Enrichr MCP Server

A Model Context Protocol (MCP) server that provides gene set enrichment analysis using the Enrichr API. This server supports all available gene set libraries from Enrichr and returns only statistically significant results (corrected-$p$ < 0.05) for LLM tools to interpret.

Installation

Claude Desktop

Download the latest MCPB bundle (.mcpb file) and install it via ☰ (top left) -> File -> Settings, then drag and drop the file into the Settings window.

Cursor / VS Code

Use the buttons below to install with default settings:

Claude Code

claude mcp add enrichr-mcp-server -- npx -y enrichr-mcp-server

Or install as a Claude Code plugin:

/plugin install enrichr-mcp-server

Smithery

npx -y @smithery/cli install enrichr-mcp-server --client claude

Manual Configuration

Add to your MCP client config (e.g., .cursor/mcp.json):

{
  "mcpServers": {
    "enrichr-server": {
      "command": "npx",
      "args": ["-y", "enrichr-mcp-server"]
    }
  }
}

Features

• Two Tools: enrichr_analysis for running enrichment, suggest_libraries for discovering relevant libraries
• Library Catalog: Browse 200+ libraries by category via MCP resources
• Guided Workflow: enrichment_analysis prompt for end-to-end analysis with interpretation
• 22 Library Categories: Programmatic category mapping for all libraries (pathways, cancer, kinases, etc.)
• Parallel Library Queries: All libraries queried in parallel for fast multi-database analysis
• Structured Output: Returns both human-readable text and structured JSON for programmatic use
• Configurable Output Formats: Detailed, compact, or minimal to manage token usage
• TSV Export: Save complete results to TSV files

Tools

suggest_libraries

Discover the most relevant Enrichr libraries for a research question. Use this before enrichr_analysis to pick the best libraries for your specific topic. No network call needed — searches locally across all library names and descriptions.

Parameters:

• query (required): Research context (e.g., "DNA repair", "breast cancer drug resistance")
• category (optional): Filter by category (e.g., cancer, pathways, kinases)
• maxResults (optional): Max results to return (default: 10, max: 50)

Returns:

• Ranked list of libraries with relevance scores, categories, and descriptions
• Structured JSON with suggestions array

enrichr_analysis

Perform enrichment analysis across multiple Enric

... View full README on GitHub