├── .gitignore ├── LICENSE ├── README.md ├── dockerfile ├── pypi_registration.sh ├── setup.py └── tmap ├── __init__.py ├── api ├── Api_cmd.example ├── Network_generator.py ├── SAFE_analysis.py ├── SAFE_visualization.py ├── __init__.py ├── envfit_analysis.py ├── general.py └── quick_vis.py ├── extra ├── Xmapper.py ├── density_es.py └── tdamapper_io.py ├── netx ├── SAFE.py ├── __init__.py ├── coenrichment_analysis.py └── driver_detect_beta.py ├── tda ├── Filter.py ├── Graph.py ├── __init__.py ├── cover.py ├── mapper.py ├── metric.py ├── plot.py └── utils.py └── test ├── __init__.py ├── case_test ├── __init__.py ├── test_Daily_saliva.py ├── test_Daily_stool.py ├── test_FGFP.py ├── test_api.py ├── test_circles.py ├── test_digits.py └── test_iris.py ├── load_data.py ├── module_test ├── __init__.py ├── test_SAFE.py ├── test_graph.py ├── test_seed.py └── test_vis.py └── test_data ├── Daily_metadata.csv ├── Daily_saliva_genus.csv ├── Daily_stool_genus.csv ├── FGFP_genus_data.csv ├── 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