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
you can test it by running
run scnapy-server locally
Refer to the following configuration in your MCP client:
run scnapy-server remotely
Refer to the following configuration in your MCP client:
run it in your server
Then configure your MCP client, like this:
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!