Scanpy
About
Provides natural language access to single-cell RNA sequencing analysis through Scanpy, enabling bioinformatics workflows like clustering, dimensionality reduction, and cell type annotation without writing code.
Details
- Author
- huang-sh
- Repository
- huang-sh/scmcp
- GitHub stars
- 3
- Downloads
- 287
- License
- BSD 3-Clause "New" or "Revised" License
- Categories
- Productivity, Design, Developer Tools, Search, Infrastructure, AI, Other
- Tags
- #mobile, #integration
Jump to
- IO module for reading/writing scRNA‑Seq data with natural language
- Preprocessing: filtering, quality control, normalization, scaling, highly variable genes, PCA, neighbors
- Tool module for clustering and differential expression analysis
- Plotting module: violin, heatmap, dotplot
- Cell‑cell communication analysis
Setting up with Highlight
This MCP is not yet compatible with Highlight’s one-click setup. However, you can still use it with Highlight by following these steps:
- Download and install Highlight from highlightai.com/download
- Navigate to the plugins tab and select "Add Custom Plugin"
-
Configure the plugin with the settings below
Plugin Name
ScanpyCommand (node, npx, python, etc.)scmcpArguments-
Argument 1
run
Please refer to the README for specific instructions on how to obtain API keys or other required environment variables.
-
Argument 1
- Enable "Start Automatically" if you want the plugin to start when Highlight launches
From the repository
Install with pip install scmcp. Run locally using scmcp run and configure your MCP client with the command scmcp run. For remote access, run scmcp run --transport sse --port 8000 and connect to http://localhost:8000/sse.
Claude Desktop / Cursor
Paste into your MCP client config file to install this server.
{
"mcpServers": {
"scanpy": {
"cwd": "string",
"env": {},
"args": [
"run"
],
"shell": false,
"command": "scmcp"
}
}
}Linux
{
"cwd": "string",
"env": [],
"args": [
"run"
],
"shell": false,
"command": "scmcp"
}Macos
{
"cwd": "string",
"env": [],
"args": [
"run"
],
"shell": false,
"command": "scmcp"
}Windows
{
"cwd": "string",
"env": [],
"args": [
"run"
],
"shell": false,
"command": "scmcp"
}> ⚠️ Important Notice: This repository is no longer maintained. Please visit SCMCPHub for the latest version of MCP servers.
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
Sign in to leave a review
Use Google, GitHub, or an email account so ratings stay tied to real people.
No reviews posted yet.
