https://github.com/huang-sh/scmcp
MCP server for single cell analysis
https://github.com/huang-sh/scmcp
Last synced: 3 months ago
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MCP server for single cell analysis
- Host: GitHub
- URL: https://github.com/huang-sh/scmcp
- Owner: huang-sh
- License: bsd-3-clause
- Created: 2025-04-14T14:38:43.000Z (6 months ago)
- Default Branch: main
- Last Pushed: 2025-05-15T11:48:14.000Z (5 months ago)
- Last Synced: 2025-05-15T12:38:04.691Z (5 months ago)
- Language: Python
- Size: 7.21 MB
- Stars: 7
- Watchers: 1
- Forks: 3
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
> â ī¸ **Important Notice**: This repository is no longer maintained. Please visit [SCMCPHub](https://github.com/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
## 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
```
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
```
## 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!