Liana-MCP

What is Liana-MCP?

Liana-MCP is a natural language interface for single-cell RNA-Seq (scRNA-Seq) analysis that uses the Model Context Protocol (MCP) to connect with the Liana analysis library. It is designed for researchers and developers who want to perform scRNA-Seq tasks—such as reading/writing data, cell-cell communication inference, and plotting—using natural language commands within MCP-compatible clients.

How to use Liana-MCP?

Install via pip: pip install Liana-mcp. Run locally with liana-mcp run and configure your MCP client with "command": "liana-mcp", "args": ["run"]. For remote access, run Liana-mcp run --transport shttp --port 8000 and set the client URL to http://localhost:8000/mcp.

Key features of Liana-MCP

• IO module for reading and writing scRNA-Seq data
• Cell-cell communication inference methods
• Plotting module including circle plot and dotplot
• Natural language interface for scRNA-Seq analysis
• Compatible with AI clients, plugins, and agent frameworks

Use cases of Liana-MCP

• Perform scRNA-Seq cell cluster analysis using natural language in an AI client like Cherry Studio
• Enable agent developers to call Liana’s functions programmatically for custom applications
• Integrate Liana analysis into MCP-compatible agent frameworks such as Agno or plugins like Cline

FAQ from Liana-MCP

What can Liana-MCP do?

It provides an IO module, cell-cell communication methods, and a plotting module (circle plot, dotplot) for scRNA-Seq analysis, all accessible via natural language through MCP.

Who is Liana-MCP for?

It is for anyone wanting to do scRNA-Seq analysis in natural language, and for agent developers who want to call Liana’s functions from their applications.

Where can Liana-MCP be used?

It can be used in MCP-compatible AI clients (e.g., Cherry Studio), plugins (e.g., Cline), and agent frameworks (e.g., Agno).

How do I install and run Liana-MCP?

Install from PyPI: pip install Liana-mcp. Then run liana-mcp run to start the local server, and configure your MCP client with the appropriate command and arguments.

How do I run Liana-MCP remotely?

Use the command Liana-mcp run --transport shttp --port 8000 on your server, then set your MCP client’s server URL to http://localhost:8000/mcp.