Omicverse
A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.
Install / Use
/learn @Starlitnightly/OmicverseREADME
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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][docs-feat-provider]
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.
[!NOTE] OmicVerse v2 is organized as a broader analysis platform rather than a single-method package. In addition to core analysis modules, it now includes agent-style workflows through J.A.R.V.I.S., MCP-based tool serving for AI clients, and a growing documentation/tutorial system under
omicverse_guide.
2 Directory structure
.
├── omicverse # Main Python package
├── omicverse_guide # Documentation files
├── omicverse_web # Web Analysis Platform
├── sample # Some test data
├── LICENSE
└── README.md
3 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.
4 J.A.R.V.I.S Getting Started
4.1 OpenClaw
OmicVerse provide an directly interact analysis with OpenClaw project. You can use
omicverse claw 'help me annotate the lung scrna-seq'
This module supported by ov.Agent function. And i think that will be convinent for you to analysis the anndata using OpenClaw.
The full tutorial could be found at here
4.2 MCP Server (Model Context Protocol)
OmicVerse provide an MCP server that exposes registered analysis tools to AI assistants (Claude Code, etc.) via the standard Model Context Protocol.
# Install with MCP dependencies
pip install -e "omicverse[mcp]"
# Start the server (stdio transport)
python -m omicverse.mcp # or: omicverse-mcp
python -m omicverse.mcp --phase P0 # core pipeline tools only
The full tutorial could be found at here
4.3 J.A.R.V.I.S Msg system
If you want to analysis the AnnData using Mobile Phone, maybe you can try
# Install with jarvis dependencies
pip install "omicverse[jarvis]"
# Start to chat with JARVIS using telegram
omicverse jarvis --channel telegram --token "$TELEGRAM_BOT_TOKEN"
The full tutorial could be found at here
4 Data Framework and Reference
The omicverse is implemented as an infrastructure based on the following four data structures.
<div align="center"> <table> <tr> <td> <a href="https://github.com/pandas-dev/pandas">pandas</a></td> <td> <a href="https://github.com/scverse/anndata">anndata</a></td> <td> <a href="https://github.com/numpy/numpy">numpy</a></td> <td> <a href="https://github.com/scverse/mudata">mudata</a></td> </tr> </table> </div>The table contains the tools have been published
<div align="center"> <table> <tr> <td align="center">Scanpy<br><a href="https://github.com/scverse/scanpy">📦</a> <a href="https://link.springer.com/article/10.1186/s13059-017-1382-0">📖</a></td> <td align="center">dynamicTreeCut<br><a href="https://github.com/kylessmith/dynamicTreeCut">📦</a> <a href="https://academic.oup.com/bioinformatics/article/24/5/719/200751">📖</a></td> <td align="center">scDrug<br><a href="https://github.com/ailabstw/scDrug">📦</a> <a href="https://www.sciencedirect.com/science/article/pii/S2001037022005505">📖</a></td> <td align="center">MOFA<br><a href="https://github.com/bioFAM/mofapy2">📦</a> <a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02015-1">📖</a></td> <td align="center">COSG<br><a href="https://github.com/genecell/COSG">📦</a> <a href="https://academic.oup.com/bib/advance-article-abstract/doi/10.1093/bib/bbab579/6511197?redirectedFrom=fulltext">📖</a></td> <td align="center">CellphoneDB<br><a href="https://github.com/ventolab/CellphoneDB">📦</a> <a href="https://www.nature.com/articles/s41586-018-0698-6">📖</a></td> </tr> <tr> <td align="center">AUCell<br><a href="https://github.com/aertslab/AUCell">📦</a> <a href="https://bioconductor.org/packages/AUCell">📖</a></td> <td align="center">Bulk2Space<br><a href="https://github.com/ZJUFanLab/bulk2space">📦</a> <a href="https://www.nature.com/articles/s41467-022-34271-z">📖</a></td> <td align="center">SCSA<br><a href="https://github.com/bioinfo-ibms-pumc/SCSA">📦</a> <a href="https://doi.org/10.3389/fgene.2020.00490">📖</a></td> <td align="center">WGCNA<br><a href="http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA">📦</a> <a href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-9-559">📖</a></td> <td align="center">StaVIA<br><a href="https://github.com/ShobiStassen/VIA">📦</a> <a href="https://www.nature.com/articles/s41467-021-25773-3">📖</a></td> <td align="center">pyDEseq2<br><a href="https://github.com/owkin/PyDESeq2">📦</a> <a href="https://www.biorxiv.org/content/10.1101/2022.12.14.520412v1">📖</a></td> </tr> <tr> <td align="center">NOCD<br><a href="ht