├── .gitattributes ├── .github ├── actions │ ├── build-docker-image │ │ └── action.yml │ ├── publish-docs │ │ └── action.yml │ └── setup-rust │ │ └── action.yml └── workflows │ ├── nightly.yml │ ├── test_python.yml │ ├── test_rust.yml │ └── wheels.yml ├── .gitignore ├── CODE_OF_CONDUCT.md ├── Cargo.toml ├── LICENSE ├── README.md ├── docker ├── README.md ├── default │ └── Dockerfile ├── docker-windows-tutorial-0.png ├── docker-windows-tutorial-1.png ├── docker-windows-tutorial-2.png └── recommend-interactive │ ├── Dockerfile │ └── entrypoint.sh ├── docs ├── _static │ ├── css │ │ └── custom.css │ ├── images │ │ ├── func+export_coverage.svg │ │ └── func+import_data.svg │ └── versions.json ├── _templates │ ├── autosummary │ │ └── class.rst │ └── layout.html ├── api │ ├── datasets.rst │ ├── export.rst │ ├── index.rst │ ├── io.rst │ ├── metrics.rst │ ├── plotting.rst │ ├── preprocessing.rst │ ├── recipes.rst │ └── tools.rst ├── changelog.md ├── conf.py ├── develop.md ├── index.rst ├── install.md ├── references.rst └── tutorials │ ├── annotation.ipynb │ ├── atlas.ipynb │ ├── diff.ipynb │ ├── hic.ipynb │ ├── index.rst │ ├── integration.ipynb │ ├── modality.ipynb │ └── pbmc.ipynb ├── pyproject.toml ├── snapatac2-contrib ├── README.md ├── pyproject.toml ├── setup.py └── snapatac2_contrib │ ├── __init__.py │ ├── _version.py │ ├── integration │ ├── README.org │ ├── __init__.py │ ├── cca.py │ ├── confusion.py │ ├── metric.py │ └── seurat_class.py │ └── metrics │ ├── __init__.py │ └── _cemba.py ├── snapatac2-core ├── Cargo.toml ├── LICENSE ├── benches │ └── benchmark.rs ├── src │ ├── embedding.rs │ ├── export.rs │ ├── feature_count │ │ ├── counter.rs │ │ ├── data_iter.rs │ │ ├── matrix.rs │ │ └── mod.rs │ ├── genome.rs │ ├── lib.rs │ ├── motif.rs │ ├── network.rs │ ├── preprocessing │ │ ├── bam.rs │ │ ├── bam │ │ │ ├── flagstat.rs │ │ │ ├── header.rs │ │ │ └── mark_duplicates.rs │ │ ├── import.rs │ │ ├── mod.rs │ │ └── qc.rs │ └── utils │ │ ├── knn.rs │ │ ├── mod.rs │ │ └── similarity.rs └── test │ ├── coverage.bdg.gz │ └── fragments.tsv.gz ├── snapatac2 ├── __init__.py ├── _io.py ├── _utils.py ├── datasets.py ├── export │ └── __init__.py ├── genome.py ├── metrics │ └── __init__.py ├── plotting │ ├── __init__.py │ ├── _base.py │ └── _network.py ├── preprocessing │ ├── __init__.py │ ├── _basic.py │ ├── _cell_calling.py │ ├── _harmony.py │ ├── _knn.py │ ├── _mnn_correct.py │ ├── _recipe.py │ ├── _scanorama.py │ └── _scrublet.py └── tools │ ├── __init__.py │ ├── _call_peaks.py │ ├── _clustering.py │ ├── _diff.py │ ├── _embedding.py │ ├── _integration.py │ ├── _misc.py │ ├── _motif.py │ ├── _network.py │ └── _smooth.py ├── src ├── call_peaks.rs ├── embedding.rs ├── export.rs ├── knn.rs ├── lib.rs ├── motif.rs ├── network.rs ├── preprocessing.rs └── utils │ ├── anndata.rs │ └── mod.rs └── tests ├── test_func.py ├── test_pipeline.py ├── test_similarity.py ├── test_tools.py └── test_tools ├── test.bam ├── test.bed.gz ├── test_clean.tsv.gz └── test_single.tsv.gz 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