├── .gitignore ├── .readthedocs.yaml ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.MD ├── Dockerfile ├── INSTALL.md ├── LICENSE ├── MANIFEST.in ├── README.md ├── _config.yml ├── docs ├── conf.py ├── figs │ ├── example_outputs.png │ ├── example_training_schematic.svg │ ├── maxatac_predict_overview.png │ ├── maxatac_predict_overview.svg │ └── quickstart.svg ├── index.rst ├── readme │ ├── average.md │ ├── benchmark.md │ ├── maxatac_predict_overview.svg │ ├── normalize.md │ ├── peaks.md │ ├── predict.md │ ├── prepare.md │ ├── train.md │ └── variants.md └── requirements.txt ├── maxatac ├── __init__.py ├── analyses │ ├── __init__.py │ ├── average.py │ ├── benchmark.py │ ├── data.py │ ├── normalize.py │ ├── peaks.py │ ├── predict.py │ ├── prepare.py │ ├── threshold.py │ ├── train.py │ └── variants.py ├── architectures │ ├── __init__.py │ └── dcnn.py ├── bin │ ├── __init__.py │ └── maxatac └── utilities │ ├── __init__.py │ ├── benchmarking_tools.py │ ├── callbacks.py │ ├── constants.py │ ├── genome_tools.py │ ├── logger.py │ ├── normalization_tools.py │ ├── parser.py │ ├── peak_tools.py │ ├── plot.py │ ├── prediction_tools.py │ ├── prepare_tools.py │ ├── system_tools.py │ ├── threshold_tools.py │ ├── training_tools.py │ └── variant_tools.py ├── packaging ├── constraints │ ├── 20211007_reqs.txt │ ├── 20220609_train_OE_reqs.txt │ ├── constraints-3.8.txt │ └── py3.9_requirements.txt └── portable │ └── linux │ ├── pack_linux_docker.sh │ └── private │ ├── maxatac.desktop │ ├── maxatac.svg │ └── pack_linux.sh ├── setup.py └── tests ├── __init__.py ├── run_tests.sh ├── test.sh ├── test_average └── test_average.py ├── test_data.py ├── test_helpers.py ├── test_normalize └── test_normalize.py ├── test_parser.py ├── test_predict └── test_predict.py ├── test_prepare └── test_prepare.py ├── test_requirements.txt └── test_tools.py /.gitignore: -------------------------------------------------------------------------------- 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