omicverse 2.4.3

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OmicVerse is the fundamental package for multi omics included bulk ,single cell and spatial RNA-seq analysis with Python. For more information, please read our paper: OmicVerse: a framework for bridging and deepening insights across bulk and single-cell sequencing

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1 Introduction

OmicVerse v2 is a unified Python project for modern transcriptomics and multi-omics analysis. It brings together bulk RNA-seq, single-cell, spatial transcriptomics, downstream visualization, model-based analysis, and AI-assisted workflows in one package and documentation system.

Speed and memory on 1.4M cells

_{CPU: omicverse 2.4.2 (storage='disk'), brisc and Seurat 6.0.0 (in-memory, setThreads(64); RunUMAP segfaulted) on the same 128-core node. GPU: omicverse on one H100. Scanpy, Seurat + BPCells and rapids-singlecell (4× H100) from the brisc paper. Scripts}

2 General Getting Started

OmicVerse can be installed via conda or pypi and you need to install pytorch at first. Please refer to the installation tutorial for more detailed installation steps and adaptations for different platforms (Windows, Linux or Mac OS).

You can use conda install omicverse -c conda-forge or pip install -U omicverse for installation.

Please checkout the documentations and tutorials at omicverse page or omicverse.readthedocs.io.

Agent workflows — OpenClaw, the MCP server and the J.A.R.V.I.S. message bots — are documented in OmicClaw.

3 Feature coverage

Feature coverage of omicverse, the scverse ecosystem and ten other frameworks over 75 audited analysis features. The full table with per-cell evidence, the data framework and the list of published tools included in OmicVerse are in the documentation.

4 Contact

• Zehua Zeng (starlitnightly@gmail.com or steorra@omicos.cn)
• Meng Xu (mengxu@omicos.cn)

5 Developer Guild and Contributing

If you would like to contribute to omicverse, please refer to our developer documentation.

Running tests locally

Install the test dependencies and execute the suite with pytest:

pip install -e .[tests]
# or install the pinned latest requirements
pip install -r requirements-latest.txt

pytest

The optional tests extra and the requirements-latest.txt file now include pytest-asyncio>=0.23, which is required for the asynchronous streaming tests under tests/utils/.

6 Citation

If you use omicverse in your work, please cite the omicverse publication as follows:

OmicVerse: a framework for bridging and deepening insights across bulk and single-cell sequencing

Zeng, Z., Ma, Y., Hu, L. et al.

Nature Communication 2024 Jul 16. doi: 10.1038/s41467-024-50194-3.

Here are some other related packages, feel free to reference them if you use them!

OmicOS: A Comprehensive Omics Ecosystem Infrastructure and Agent System for the AI Era

Zeng, Z., Meng, X., Hu, L. et al.

Biorxiv 2026 Jun 16. doi: 10.64898/2026.06.11.731775.

CellOntologyMapper: Consensus mapping of cell type annotation

Zeng, Z., Wang, X., Du, H. et al.

imetaomics 2025 Nov 06. doi: 10.1002/imo2.70064.

7 Other

If you would like to sponsor the development of our project, you can go to the afdian website (https://ifdian.net/a/starlitnightly) and sponsor us.

Copyright © 2024 112 Lab.
This project is GPL3.0 licensed.