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# Scanpy – Single-Cell Analysis in Python

Scanpy is a scalable toolkit for analyzing single-cell gene expression data
built jointly with [anndata](https://anndata.readthedocs.io).  It includes
preprocessing, visualization, clustering, trajectory inference and differential
expression testing.  The Python-based implementation efficiently deals with
datasets of more than one million cells.

Discuss usage on the scverse [Discourse]. Read the [documentation].
If you'd like to contribute by opening an issue or creating a pull request, please take a look at our [contributing guide].
If Scanpy is useful for your research, consider citing [Genome Biology (2018)].

[contributing guide]: CONTRIBUTING.md
[discourse]: https://discourse.scverse.org/
[documentation]: https://scanpy.readthedocs.io
[genome biology (2018)]: https://doi.org/10.1186/s13059-017-1382-0