Scanpy MCP server
MCP server for Scanpy
huang-sh
README
Scanpy MCP server
An MCP server for scRNA-Seq analysis software Scanpy 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
❓ 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 scanpy-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
🎬 Demo
A demo showing scRNA-Seq cell cluster analysis in a AI client Cherry Studio using natural language based on scanpy-mcp
https://github.com/user-attachments/assets/93a8fcd8-aa38-4875-a147-a5eeff22a559
🏎️ Quickstart
Install
Install from PyPI
pip install scanpy-mcp
you can test it by running
scmcp run
run scnapy-server locally
Refer to the following configuration in your MCP client:
"mcpServers": {
"scanpy-mcp": {
"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!
Recommended Servers
Crypto Price & Market Analysis MCP Server
A Model Context Protocol (MCP) server that provides comprehensive cryptocurrency analysis using the CoinCap API. This server offers real-time price data, market analysis, and historical trends through an easy-to-use interface.
MCP PubMed Search
Server to search PubMed (PubMed is a free, online database that allows users to search for biomedical and life sciences literature). I have created on a day MCP came out but was on vacation, I saw someone post similar server in your DB, but figured to post mine.
dbt Semantic Layer MCP Server
A server that enables querying the dbt Semantic Layer through natural language conversations with Claude Desktop and other AI assistants, allowing users to discover metrics, create queries, analyze data, and visualize results.
mixpanel
Connect to your Mixpanel data. Query events, retention, and funnel data from Mixpanel analytics.
Sequential Thinking MCP Server
This server facilitates structured problem-solving by breaking down complex issues into sequential steps, supporting revisions, and enabling multiple solution paths through full MCP integration.
Nefino MCP Server
Provides large language models with access to news and information about renewable energy projects in Germany, allowing filtering by location, topic (solar, wind, hydrogen), and date range.
Vectorize
Vectorize MCP server for advanced retrieval, Private Deep Research, Anything-to-Markdown file extraction and text chunking.
Mathematica Documentation MCP server
A server that provides access to Mathematica documentation through FastMCP, enabling users to retrieve function documentation and list package symbols from Wolfram Mathematica.
kb-mcp-server
An MCP server aimed to be portable, local, easy and convenient to support semantic/graph based retrieval of txtai "all in one" embeddings database. Any txtai embeddings db in tar.gz form can be loaded
Research MCP Server
The server functions as an MCP server to interact with Notion for retrieving and creating survey data, integrating with the Claude Desktop Client for conducting and reviewing surveys.