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Scanpy is a scalable toolkit for analyzing single-cell gene expression databuilt jointly withanndata. It includespreprocessing, visualization, clustering, trajectory inference and differentialexpression testing. The Python-based implementation efficiently deals withdatasets of more than one million cells.

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scanpy is part of the scverse® project (website,governance) and is fiscally sponsored byNumFOCUS.If you like scverse® and want to support our mission, please consider making a tax-deductibledonation to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.

If you usescanpy in your work, please cite thescanpy publication as follows:

SCANPY: large-scale single-cell gene expression data analysis

F. Alexander Wolf, Philipp Angerer, Fabian J. Theis

Genome Biology 2018 Feb 06. doi:10.1186/s13059-017-1382-0.

You can cite the scverse publication as follows:

The scverse project provides a computational ecosystem for single-cell omics data analysis

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 & Fabian J. Theis

Nat Biotechnol. 2023 Apr 10. doi:10.1038/s41587-023-01733-8.