About scverse

scverse® is a consortium of foundational Python packages for the analysis of omics data in the life sciences.

Scanpy, AnnData and the tools around them each started out in a single lab. The consortium was founded to keep them alive well past that, and to extend the same interoperable tooling to new modalities: shared maintenance in one organisation, around a common set of data structures.

Read the mission statement Browse the packages Meet the team
63M downloads of the core packages 124 packages in the registry 394 people have contributed code 11,330 citations of scverse papers

How the pieces fit together

Every package agrees on the same data structures, so an AnnData object written by scanpy can be passed straight to scvi-tools, squidpy or anything in the ecosystem.

Layer 1

Data structures

Annotated data matrices with documented on-disk formats. Every package below reads and writes them, and that is what makes the ecosystem interoperable.

Read the format docs
AnnData anndata is a Python package for handling annotated data matrices in memory and on disk, positioned between pandas and xarray. MuData MuData is a format for annotated multimodal datasets where each modality is represented by an AnnData object. SpatialData SpatialData is a data framework that comprises a FAIR storage format and a collection of python libraries for performant access, alignment, and processing of uni- and multi-modal spatial omics datasets.
Layer 2

Core frameworks

Analysis toolkits under the shared maintenance of the core team, each covering a modality or an analysis task.

See what each one does
Scanpy Muon Squidpy scvi-tools Scirpy SnapATAC2 rapids-singlecell Pertpy decoupler
Layer 3

Ecosystem

Packages written on top of the core by labs and developers across the field. Each is maintained by its own authors and listed in the registry.

Browse all 105 packages
AESTETIK AlphaPeptTools anndata for R anndataR annsel ATLAS benGRN bento-tools biolord cell2location Cell_BLAST CellAnnotator CellCharter CellMapper CellOracle CellphoneDB CellRank cellxgene Cirrocumulus clone2vec dandelion delnx DOTools_py DoubletDetection DRVI dvp-io dynamo-release epiScanpy eschr fava flashdeconv flowsom GPTBioInsightor grassp GRnnData gssnng hotspot illico infercnvpy kompot LazySlide liana Marsilea maxspin moscot Mowgli Multivelo ncountr NicheNetPy nichepca novae omicverse Palantir Panpipes ParTIpy PathML pcdl PEAKQC pegasus PILOT popV pycea pychromVAR pyCrossTalkeR PyDESeq2 pyLemur pySCENIC pytximport pyUCell Rectangle SC2Spa SCALEX scanpro scCellFie scDataLoader scFates scGen schist scib scib-metrics scib-rapids scmcp scPRINT scPRINT-2 scTriangulate scVelo scviva-tools scxmatch scXpand scyan sift-sc sincei Sobolev Alignment sopa spatial-eggplant spatialproteomics spatiomic STMiner Symphonypy tangram TAU Community Detection TreeData vitessce wsidata zellkonverter

How scverse is run

We are a consensus-based community project and do our work in the open. Anyone with an interest can join the discussion that leads to a decision. These documents record who does what, and what we expect of each other.

24 core team members 74 GitHub organisation members 2,123 pull requests in the last year

Mission statement The goals we hold ourselves to, and the vision behind the consortium. Roles and decisions Contributors, core team, steering council, and how decisions are reached. Code of conduct The NumFOCUS code of conduct we all sign up to, and how to report a violation. AI policy Where we stand on AI-assisted contributions, and what we ask of you before you open the pull request. People Everyone holding a role in the project today, and the packages they work on. Statistics Downloads, contributors and repository activity, collected automatically and published in full.

Take part

Questions, bug reports and pull requests are all welcome, and so is turning up to ask a question. The forum and the chat are the quickest way to reach the people who maintain the packages.

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