OmicVerse

About

A unified Python ecosystem for multi-omics, with Rust and Torch underneath.

What this org is

OmicVerse is a Python ecosystem for multi-omics analysis built around three principles:

  • One unified API across bulk, single-cell, spatial, and multi-modal data.
  • AnnData-native throughout, so it plugs into existing scanpy pipelines without rewrites.
  • Rust and Torch underneath — hot loops in Rust, tensor methods on Torch, classical methods on NumPy / SciPy.

The core library, omicverse, exposes the unified surface. Around it, the organization maintains pure-Python and pure-Rust re-implementations of widely-cited methods (CopyKAT, hdWGCNA, inferCNV, Monocle, scDblFinder, DoubletFinder, DADA2, mclust, Milo, scHiCluster, BandNorm, NMF…) so users have a parity-audited alternative that doesn't depend on R or rpy2.

An agent layer on top — omicverse-skills and omicclaw — exposes the same methods as callable skills for agent-driven analysis. The project is open-source, community-led, and aligned with the broader scverse ecosystem.

At a glance

  • One unified Python API · AnnData-native
  • Rust hot loops · Torch tensors · GPU support
  • 14 method ports · 11 Python, 3 Rust · parity-audited
  • Bit-equivalent to the R reference at published defaults
  • Up to ~200× faster than R on the compute-heavy paths
  • 979★ on GitHub · Apache-2.0 · scverse-aligned

Governance

OmicVerse follows a lightweight model: maintainers own tracks, contributions are reviewed in the open, breaking changes go through an RFC.

/01

Track maintainers

Each track (ports, runtime, agents, docs) has a named maintainer who reviews PRs and signs off releases.

/02

Open review

All design discussion happens in GitHub Issues and Discussions. Contributing doesn't require maintainer status.

/03

RFC for breaking changes

Anything that changes a public API, AnnData contract, or benchmark methodology requires a public RFC.

/04

Code of conduct

The project follows the Contributor Covenant. Reports go to the maintainer contact in the org README.

/05

Release cadence

Stable releases monthly, patch releases as needed. Each release ships changelog, parity diffs, updated benchmarks.

/06

Funding

OmicVerse is independent. Acknowledgments to research groups and funding sources live next to the code they support.

Citation

If you use OmicVerse in published work, please cite the framework paper. For specific method ports, also cite the original method.

@article{omicverse,
  title   = "OmicVerse: a unified multi-omics analysis framework",
  author  = "Zeng, Zehua and others",
  journal = "Nature Communications",
  year    = "2024",
  url     = "https://github.com/omicverse/omicverse"
}

Replace this entry with the canonical citation from the project README before publishing.