SCMCP

An MCP server for scRNA-Seq analysis with natural language!

What can it do?

• IO module like read and write scRNA-Seq data with natural language
• Preprocessing module,like filtering, quality control, normalization, scaling, highly-variable genes, PCA, Neighbors,…
• Tool module, like clustering, differential expression etc.
• Plotting module, like violin, heatmap, dotplot
• cell-cell communication analysis

Who is this for?

• Anyone who wants to do scRNA-Seq analysis natural language!
• Agent developers who want to call scanpy’s functions for their applications

Where to use it?

You can use scmcp 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 scmcp

https://github.com/user-attachments/assets/93a8fcd8-aa38-4875-a147-a5eeff22a559

Quickstart

Install

Install from PyPI

pip install scmcp

you can test it by running

scmcp run

run scnapy-server locally

Refer to the following configuration in your MCP client:

"mcpServers": {
  "scmcp": {
    "command": "scmcp",
    "args": [
      "run"
    ]
  }
}

run scnapy-server remotely

Refer to the following configuration in your MCP client:

run it in your server

scmcp run --transport sse --port 8000

Then configure your MCP client, like this:

http://localhost:8000/sse

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!