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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 <>__. 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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