├── .gitignore ├── LICENSE ├── README.md ├── comut ├── __init__.py ├── comut.py └── fileparsers.py ├── examples ├── documentation.ipynb ├── images │ ├── melanoma_comut.png │ ├── melanoma_comut.svg │ └── tutorial_comut.svg ├── quickstart.ipynb └── tutorial_data │ ├── data_types.png │ ├── melanoma_example │ ├── best_response.tsv │ ├── copy_number_alterations.tsv │ ├── melanoma.maf │ ├── melanoma_comut.png │ ├── merged_clinical_data.tsv │ ├── mutation_frequency.tsv │ ├── mutation_signatures.tsv │ ├── mutational_burden.tsv │ ├── mutational_signatures.tsv │ ├── primary_type.tsv │ ├── purity.tsv │ └── whole_genome_doubling.tsv │ ├── tutorial_biopsy_site.tsv │ ├── tutorial_comut.png │ ├── tutorial_indicator.tsv │ ├── tutorial_mutation_burden.tsv │ ├── tutorial_mutation_data.tsv │ ├── tutorial_mutsig_qvals.tsv │ └── tutorial_purity.tsv ├── reqs └── base-requirements.txt └── setup.py /.gitignore: -------------------------------------------------------------------------------- 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