├── .gitattributes ├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ ├── custom.md │ └── feature_request.md └── workflows │ └── ci.yml ├── .gitignore ├── CHANGELOG.md ├── CONTRIBUTING.md ├── LICENSE ├── README.md ├── config ├── README.md ├── config.yaml ├── project │ ├── aml.yaml │ ├── bmmc.yaml │ └── poised.yaml ├── sweeper │ └── optuna.yaml └── trainer │ ├── all_params.yaml │ ├── debug.yaml │ ├── default.yaml │ └── gpu.yaml ├── docs ├── advanced │ ├── data.md │ ├── hydra_wandb.md │ ├── parameters.md │ └── scripts.md ├── advice.md ├── api │ ├── coupling_layer.md │ ├── datasets.md │ ├── io.md │ ├── model.md │ ├── module.md │ ├── plots.md │ ├── preprocess.md │ ├── prior.md │ ├── real_nvp.md │ └── tools.md ├── assets │ ├── example_scatterplot.png │ ├── favicon.png │ ├── logo.png │ ├── logo_white.svg │ ├── overview.png │ ├── overview_b.png │ └── overview_c.png ├── cite.md ├── getting_started.md ├── index.md ├── javascripts │ └── mathjax.js ├── math.md └── tutorials │ ├── batch_effect_correction.ipynb │ ├── debarcoding.ipynb │ ├── population_discovery.ipynb │ ├── preprocessing.ipynb │ └── usage.ipynb ├── mkdocs.yml ├── poetry.lock ├── pyproject.toml ├── scripts ├── README.md ├── __init__.py ├── lisi.py ├── run.py ├── timing.py └── utils.py ├── scyan ├── __init__.py ├── _io.py ├── baseline.py ├── data │ ├── __init__.py │ ├── datasets.py │ └── tensors.py ├── model.py ├── module │ ├── __init__.py │ ├── coupling_layer.py │ ├── distribution.py │ ├── real_nvp.py │ └── scyan_module.py ├── plot │ ├── __init__.py │ ├── _scanpy_plot │ │ ├── README.md │ │ ├── __init__.py │ │ ├── palettes.py │ │ ├── plot_settings.py │ │ └── umap.py │ ├── density.py │ ├── dot.py │ ├── expressions.py │ ├── graph.py │ ├── heatmap.py │ ├── ratios.py │ └── utils.py ├── preprocess.py ├── tools │ ├── __init__.py │ ├── biomarkers.py │ ├── colors.py │ ├── gating.py │ └── representation.py └── utils.py ├── setup.py └── tests ├── test_analysis.py ├── test_plots.py ├── test_preprocess.py └── 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