├── .coveragerc ├── .gitattributes ├── .github └── workflows │ ├── publish-to-pypi.yml │ ├── publish-to-test-pypi.yml │ └── run_tests.yml ├── .gitignore ├── .travis.yml ├── LICENSE ├── LICENSE-GPL3.txt ├── README.md ├── comparison └── comparison.py ├── data └── Klein_parameter_search_results.pickle.gz ├── doc ├── Makefile └── source │ ├── conf.py │ ├── index.rst │ ├── installation.rst │ ├── reference.rst │ └── requirements.txt ├── meld ├── __init__.py ├── benchmark.py ├── cluster.py ├── filter.py ├── meld.py ├── utils.py └── version.py ├── notebooks ├── .ipynb_checkpoints │ └── meld_txclustering-checkpoint.ipynb ├── MELD_Quickstart.ipynb ├── MELD_thresholding.Tcell.ipynb ├── Wagner2018_Chordin_Cas9_Mutagenesis.ipynb ├── cells_per_sample.png ├── excluded_cells.txt └── meld_txclustering.ipynb ├── requirements.txt ├── setup.cfg ├── setup.py ├── test ├── test_benchmark.py ├── test_meld.py ├── test_utils.py └── utils │ └── __init__.py └── unittest.cfg /.coveragerc: 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