scverse
Foundational tools for single-cell omics data analysisScverse is an open-source, community-governed ecosystem of packages for single-cell and spatial omics. Shared data structures like AnnData, MuData, and SpatialData let tools such as Scanpy, scvi-tools, and Squidpy compose into a single powerful analysis.
Well-documented, actively maintained tools that interoperate out of the box.
Shared data structures and conventions, so your package fits the ecosystem from day one.
A community-governed foundation ensuring the long-term maintenance of critical infrastructure.
Extensive documentation covering installation, usage, and API references for every core package.
Semantic versioning and changelogs for every release.
Freely licensed and hosted on GitHub — use it, modify it, fork it.
Every change runs through CI before release.
Shared data structures mean output from one tool works as input to the next.
Roadmap and priorities are set by the community and core developers, not a single company.
Core packages
scverse develops a set of interoperable packages spanning every step of single-cell and spatial omics analysis, from data structures to modeling.
Ecosystem
A broader ecosystem of packages builds on the scverse core, extending it with domain-specific models and analysis methods.
Events
scverse hosts hackathons, workshops, and an annual conference to bring the community together throughout the year.
Mission
Scverse builds the community that sustains foundational tools for omics data in the life sciences.
Team
Scverse is a community project currently governed by a core team. Please reach out if you’d like to be involved!
References
scverse tools are used in research and industry across the globe. If they are useful in your work, please cite the scverse paper along with the individual packages you used.