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 [contributing 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.
Follow changes in the release notes.
Check out our contributing guide for development practices.
Scanpy hits 100 contributors! 2022-03-31#
Of course, contributions to the project are not limited to direct modification of the source code. Many others have improved the project by building on top of it, participating in development discussions, helping others with usage, or by showing off what it’s helped them accomplish.
Thanks to all our contributors for making this project possible!
New community channels 2022-03-31#
We’ve moved our forums and have a new publicly available chat!
Toolkit for spatial (squidpy) and multimodal (muon) published 2022-02-01#
Two large toolkits extending our ecosystem to new modalities have had their manuscripts published!