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It includes\npreprocessing, visualization, clustering, trajectory inference and differential\nexpression testing.  The Python-based implementation efficiently deals with\ndatasets of more than one million cells.\n\nDiscuss usage on the scverse [Discourse][]. Read the [documentation][].\nIf you'd like to contribute by opening an issue or creating a pull request, please take a look at our [contribution guide][].\n\n[anndata]: https://anndata.readthedocs.io\n[discourse]: https://discourse.scverse.org/\n[documentation]: https://scanpy.readthedocs.io\n\n[//]: # (numfocus-fiscal-sponsor-attribution)\n\nscanpy is part of the scverse® project ([website](https://scverse.org), [governance](https://scverse.org/about/roles)) and is fiscally sponsored by [NumFOCUS](https://numfocus.org/).\nIf you like scverse® and want to support our mission, please consider making a tax-deductible [donation](https://numfocus.org/donate-to-scverse) to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.\n\n\u003cdiv align=\"center\"\u003e\n\u003ca href=\"https://numfocus.org/project/scverse\"\u003e\n  \u003cimg\n    src=\"https://raw.githubusercontent.com/numfocus/templates/master/images/numfocus-logo.png\"\n    width=\"200\"\n  \u003e\n\u003c/a\u003e\n\u003c/div\u003e\n\n\n## Citation\n\nIf you use `scanpy` in your work, please cite the `scanpy` publication as follows:\n\n\u003e **SCANPY: large-scale single-cell gene expression data analysis**\n\u003e\n\u003e F. Alexander Wolf, Philipp Angerer, Fabian J. Theis\n\u003e\n\u003e _Genome Biology_ 2018 Feb 06. doi: [10.1186/s13059-017-1382-0](https://doi.org/10.1186/s13059-017-1382-0).\n\nYou can cite the scverse publication as follows:\n\n\u003e **The scverse project provides a computational ecosystem for single-cell omics data analysis**\n\u003e\n\u003e Isaac Virshup, Danila Bredikhin, Lukas Heumos, Giovanni Palla, Gregor Sturm, Adam Gayoso, Ilia Kats, Mikaela Koutrouli, Scverse Community, Bonnie Berger, Dana Pe’er, Aviv Regev, Sarah A. Teichmann, Francesca Finotello, F. Alexander Wolf, Nir Yosef, Oliver Stegle \u0026 Fabian J. Theis\n\u003e\n\u003e _Nat Biotechnol._ 2023 Apr 10. doi: [10.1038/s41587-023-01733-8](https://doi.org/10.1038/s41587-023-01733-8).\n\n\n[contribution guide]: CONTRIBUTING.md\n","funding_links":[],"categories":["Software \u0026 Tools","Software packages","Ranked by starred repositories"],"sub_categories":["Deep Learning Approaches","RNA-seq"],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fscverse%2Fscanpy","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fscverse%2Fscanpy","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fscverse%2Fscanpy/lists"}