decoupler-MCP
About
A natural language interface for biological activities analysis using the decoupler tool.
Details
- Author
- scmcphub
- GitHub stars
- 4
- Downloads
- 150
- Categories
- Developer Tools, Other
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- IO module for reading and writing scRNA-Seq data
- Pathway activity and transcription factor inference
- Tool module including clustering and differential expression
- Plotting module with violin, UMAP, and t-SNE visuals
- Runs locally or remotely via SSE HTTP transport
- Plugs into multiple MCP-compatible AI clients and frameworks
Install the package via pip (pip install decoupler-mcp) and test it by running decoupler-mcp run. For local use, configure your MCP client with the command path and arguments; for remote use, run the server with --transport shttp --port 8000 and point your client to the corresponding URL. The server is supported in AI clients (e.g., Cherry Studio), plugins (e.g., Cline), and agent frameworks (e.g., Agno).
Natural language interface for scRNA-Seq analysis with decoupler through MCP.
- IO module like read and write scRNA-Seq data
- Pathway activity/Transcription factor inference
- Tool module, like clustering, differential expression etc.
- Plotting module, like violin, umap/tsne
- Anyone who wants to do scRNA-Seq analysis natural language!
- Agent developers who want to call decoupler's functions for their applications
You can use decoupler-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
A demo showing scRNA-Seq cell cluster analysis in a AI client Cherry Studio using natural language based on decoupler-mcp
scmcphub's complete documentation is available athttps://docs.scmcphub.org
Refer to the following configuration in your MCP client:
$ which decoupler /home/test/bin/decoupler-mcp
"mcpServers": { "decoupler-mcp": { "command": "/home/test/bin/decoupler-mcp", "args": [ "run" ] } }
Refer to the following configuration in your MCP client:
decoupler-mcp run --transport shttp --port 8000
Then configure your MCP client in local AI client, like this:
"mcpServers": { "decoupler-mcp": { "url": "http://localhost:8000/mcp" } }
If you have any questions, welcome to submit an issue, or contact me(hsh-me@outlook.com). Contributions to the code are also welcome!
If you use decoupler-mcp in for your research, please consider citing following work:
Badia-i-Mompel P., Vélez Santiago J., Braunger J., Geiss C., Dimitrov D., Müller-Dott S., Taus P., Dugourd A., Holland C.H., Ramirez Flores R.O. and Saez-Rodriguez J. 2022. decoupleR: ensemble of computational methods to infer biological activities from omics data. Bioinformatics Advances.https://doi.org/10.1093/bioadv/vbac016
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