├── .gitignore ├── .readthedocs.yaml ├── .travis.yml ├── 2020plus.py ├── LICENSE ├── README.md ├── Snakefile ├── cluster.yaml ├── config.yaml ├── config ├── db.cfg ├── input.cfg └── output.cfg ├── data ├── README.rst ├── banned.samples.txt ├── biogrid_stats.txt ├── gene_lists │ ├── oncogenes.txt │ └── tsgs.txt └── mutsigcv_gene_features.txt ├── doc ├── Makefile ├── advanced_tutorial.rst ├── conf.py ├── download.rst ├── faq.rst ├── images │ ├── final_result.png │ ├── mlfc.png │ ├── null_distribution.png │ ├── pancan_feat_matrix.png │ ├── pancan_trained_classifier.png │ └── simulated_features.png ├── index.rst ├── installation.rst ├── quickstart.rst ├── tutorial.rst └── user_doc.rst ├── environment_python.yml ├── requirements.txt ├── requirements_rtd.txt ├── scripts ├── python │ ├── biogrid_network.py │ ├── convert_gene_names.py │ ├── davoli2maf.py │ ├── davoli_performance.py │ ├── filter_davoli_maf.py │ ├── lawrence2maf.py │ ├── maf2cravat.py │ ├── pr_curve.py │ ├── prob2020_to_2020plus.py │ ├── remove_banned_samples.py │ └── venn_diagram.py └── shell │ └── filter_maf.sh ├── src ├── __init__.py ├── classify │ ├── __init__.py │ └── python │ │ ├── __init__.py │ │ ├── classifier.py │ │ ├── dummy_clf.py │ │ ├── generic_classifier.py │ │ ├── multinomial_nb_clf.py │ │ ├── plot_data.py │ │ ├── r_random_forest_clf.py │ │ ├── random_forest_clf.py │ │ └── vogelstein_classifier.py ├── features │ ├── __init__.py │ └── python │ │ ├── __init__.py │ │ ├── feature_utils.py │ │ ├── features.py │ │ └── plot_data.py ├── savedb │ ├── __init__.py │ └── python │ │ ├── __init__.py │ │ ├── gene_features.py │ │ ├── gene_maf.py │ │ ├── gene_tsv.py │ │ └── merge_mutations.py ├── train │ ├── __init__.py │ └── python │ │ ├── __init__.py │ │ └── train.py └── utils │ ├── __init__.py │ └── python │ ├── __init__.py │ ├── amino_acid.py │ ├── math.py │ ├── nucleotide.py │ ├── p_value.py │ ├── plot.py │ └── util.py └── tests ├── data ├── example_sim_features.txt ├── features_pancan_subset.txt ├── og_example.txt ├── pancan.Rdata ├── summary_example.txt └── tsg_example.txt ├── test_classify.py ├── test_features.py └── test_train.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KarchinLab/2020plus/HEAD/.gitignore -------------------------------------------------------------------------------- /.readthedocs.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KarchinLab/2020plus/HEAD/.readthedocs.yaml -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KarchinLab/2020plus/HEAD/.travis.yml -------------------------------------------------------------------------------- /2020plus.py: 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