enrichr

This MCP server provides multi-library gene set enrichment analysis by interfacing with the Enrichr API. It can query hundreds of Enrichr libraries (GO, pathways, diseases, tissues, drugs, transcription factors, microRNA targets, etc.) in a single request and return only statistically significant results (adjustable via CLI and library filters). The server is designed to work with MCP clients and can be added to your MCP configuration to expose enrichment capabilities to LLM-assisted workflows. Typical usage involves invoking the server via an MCP client command (for example by adding enrichr-mcp-server to your MCP config) and then passing a gene list to one or more configured libraries. You can also tailor which libraries are exposed by using the CLI options when starting the server, enabling you to limit or expand the available results for your LLM deployments.

Prerequisites:

• Node.js (recommended latest LTS) and npm installed on your system
• Internet access to fetch the Enrichr MCP server package

Installation steps:

1. Ensure Node.js and npm are installed. Verify with:

node -v
npm -v

2. Install the Enrichr MCP server package via npx or installable package name (recommended during MCP setup):

npx -y enrichr-mcp-server

3. Add the server to your MCP client configuration (example shown). If you use Claude or other MCP-integrated tools, you can register the server as:

# Example: add enrichr-mcp-server with default settings
claude mcp add enrichr-server -- npx -y enrichr-mcp-server

4. Run your MCP client or start the server as part of your environment, depending on your integration. The default configuration uses the enrichr-mcp-server package name to pull available libraries from Enrichr. Adjust libraries via CLI (--libraries or environment variables) as needed.

Notes and tips:

• The default configuration exposes enrichr-server with the basic setup using npx -y enrichr-mcp-server. You can customize the libraries exposed to the LLM by editing the mcp.json file in your MCP client or by passing CLI options (e.g., --libraries or -l) when starting the server.
• Environment variables supported include ENRICHR_LIBRARIES, ENRICHR_MAX_TERMS, ENRICHR_FORMAT, and ENRICHR_OUTPUT_FILE. CLI arguments take precedence over environment variables when both are specified.
• If you encounter HTTP or API rate limits from Enrichr, consider staggering requests across multiple libraries or reducing the number of libraries requested in a single call.
• For best results with large gene lists, consider using the compact or minimal output formats to reduce token usage in the LLM context, then parse and summarize as needed on the client side.