What is Scmcp

scmcp is an MCP server designed for single-cell RNA sequencing (scRNA-Seq) analysis using natural language, making it accessible for users without extensive programming knowledge.

Use cases

Use cases for scmcp include performing scRNA-Seq analysis in a user-friendly manner, enabling agent developers to integrate scanpy functions into their applications, and facilitating data analysis in research and clinical settings.

How to use

To use scmcp, install it via PyPI with ‘pip install scmcp’. You can run it locally or remotely by configuring your MCP client appropriately. For local use, simply execute ‘scmcp run’. For remote access, start the server with ‘scmcp run --transport sse --port 8000’ and configure your MCP client to connect.

Key features

Key features of scmcp include an IO module for reading and writing scRNA-Seq data, preprocessing capabilities (filtering, quality control, normalization), analytical tools (clustering, differential expression), and visualization options (violin plots, heatmaps, dot plots).

Where to use

scmcp can be utilized in various AI clients, plugins, and agent frameworks that support MCP, such as Cherry Studio, Cline, and Agno.

⚠️ Important Notice: This repository is no longer maintained.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([email protected]). Contributions to the code are also welcome!