Scanpy MCP Server

@scmcphub

Repository

Basic information

About Scanpy MCP Server

MCP server for scanpy

#scanpy#scrna-seq #data-analysis

Scanpy MCP Server config

No standard config provided

This server doesn't expose a parseable MCP config block in its README. See the repository for install instructions.

Repository

Scanpy MCP Server tools

Tool list not available yet

This listing does not currently have a tool list to display. This does not mean the server has no tools; check its documentation for supported capabilities.

We auto-extract tools from the README. The maintainer can list them under a ## Tools heading to populate this section.

Overview

What is Scanpy-MCP?

Scanpy-MCP is a natural language interface for single-cell RNA-Seq (scRNA-Seq) analysis that wraps Scanpy functions through the Model Context Protocol (MCP). It allows users and agent developers to perform IO, preprocessing, clustering, differential expression, and plotting using plain language.

How to use Scanpy-MCP?

Install via pip install scanpy-mcp and run scanpy-mcp run to start the server. Configure it in any MCP-compatible client (e.g., Cherry Studio, Cline) using either a local command or a remote SHTTP endpoint.

Key features of Scanpy-MCP

IO module: read and write scRNA-Seq data
Preprocessing: filtering, QC, normalization, scaling, HVG, PCA, Neighbors
Tool module: clustering, differential expression
Plotting module: violin, heatmap, dotplot
Works with any MCP-supporting AI client or framework
Supports local and remote (SHTTP) transport

Use cases of Scanpy-MCP

Perform complete scRNA-Seq analysis using natural language commands
Integrate Scanpy functions into AI agent applications
Run analysis interactively in MCP-aware chatbots like Cherry Studio
Automate single-cell data processing pipelines through agent frameworks

Frequently asked questions

How do I install Scanpy-MCP?

Install from PyPI using `pip install scanpy-mcp` and run `scanpy-mcp run` to test.

What transport options does Scanpy-MCP support?

It supports standard input/output (stdio) for local use and SHTTP for remote access.

Which MCP clients can I use with Scanpy-MCP?

It works with any MCP client, such as Cherry Studio, Cline, and agent frameworks like Agno.

What analysis modules are available in Scanpy-MCP?

It provides IO, preprocessing, clustering/differential expression (tools), and plotting modules.

Comments

More Other MCP servers

The Living Bread

A free remote MCP server for The Living Bread. Bible passages read word for word from a stored public domain text with an evidence label, keyword search and cross references, real churches, gatherings and prayer groups w

Senso MCP for Joomla

sensomedia

Senso MCP turns a Joomla 5 or 6 site into a remote MCP server. It runs inside Joomla itself (no extra server, no Node.js bridge) and is secured with OAuth 2.1 and Joomla's own ACL. The free pack lets an AI assistant crea

YOUB

Connect your AI assistant to your own YOUB endurance training account. Read recorded activities with full analysis, planned sessions, race goals, wellness (HRV, sleep, resting HR) and your athletic profile. Create or mov

Figs, Relationship Expert

Figs O'Sullivan, LMFT

Couples therapist Figs O'Sullivan (LMFT, 17 years, endorsed by Sue Johnson, creator of EFT) inside your AI. Ask relationship questions answered from his clinical writing, name the pattern in a fight, get a three-step rep

Handl

Handl speaks the Model Context Protocol. Your whole billing operation — projects, invoices, clients, reports, approvals — as tools any AI assistant can call, inside your autonomy rules.