├── .codecov.yaml ├── .cruft.json ├── .editorconfig ├── .flake8 ├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.yml │ ├── config.yml │ └── feature_request.yml └── workflows │ ├── build.yaml │ ├── release.yaml │ └── test.yaml ├── .gitignore ├── .pre-commit-config.yaml ├── .readthedocs.yaml ├── CHANGELOG.md ├── LICENSE ├── README.md ├── docs ├── Makefile ├── _static │ ├── .gitkeep │ ├── cellcharter.png │ ├── cellcharter_workflow.png │ ├── css │ │ └── custom.css │ └── spatial_clusters.png ├── _templates │ ├── .gitkeep │ └── autosummary │ │ └── class.rst ├── api.md ├── changelog.md ├── conf.py ├── contributing.md ├── extensions │ └── typed_returns.py ├── graph.md ├── index.md ├── notebooks │ ├── codex_mouse_spleen.ipynb │ ├── cosmx_human_nsclc.ipynb │ ├── data │ │ └── .gitkeep │ ├── example.ipynb │ └── tutorial_models │ │ └── codex_mouse_spleen_trvae │ │ ├── attr.pkl │ │ ├── model_params.pt │ │ └── var_names.csv ├── plotting.md ├── references.bib ├── references.md └── tools.md ├── pyproject.toml ├── src └── cellcharter │ ├── __init__.py │ ├── _constants │ └── _pkg_constants.py │ ├── _utils.py │ ├── datasets │ ├── __init__.py │ └── _dataset.py │ ├── gr │ ├── __init__.py │ ├── _aggr.py │ ├── _build.py │ ├── _group.py │ ├── _nhood.py │ └── _utils.py │ ├── pl │ ├── __init__.py │ ├── _autok.py │ ├── _group.py │ ├── _nhood.py │ ├── _shape.py │ └── _utils.py │ └── tl │ ├── __init__.py │ ├── _autok.py │ ├── _gmm.py │ ├── _shape.py │ ├── _trvae.py │ └── _utils.py └── tests ├── _data └── test_data.h5ad ├── _models ├── cellcharter_autok_imc │ ├── attributes.pickle │ ├── best_models │ │ ├── GaussianMixture_k1 │ │ │ ├── attributes.pickle │ │ │ ├── model │ │ │ │ ├── config.json │ │ │ │ └── parameters.pt │ │ │ └── params.pickle │ │ ├── GaussianMixture_k10 │ │ │ ├── attributes.pickle │ │ │ ├── model │ │ │ │ ├── config.json │ │ │ │ └── parameters.pt │ │ │ └── params.pickle │ │ ├── GaussianMixture_k11 │ │ │ ├── attributes.pickle │ │ │ ├── model │ │ │ │ ├── config.json │ │ │ │ └── parameters.pt │ │ │ └── params.pickle │ │ ├── GaussianMixture_k12 │ │ │ ├── attributes.pickle │ │ │ ├── model │ │ │ │ ├── config.json │ │ │ │ └── parameters.pt │ │ │ └── params.pickle │ │ ├── GaussianMixture_k13 │ │ │ ├── attributes.pickle │ │ │ ├── model │ │ │ │ ├── config.json │ │ │ │ └── parameters.pt │ │ │ └── params.pickle │ │ ├── GaussianMixture_k14 │ │ │ ├── attributes.pickle │ │ │ ├── model │ │ │ │ ├── config.json │ │ │ │ └── parameters.pt │ │ │ └── params.pickle │ │ ├── GaussianMixture_k15 │ │ │ ├── attributes.pickle │ │ │ ├── model │ │ │ │ ├── config.json │ │ │ │ └── parameters.pt │ │ │ └── params.pickle │ │ ├── GaussianMixture_k16 │ │ │ ├── attributes.pickle │ │ │ ├── model │ │ │ │ ├── config.json │ │ │ │ └── parameters.pt │ │ │ └── params.pickle │ │ ├── GaussianMixture_k2 │ │ │ ├── attributes.pickle │ │ │ ├── model │ │ │ │ ├── config.json │ │ │ │ └── parameters.pt │ │ │ └── params.pickle │ │ ├── GaussianMixture_k3 │ │ │ ├── attributes.pickle │ │ │ ├── model │ │ │ │ ├── config.json │ │ │ │ └── parameters.pt │ │ │ └── params.pickle │ │ ├── GaussianMixture_k4 │ │ │ ├── attributes.pickle │ │ │ ├── model │ │ │ │ ├── config.json │ │ │ │ └── parameters.pt │ │ │ └── params.pickle │ │ ├── GaussianMixture_k5 │ │ │ ├── attributes.pickle │ │ │ ├── model │ │ │ │ ├── config.json │ │ │ │ └── parameters.pt │ │ │ └── params.pickle │ │ ├── GaussianMixture_k6 │ │ │ ├── attributes.pickle │ │ │ ├── model │ │ │ │ ├── config.json │ │ │ │ └── parameters.pt │ │ │ └── params.pickle │ │ ├── GaussianMixture_k7 │ │ │ ├── attributes.pickle │ │ │ ├── model │ │ │ │ ├── config.json │ │ │ │ └── parameters.pt │ │ │ └── params.pickle │ │ ├── GaussianMixture_k8 │ │ │ ├── attributes.pickle │ │ │ ├── model │ │ │ │ ├── config.json │ │ │ │ └── parameters.pt │ │ │ └── params.pickle │ │ └── GaussianMixture_k9 │ │ │ ├── attributes.pickle │ │ │ ├── model │ │ │ ├── config.json │ │ │ └── parameters.pt │ │ │ └── params.pickle │ └── params.pickle └── cellcharter_autok_mibitof │ ├── attributes.pickle │ ├── best_models │ ├── GaussianMixture_k1 │ │ ├── attributes.pickle │ │ ├── model │ │ │ ├── config.json │ │ │ └── parameters.pt │ │ └── params.json │ ├── GaussianMixture_k2 │ │ ├── attributes.pickle │ │ ├── model │ │ │ ├── config.json │ │ │ └── parameters.pt │ │ └── params.json │ ├── GaussianMixture_k3 │ │ ├── attributes.pickle │ │ ├── model │ │ │ ├── config.json │ │ │ └── parameters.pt │ │ └── params.json │ ├── GaussianMixture_k4 │ │ ├── attributes.pickle │ │ ├── model │ │ │ ├── config.json │ │ │ └── parameters.pt │ │ └── params.json │ ├── GaussianMixture_k5 │ │ ├── attributes.pickle │ │ ├── model │ │ │ ├── config.json │ │ │ └── parameters.pt │ │ └── params.json │ └── GaussianMixture_k6 │ │ ├── attributes.pickle │ │ ├── model │ │ ├── config.json │ │ └── parameters.pt │ │ └── params.json │ └── params.pickle ├── conftest.py ├── graph ├── test_aggregate_neighbors.py ├── test_build.py ├── test_diff_nhood.py ├── test_group.py └── test_nhood.py ├── plotting ├── test_group.py ├── test_plot_nhood.py ├── test_plot_stability.py └── test_shape.py └── tools ├── test_autok.py ├── test_gmm.py └── test_shape.py /.codecov.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSOgroup/cellcharter/HEAD/.codecov.yaml -------------------------------------------------------------------------------- /.cruft.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSOgroup/cellcharter/HEAD/.cruft.json -------------------------------------------------------------------------------- /.editorconfig: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSOgroup/cellcharter/HEAD/.editorconfig -------------------------------------------------------------------------------- /.flake8: -------------------------------------------------------------------------------- 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