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868 Stars 324 Forks BSD 3-Clause "New" or "Revised" License 3.0K Commits 368 Opened issues


Single-Cell Analysis in Python. Scales to >1M cells.

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.. |Stars| image:: :target: .. |PyPI| image:: :target: .. |PyPIDownloads| image:: :target: .. doesn't really add anything .. |Bioconda| image:: :target: .. |BiocondaDownloads| image:: :target: .. |Docs| image:: :target: .. |Build Status| image:: :target: .. wait until we have better coverage ;-) .. |Coverage| image:: :target:

Scanpy – Single-Cell Analysis in Python

Scanpy is a scalable toolkit for analyzing single-cell gene expression data built jointly with

__. 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 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)

.. _Discourse: .. _documentation: .. _contributing guide: .. _Genome Biology (2018):

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