├── .codecov.yaml ├── .editorconfig ├── .github └── workflows │ ├── deployment.yml │ └── test.yml ├── .gitignore ├── .pre-commit-config.yaml ├── .readthedocs.yaml ├── LICENSE.txt ├── MANIFEST.in ├── README.md ├── VERSION.txt ├── docs ├── Makefile └── source │ ├── .gitignore │ ├── _static │ ├── figure.png │ └── metrics_workflow.png │ ├── api.rst │ ├── conf.py │ ├── index.rst │ ├── installation.rst │ └── user_guide.rst ├── pyproject.toml ├── scib ├── __init__.py ├── _package_tools.py ├── exceptions.py ├── integration.py ├── knn_graph │ ├── .gitignore │ ├── README.md │ ├── knn_graph.cpp │ └── makefile ├── metrics │ ├── __init__.py │ ├── ari.py │ ├── cell_cycle.py │ ├── clustering.py │ ├── graph_connectivity.py │ ├── highly_variable_genes.py │ ├── isolated_labels.py │ ├── kbet.py │ ├── lisi.py │ ├── metrics.py │ ├── nmi.py │ ├── pcr.py │ ├── silhouette.py │ ├── trajectory.py │ └── utils.py ├── preprocessing.py ├── resources │ ├── cell_cycle_genes_caenorhabditis_elegans.tsv │ ├── cell_cycle_genes_danio_rerio.tsv │ ├── cell_cycle_genes_homo_sapiens.tsv │ ├── cell_cycle_genes_mus_musculus.tsv │ ├── convert_genes.py │ ├── g2m_genes_tirosh.txt │ ├── g2m_genes_tirosh_hm.txt │ ├── s_genes_tirosh.txt │ └── s_genes_tirosh_hm.txt ├── trajectory_inference.py └── utils.py ├── setup.cfg ├── setup.py └── tests ├── __init__.py ├── common.py ├── conftest.py ├── integration ├── test_harmony.py ├── test_scanorama.py ├── test_scanvi.py └── test_scvi.py ├── metrics ├── rpy2 │ └── test_kbet.py ├── test_all.py ├── test_beyond_label_metrics.py ├── test_clisi.py ├── test_cluster_metrics.py ├── test_graph_connectivity.py ├── test_ilisi.py ├── test_isolated_label.py ├── test_pcr_metrics.py ├── test_silhouette_metrics.py └── test_trajectory.py └── preprocessing ├── test_clustering.py ├── test_gene_scoring.py └── test_preprocessing.py /.codecov.yaml: -------------------------------------------------------------------------------- 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