Project Links

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Author: Alex Wolf, Philipp Angerer, Fidel Ramirez, Isaac Virshup, Sergei Rybakov, Gokcen Eraslan, Tom White, Malte Luecken, Davide Cittaro, Tobias Callies, Marius Lange, Andrés R. Muñoz-Rojas

Maintainer: Severin Dicks

Requires Python: >=3.10

Classifiers

Development Status

5 - Production/Stable

Environment

Console

Framework

Jupyter

Intended Audience

Developers
Science/Research

License

OSI Approved :: BSD License

Natural Language

English

Operating System

MacOS :: MacOS X
Microsoft :: Windows
POSIX :: Linux

Programming Language

Python :: 3
Python :: 3.10
Python :: 3.11
Python :: 3.12

Topic

Scientific/Engineering :: Bio-Informatics
Scientific/Engineering :: Visualization

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 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 contribution guide.

scanpy is part of the scverse project (website, governance) and is fiscally sponsored by NumFOCUS. If you like scverse and want to support our mission, please consider making a donation to support our efforts.

Citation

If you use scanpy in your work, please cite the scanpy 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.