uvx anndata-mcp

{
  "mcpServers": {
    "anndata-mcp": {
      "command": "uvx",
      "args": ["anndata-mcp"]
    }
  }
}

pip install --user anndata-mcp

pip install git+https://github.com/biocontext-ai/anndata-mcp.git@main

@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},
}

@article{Virshup2024,
  title = {anndata: Access and store annotated data
matrices},
  volume = {9},
  ISSN = {2475-9066},
  url = {http://dx.doi.org/10.21105/joss.04371},
  DOI = {10.21105/joss.04371},
  number = {101},
  journal = {Journal of Open Source Software},
  publisher = {The Open Journal},
  author = {Virshup,  Isaac and Rybakov,  Sergei and Theis,  Fabian J. and Angerer,  Philipp and Wolf,  F. Alexander},
  year = {2024},
  month = sep,
  pages = {4371}
}