SCMCP Server

You have access to an MCP server that lets you control scRNA-Seq analysis through natural language. It provides IO, preprocessing, analysis tools, plotting, cell-cell communication and more, all orchestrated via a flexible client interface so you can focus on the science while the server handles the heavy lifting.

How to use

You interact with the SCMCP server through an MCP client. Start the server in one of two run modes: tool mode for a stable, predefined set of functions, or code mode for flexible, custom code generation and notebook workflows. You can run locally or expose the server remotely and connect your client to the appropriate URL.

• Tool mode provides a curated set of functions that the client can select and execute to perform standard workflows like data loading, preprocessing, clustering, differential expression, and visualization. This mode emphasizes stability and safety, with predictable results.

• Code mode enables the client to generate and run custom Python code, including complete Jupyter notebooks. This mode offers high flexibility for bespoke analyses but may be less stable across runs.

To connect your client, you can either use a local stdio configuration or point the client at a remote HTTP endpoint. The HTTP URL maps to the MCP API, while the stdio setup runs the server process locally.

How to install

Prerequisites: you need Python and a package manager to install the MCP server package. Ensure you have access to a shell with Python and pip available.

Install the SCMCP package from PyPI.

pip install scmcp

Configuration and usage patterns

You can run SCMCP locally in two modes or expose it remotely for client access. The following configurations show the supported patterns.

{
  "mcpServers": {
    "scmcp": {
      "command": "/home/test/bin/scmcp",
      "args": ["run", "--run-mode", "tool"]
    }
  }
}

Remote access and usage

If you want to run SCMCP so a client can reach it over HTTP, start the server with the HTTP transport and specify a port. Then connect your client to the HTTP URL.

Example command to start in tool mode remotely:

scmcp run --transport shttp --port 8000 --run-mode tool

Additional notes

You can also start in code mode remotely by changing the run mode to code. The HTTP URL for client configuration remains the same pattern.

Example configuration for code mode in the MCP client:

{
  "mcpServers": {
    "scmcp": {
      "url": "http://localhost:8000/mcp"
    }
  }
}