scanpy-mcp
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Scanpy MCP server is designed for scRNA-Seq analysis using natural language.
⚠️ Important Notice: This repository is no longer maintained. Please visit scmcphub for the latest version of MCP servers.
Scanpy MCP server
An MCP server for scRNA-Seq analysis software Scanpy 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
❓ 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 scanpy-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 scanpy-mcp
https://github.com/user-attachments/assets/93a8fcd8-aa38-4875-a147-a5eeff22a559
🏎️ Quickstart
Install
Install from PyPI
pip install scanpy-mcp
you can test it by running
scmcp run
run scnapy-server locally
Refer to the following configuration in your MCP client:
"mcpServers": {
"scanpy-mcp": {
"command": "scanpy-mcp",
"args": [
"run"
]
}
}
run scnapy-server remotely
Refer to the following configuration in your MCP client:
run it in your server
scmcp run --transport shttp --port 8000
Then configure your MCP client, like this:
http://localhost:8000/mcp
🤝 Contributing
If you have any questions, welcome to submit an issue, or contact me(). Contributions to the code are also welcome!
