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⚠️ Important Notice: This repository is no longer maintained. Please visit SCMCPHub for the latest version of MCP servers.

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!

Install Server
A
security – no known vulnerabilities
A
license - permissive license
A
quality - confirmed to work

hybrid server

The server is able to function both locally and remotely, depending on the configuration or use case.

An MCP server that enables single-cell RNA sequencing analysis through natural language, supporting data processing, visualization, and analysis tasks without requiring coding knowledge.

  1. 🪩 What can it do?
    1. ❓ Who is this for?
      1. 🌐 Where to use it?
        1. 🎬 Demo
          1. 🏎️ Quickstart
            1. Install
          2. 🤝 Contributing

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