Infercnv MCP Server

What is Infercnv-MCP?

Infercnv-MCP is a natural language interface for Copy Number Variation (CNV) inference from single-cell RNA-Seq (scRNA-Seq) data, powered by the infercnvpy library and the Model Context Protocol (MCP). It provides modules for reading/writing scRNA-Seq data, preprocessing, CNV inference and scoring, and plotting (chromosome heatmaps, UMAP, t-SNE). The tool targets researchers and agent developers who want to perform or integrate CNV analysis using natural‑language commands.

How to use Infercnv-MCP?

Install the package from PyPI (pip install infercnv-mcp), then run it either locally (infercnv-mcp run) or as a remote HTTP server (infercnv-mcp run --transport shttp --port 8000). Configure your MCP client (e.g., Cherry Studio, Cline, Agno) with the appropriate command or endpoint.

Key features of Infercnv-MCP

• Natural language interface for CNV analysis
• IO module: read/write scRNA-Seq data and load gene positions
• Preprocessing module: neighbors computation and data preparation
• Tool module: CNV inference and CNV scoring
• Plotting module: chromosome heatmaps, UMAP, and t‑SNE visualizations
• Supports both local (stdio) and remote (shttp) transports

Use cases of Infercnv-MCP

• Researchers inferring CNVs from scRNA‑Seq data without writing code
• Agent developers integrating CNV analysis into AI-powered applications
• Interactive exploration of copy number alterations in tumor transcriptomes
• Automated preprocessing, inference, and visualization in reproducible workflows