SCMCP MCP Server

What is SCMCP?

SCMCP is an MCP server that enables scRNA‑Seq analysis through natural language commands. It wraps common scanpy functions, providing modules for IO, preprocessing, clustering, differential expression, plotting, and cell‑cell communication analysis.

How to use SCMCP?

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.

Key features of SCMCP

• 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

Use cases of SCMCP

• Perform scRNA‑Seq analysis via natural language in an AI chat client
• Integrate scanpy functions into agent or plugin workflows
• Quickly generate plots and summary statistics without writing code