682_logits.png │ │ ├── chr8_86367684_86367955_logits.png │ │ ├── chr8_89567533_89567765_logits.png │ │ ├── chr9_105314161_105314330_logits.png │ │ ├── chr9_14470510_14470698_logits.png │ │ ├── chr9_17178152_17178479_logits.png │ │ ├── chr9_22026730_22026920_logits.png │ │ ├── chr9_68629029_68629370_logits.png │ │ ├── chr9_6998075_6998252_logits.png │ │ ├── chr9_83327829_83328084_logits.png │ │ └── chr9_93453166_93453731_logits.png ├── case2 │ ├── 1_train_with_deepsea_mats │ │ ├── train.sh │ │ └── train_deepsea_mat.yml │ ├── 1_train_with_online_sampler │ │ ├── data │ │ │ ├── README.md │ │ │ ├── create_TF_intervals_file.py │ │ │ ├── process_chromatin_profiles.py │ │ │ └── process_data.sh │ │ ├── train.sh │ │ └── train_online_sampler.yml │ ├── 2_model_comparison │ │ ├── eval.sh │ │ └── evaluate.yml │ ├── 3_kipoi_export │ │ ├── ExampleDeeperDeepSEA │ │ │ ├── class_names.txt │ │ │ ├── model.yaml │ │ │ └── model_arch │ │ │ │ ├── __init__.py │ │ │ │ ├── deeper_deepsea_arch.py │ │ │ │ └── wrapped_deeper_deepsea.py │ │ ├── README.md │ │ ├── example_inputs │ │ │ ├── class_names.txt │ │ │ ├── config.yaml │ │ │ ├── deeper_deepsea_arch.py │ │ │ └── non_strand_specific_module.py │ │ ├── kipoi_export.py │ │ └── model-template.yaml │ ├── README.md │ ├── deeper_deepsea_arch.py │ └── download_data.sh └── case3 │ ├── 1_variant_effect_prediction │ ├── variant_effect_prediction.sh │ └── variant_effect_prediction.yml │ ├── 2_variant_groups_comparison.sh │ ├── README.md │ ├── deeper_deepsea_arch.py │ ├── download_data.sh │ ├── scores_as_npz.py │ └── variant_groups_comparison.py ├── models ├── README.md ├── danQ.py ├── deepsea.py ├── heartenn.py └── seqweaver.py ├── pyproject.toml ├── scripts ├── sampler_write_to_h5.py └── update_seqweaver.py ├── selene-cpu.yml ├── selene-gpu-snapshot.yml ├── selene-gpu.yml ├── selene_sdk ├── __init__.py ├── __main__.py ├── cli.py ├── evaluate_model.py ├── interpret │ ├── __init__.py │ ├── data │ │ ├── filter_gencode_gtf.py │ │ ├── gencode_v28_hg19 │ │ │ ├── protein_coding_l12_genes.bed │ │ │ ├── protein_coding_l12_genes.bed.gz │ │ │ └── protein_coding_l12_genes.bed.gz.tbi │ │ └── gencode_v28_hg38 │ │ │ ├── .nfs0000000002f5f562000003b3 │ │ │ ├── protein_coding_l12_genes.bed │ │ │ ├── protein_coding_l12_genes.bed.gz │ │ │ └── protein_coding_l12_genes.bed.gz.tbi │ ├── ism_result.py │ └── vis.py ├── predict │ ├── __init__.py │ ├── _common.py │ ├── _in_silico_mutagenesis.py │ ├── _variant_effect_prediction.py │ ├── model_predict.py │ ├── predict_handlers │ │ ├── __init__.py │ │ ├── absolute_diff_score_handler.py │ │ ├── diff_score_handler.py │ │ ├── handler.py │ │ ├── logit_score_handler.py │ │ ├── write_predictions_handler.py │ │ └── write_ref_alt_handler.py │ └── tests │ │ ├── test__common.py │ │ └── test_model_predict.py ├── samplers │ ├── __init__.py │ ├── dataloader.py │ ├── file_samplers │ │ ├── __init__.py │ │ ├── bed_file_sampler.py │ │ ├── file_sampler.py │ │ └── mat_file_sampler.py │ ├── intervals_sampler.py │ ├── multi_sampler.py │ ├── online_sampler.py │ ├── random_positions_sampler.py │ └── sampler.py ├── sequences │ ├── __init__.py │ ├── _sequence.pyx │ ├── data │ │ ├── hg19_blacklist_ENCFF001TDO.bed.gz │ │ ├── hg19_blacklist_ENCFF001TDO.bed.gz.tbi │ │ ├── hg38.blacklist.bed.gz │ │ └── hg38.blacklist.bed.gz.tbi │ ├── genome.py │ ├── proteome.py │ ├── sequence.py │ └── tests │ │ ├── files │ │ ├── small.faa │ │ ├── small.faa.fai │ │ ├── small.fasta │ │ └── small.fasta.fai │ │ ├── test_genome.py │ │ └── test_proteome.py ├── targets │ ├── __init__.py │ ├── _genomic_features.pyx │ ├── genomic_features.py │ ├── genomic_features_h5.py │ ├── target.py │ └── tests │ │ ├── files │ │ ├── sorted_aggregate.bed │ │ ├── sorted_aggregate.bed.gz │ │ └── sorted_aggregate.bed.gz.tbi │ │ └── test_genomic_features.py ├── train_model.py ├── utils │ ├── __init__.py │ ├── config.py │ ├── config_utils.py │ ├── example_model.py │ ├── multi_model_wrapper.py │ ├── non_strand_specific_module.py │ ├── performance_metrics.py │ └── utils.py └── version.py ├── setup.py 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