MCP Servers

Scanpy MCP server

MCP server for Scanpy

huang-sh

Research & Data

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

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.

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.

Vectorize

Vectorize MCP server for advanced retrieval, Private Deep Research, Anything-to-Markdown file extraction and text chunking.

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.

MATLAB MCP Server

Integrates MATLAB with AI to execute code, generate scripts from natural language, and access MATLAB documentation seamlessly.

Macrostrat MCP Server

Enables Claude to query comprehensive geologic data from the Macrostrat API, including geologic units, columns, minerals, and timescales through natural language.

MCP Word Counter

A Model Context Protocol server that provides tools for analyzing text documents, including counting words and characters. This server helps LLMs perform text analysis tasks by exposing simple document statistics functionality.