Scanpy MCP Server

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