What is Infercnv Mcp

infercnv-mcp is an MCP server designed for Copy Number Variation (CNV) analysis using infercnvpy, enabling users to infer CNVs from single-cell RNA sequencing (scRNA-Seq) data through a natural language interface.

Use cases

Use cases for infercnv-mcp include academic research for inferring CNVs from scRNA-Seq data and integration of CNV analysis into applications by agent developers.

How to use

To use infercnv-mcp, install it via PyPI with ‘pip install infercnv-mcp’. You can run it locally or remotely by configuring your MCP client accordingly. For local use, check the path and run ‘infercnv-mcp run’. For remote use, start the server with ‘infercnv-mcp run --transport shttp --port 8000’ and configure your MCP client to connect to it.

Key features

Key features include an IO module for scRNA-Seq data handling, a preprocessing module for neighbor computation, a tool module for CNV inference and scoring, and a plotting module for visualizations such as chromosome heatmaps, UMAP, and t-SNE.

Where to use

infercnv-mcp can be used in various AI clients, plugins, or agent frameworks that support MCP, including Cherry Studio, Cline, and Agno.

Infercnv-MCP

Natural language interface for Copy Number Variation (CNV) inference from scRNA-Seq data with infercnvpy through MCP.

🪩 What can it do?

• IO module for reading and writing scRNA-Seq data, load gene position
• Preprocessing module for neighbors computation and data preparation
• Tool module for CNV inference, cnv score
• Plotting module for chromosome heatmaps, UMAP, and t-SNE visualizations

❓ Who is this for?

• Researchers who want to infer CNVs from scRNA-Seq data using natural language
• Agent developers who want to integrate CNV analysis into their applications

🌐 Where to use it?

You can use infercnv-mcp in most AI clients, plugins, or agent frameworks that support the MCP:

• AI clients, like Cherry Studio
• Plugins, like Cline
• Agent frameworks, like Agno

📚 Documentation

scmcphub’s complete documentation is available at https://docs.scmcphub.org

🏎️ Quickstart

Install

Install from PyPI

pip install infercnv-mcp

you can test it by running

infercnv-mcp run

run infercnv-mcp locally

Refer to the following configuration in your MCP client:

check path

$ which infercnv 
/home/test/bin/infercnv-mcp

"mcpServers": {
  "infercnv-mcp": {
    "command": "/home/test/bin/infercnv-mcp",
    "args": [
      "run"
    ]
  }
}

Run infercnv-server remotely

Refer to the following configuration in your MCP client:

Run it in your server

infercnv-mcp run --transport shttp --port 8000

Then configure your MCP client, like this:

http://localhost:8000/mcp

🤝 Contributing

If you have any questions, welcome to submit an issue, or contact me([email protected]). Contributions to the code are also welcome!

Citing

If you use infercnv-mcp in your research, please consider citing following work:

https://github.com/icbi-lab/infercnvpy