Liana-MCP

Natural language interface for scRNA-Seq analysis with Liana through MCP.

🪩 What can it do?

• IO module like read and write scRNA-Seq data

• Cell-cell communication method

• Plotting module, circle plot, dotplot

Related MCP server: ChatSpatial

❓ Who is this for?

• Anyone who wants to do scRNA-Seq analysis natural language!

• Agent developers who want to call Liana's functions for their applications

🌐 Where to use it?

You can use Liana-mcp in most AI clients, plugins, or agent frameworks that support the MCP:

• AI clients, like Cherry Studio

• Plugins, like Cline

• Agent frameworks, like Agno

🎬 Demo

A demo showing scRNA-Seq cell cluster analysis in a AI client Cherry Studio using natural language based on Liana-mcp

https://github.com/user-attachments/assets/40fb5bd8-a166-4993-9979-3258ef6646a0

📚 Documentation

scmcphub's complete documentation is available at https://docs.scmcphub.org

🏎️ Quickstart

Install

Install from PyPI

pip install liana-mcp

you can test it by running

liana-mcp run

run liana-mcp locally

Refer to the following configuration in your MCP client:

check path

$ which liana 
/home/test/bin/liana-mcp

"mcpServers": {
  "liana-mcp": {
    "command": "/home/test/bin/liana-mcp",
    "args": [
      "run"
    ]
  }
}

run liana-server remotely

Refer to the following configuration in your MCP client:

run it in your server

liana-mcp run --transport shttp --port 8000

Then configure your MCP client in local AI client, like this:

"mcpServers": {
  "liana-mcp": {
    "url": "http://localhost:8000/mcp"
  }
}

🤝 Contributing

If you have any questions, welcome to submit an issue, or contact me(hsh-me@outlook.com). Contributions to the code are also welcome!

Citing

If you use liana-mcp in for your research, please consider citing following work:

Dimitrov D., Schäfer P.S.L, Farr E., Rodriguez Mier P., Lobentanzer S., Badia-i-Mompel P., Dugourd A., Tanevski J., Ramirez Flores R.O. and Saez-Rodriguez J. LIANA+ provides an all-in-one framework for cell–cell communication inference. Nat Cell Biol (2024). https://doi.org/10.1038/s41556-024-01469-w