├── .bumpversion.cfg ├── .github └── workflows │ ├── ci-cd.yaml │ └── sphinx-autodoc.yaml ├── .gitignore ├── .readthedocs.yaml ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── DEVELOPER.md ├── LICENSE ├── README.md ├── coverage.svg ├── docs ├── Makefile ├── api.rst ├── conf.py ├── contents.rst ├── index.rst ├── make.bat ├── notebooks │ ├── automatic_qc.ipynb │ └── scautoqc_logo.png └── requirements.txt ├── poetry.lock ├── pyproject.toml ├── sctk ├── __init__.py ├── _annot.py ├── _diffexp.py ├── _diffmap.py ├── _doublets.py ├── _dpt.py ├── _fdg.py ├── _filter.py ├── _highly_deviant_genes.py ├── _hvg.py ├── _leiden.py ├── _louvain.py ├── _markers.py ├── _neighbors.py ├── _norm.py ├── _obj_utils.py ├── _paga.py ├── _pca.py ├── _pipeline.py ├── _plot.py ├── _read.py ├── _tsne.py ├── _umap.py ├── _utils.py └── _velocity.py └── test └── test_pipeline.py /.bumpversion.cfg: -------------------------------------------------------------------------------- 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