Skip to content
Conduit

mcp server

scanpy-mcp

MCP server for Scanpy

huang-sh/scanpy-mcpcommunitylistedunreviewed
Use tool

Set up

Runs on your computer. Pick your agent and operating system.

Before you start

  • uv (`curl -LsSf https://astral.sh/uv/install.sh | sh`)
~/Library/Application Support/Claude/claude_desktop_config.json
{
  "mcpServers": {
    "huang-sh-scanpy-mcp": {
      "command": "uvx",
      "args": [
        "scanpy-mcp"
      ]
    }
  }
}

same format Cursor, GitHub Copilot CLI, Junie, JetBrains AI Assistant, Augment (Auggie CLI), Factory Droid, Kiro, Devin CLI +12

Values in angle brackets are placeholders. Restart Claude Desktop after editing its config.Claude Desktop docs

README

synced Oct 15, 2026

⚠️ Important Notice: This repository is no longer maintained. Please visit scmcphub for the latest version of MCP servers.

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": "scanpy-mcp",
    "args": [
      "run"
    ]
  }
}

run scnapy-server remotely

Refer to the following configuration in your MCP client:

run it in your server

scmcp run --transport shttp --port 8000

Then configure your MCP client, like this:

http://localhost:8000/mcp

🤝 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!

↑↓ navigate openesc close