Infercnv-MCP

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

FAQ from Infercnv-MCP

What does Infercnv-MCP do?

It provides a natural language interface to the infercnvpy library, enabling users to perform CNV inference from scRNA‑Seq data, including preprocessing, scoring, and visualization, through any MCP‑compatible client.

How do I install Infercnv-MCP?

Install it via pip: pip install infercnv-mcp. After installation, you can test the server by running infercnv-mcp run.

Can I run Infercnv-MCP on a remote server?

Yes. Start the server with infercnv-mcp run --transport shttp --port 8000, then point your MCP client to http://localhost:8000/mcp (or the appropriate URL).

What data formats does Infercnv-MCP work with?

The IO module handles reading and writing scRNA‑Seq data; specific file formats are not detailed, but it loads gene position information for downstream analysis.

Who is Infercnv-MCP intended for?

It is built for researchers who want to infer CNVs from scRNA‑Seq data using natural language, and for agent developers who need to embed CNV analysis into their applications.