├── .gitignore ├── .pre-commit-config.yaml ├── .readthedocs.yml ├── .vscode ├── launch.json └── settings.json ├── LICENSE ├── Makefile ├── README.rst ├── _static ├── css │ └── warning.css └── img │ └── Scanpy_Logo_BrightFG.svg ├── basic-scrna-tutorial.ipynb ├── biome.jsonc ├── conf.py ├── dask.ipynb ├── how-to ├── cell-cycle.ipynb ├── knn-transformers.ipynb └── plotting-with-marsilea.ipynb ├── index.rst ├── integrating-data-using-ingest.ipynb ├── paga-paul15.ipynb ├── pbmc3k.ipynb ├── plotting ├── advanced.ipynb └── core.ipynb ├── pyproject.toml ├── scanpy_workshop ├── README.md ├── day1_01.ipynb ├── day1_01_GColab.ipynb ├── day1_01_GColabs_solutions.ipynb ├── day1_01_solutions.ipynb ├── day2_01_DE_Colabs.ipynb ├── day2_01_DifferentialExpression.ipynb ├── day2_02_GSEA_Colabs.ipynb ├── day2_02_GeneSetEnrichmentAnalysis.ipynb └── day2_03_RNAvelocity.ipynb ├── spatial ├── basic-analysis.ipynb └── integration-scanorama.ipynb ├── tutorial_pearson_residuals.ipynb └── 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