Infercnv-MCP

Infer Copy Number Variations (CNVs) from single-cell RNA-Seq data using a natural language interface.

GitHub

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

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