What is SCMCP?
SCMCP is an MCP server designed for single-cell RNA sequencing (scRNA-Seq) analysis using natural language processing.
How to use SCMCP?
To use SCMCP, install it via PyPI with pip install scmcp, and run it locally or remotely as per your configuration needs.
Key features of SCMCP?
- IO module for reading and writing scRNA-Seq data using natural language.
- Preprocessing capabilities including filtering, quality control, normalization, and PCA.
- Tool modules for clustering and differential expression analysis.
- Plotting options such as violin plots, heatmaps, and dot plots.
Use cases of SCMCP?
- Performing scRNA-Seq analysis with natural language queries.
- Integrating with AI clients and agent frameworks for enhanced data analysis.
- Facilitating data preprocessing and visualization in single-cell studies.
FAQ from SCMCP?
- Who can use SCMCP?
Anyone interested in scRNA-Seq analysis using natural language, including developers of AI clients and plugins.
- Is there a demo available?
Yes! A demo showcasing scRNA-Seq cell cluster analysis is available on the project's GitHub page.
- How can I contribute to SCMCP?
Contributions are welcome! You can submit issues or contact the author for collaboration.
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(hsh-me@outlook.com). Contributions to the code are also welcome!