Information
# anndata-mcp
[](https://biocontext.ai/registry)
[![Tests][badge-tests]][tests]
[![Documentation][badge-docs]][documentation]
[badge-tests]: https://img.shields.io/github/actions/workflow/status/dschaub95/anndata-mcp/test.yaml?branch=main
[badge-docs]: https://img.shields.io/readthedocs/anndata-mcp
Allows to retrieve information about an AnnData object via MCP
## Getting started
Please refer to the [documentation][],
in particular, the [API documentation][].
You can also find the project on [BioContextAI](https://biocontext.ai), the community-hub for biomedical MCP servers: [anndata-mcp on BioContextAI](https://biocontext.ai/registry/dschaub95/anndata-mcp).
## Installation
You need to have Python 3.10 or newer installed on your system.
If you don't have Python installed, we recommend installing [uv][].
There are several alternative options to install anndata-mcp:
1. Use \`uvx\` to run it immediately:
\`\`\`bash
uvx anndata_mcp
\`\`\`
2. Include it in one of various clients that supports the \`mcp.json\` standard, please use:
\`\`\`json
\{
"mcpServers": \{
"server-name": \{
"command": "uvx",
"args": ["anndata_mcp"],
\}
\}
\}
\`\`\`
3. Install it through \`pip\`:
\`\`\`bash
pip install --user anndata_mcp
\`\`\`
4. Install the latest development version:
\`\`\`bash
pip install git+https://github.com/dschaub95/anndata-mcp.git@main
\`\`\`
## Contact
If you found a bug, please use the [issue tracker][].
## Citation
If this MCP server is useful to your research, please cite it as below.
\`\`\`bibtex
@article\{BioContext_AI_Kuehl_Schaub_2025,
title=\{BioContextAI is a community hub for agentic biomedical systems\},
url=\{http://dx.doi.org/10.1038/s41587-025-02900-9\},
urldate = \{2025-11-06\},
doi=\{10.1038/s41587-025-02900-9\},
year = \{2025\},
month = nov,
journal=\{Nature Biotechnology\},
publisher=\{Springer Science and Business Media LLC\},
author=\{Kuehl, Malte and Schaub, Darius P. and Carli, Francesco and Heumos, Lukas and Hellmig, Malte and Fernández-Zapata, Camila and Kaiser, Nico and Schaul, Jonathan and Kulaga, Anton and Usanov, Nikolay and Koutrouli, Mikaela and Ergen, Can and Palla, Giovanni and Krebs, Christian F. and Panzer, Ulf and Bonn, Stefan and Lobentanzer, Sebastian and Saez-Rodriguez, Julio and Puelles, Victor G.\},
year=\{2025\},
month=nov,
language=\{en\},
\}
\`\`\`
[uv]: https://github.com/astral-sh/uv
[issue tracker]: https://github.com/dschaub95/anndata-mcp/issues
[tests]: https://github.com/dschaub95/anndata-mcp/actions/workflows/test.yaml
[documentation]: https://anndata-mcp.readthedocs.io
[changelog]: https://anndata-mcp.readthedocs.io/en/latest/changelog.html
[api documentation]: https://anndata-mcp.readthedocs.io/en/latest/api.html
[pypi]: https://pypi.org/project/anndata-mcp