Scanpy

SCMCP is an MCP server that provides natural language access to single-cell RNA sequencing analysis through the Scanpy library. Developed by Shenghui Huang, it exposes a comprehensive set of tools organized into modules for input/output operations, preprocessing, visualization, trajectory inference, and utility functions. The server supports both stdio and server-sent events (SSE) transport protocols, making it flexible for different integration scenarios. SCMCP handles AnnData objects internally, allowing users to perform complex bioinformatics workflows like clustering, dimensionality reduction, differential expression analysis, and cell type annotation through conversational interfaces, making it particularly valuable for researchers who want to analyze single-cell data without writing code.