Allows installation of the scmcp package directly from PyPI using pip, making it easy to set up the MCP server for scRNA-Seq analysis.
Click on "Install Server".
Wait a few minutes for the server to deploy. Once ready, it will show a "Started" state.
In the chat, type
@followed by the MCP server name and your instructions, e.g.,@SCMCP what is the weather in Tokyo?
That's it! The server will respond to your query, and you can continue using it as needed.
Here is a step-by-step guide with screenshots.
You can also use deployed servers via HTTP endpoints. For instructions, see How to Test MCP Streamable HTTP Endpoints Using cURL.
â ī¸ Important Notice: This repository is no longer maintained.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!
đĒŠ 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
Related MCP server: Zanny's Persistent Memory Manager
â 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
đ 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
đŦ 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
đī¸ 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:
đ¤ 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!