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
• Custom Background Correction: Test against your own background gene set (e.g. only the genes expressed in your assay) instead of the whole genome
• Live Library Catalog: The library list is fetched from Enrichr at runtime, so new releases appear automatically and retired libraries are never suggested
• 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. Searches Enrichr's live library catalog, so it never recommends a library that Enrichr has retired. When two libraries are equally relevant, the newer vintage ranks first (GO_Biological_Process_2026 over ..._2021).

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 Enrichr libraries in parallel.

Parameters:

• genes (required): Array of gene symbols (e.g., ["TP53", "BRCA1", "EGFR"]) — minimum 2
• libraries (optional): Array of Enrichr library names to query (defaults to configured libraries)
• background (optional): Custom background gene set — minimum 20 genes. See below.
• description (optional): Description for the gene list
• maxTerms (optional): Maximum terms per library (default: 50)
• format (optional): Output format: detailed, compact, minimal
• outputFile (optional): Path to save complete results as TSV file

Returns:

• Text content with formatted significant terms (name, p-values, odds ratio, combined score, overlapping genes)
• Structured JSON output with full result data, including backgroundCorrected per library

Background correction

By default Enrichr tests your gene list against the whole genome. If your genes were drawn from a restricted universe — only the genes expressed in your tissue, or a targeted panel — the whole-genome default overstates significance, often by many orders of magnitude. Pass background with the universe the list was drawn from:

{
  "genes": ["TP53", "BRCA1", "ATM", "CHEK2"],
  "background": ["TP53", "BRCA1", "ATM", "CHEK2", "ACTB", "GAPDH", "..."],
  "libraries": ["GO_Biological_Process_2026"]
}

The difference is not cosmetic. For a 16-gene DNA-damage list, the top GO term moves from an adjusted p of 1.2e-16 (whole genome) to 1.8e-5 (48-gene background), and the number of "significant" terms drops from 359 to 10.

Background correction runs against Enrichr's separate speedrichr service, which is intermittently unavailable. Failures are retried; if they persist, the library falls back to uncorrected whole-genome p-values, and the result is flagged backgroundCorrected: false with a loud WARNING in the text output. A fallback result is never presented as if it were background-corrected.

Resources

Prompts

enrichment_analysis

Guided workflow for gene set enrichment analysis. Accepts a gene list and optional research context, then walks through library selection, analysis, and interpretation.

Arguments:

• genes (required): Gene symbols, comma or newline separated
• context (optional): Research context for library selection (triggers suggest_libraries step)

Library Categories

All 200+ libraries are organized into 22 categories:

Use suggest_libraries to search across all categories, or read enrichr://libraries/{category} for the full list in any category.

Configuration

Command Line Options

Format Options

• detailed: Full details including p-values, odds ratios, and gene lists (default)
• compact: Term name + p-value + gene count (saves ~50% tokens)
• minimal: Just term name + p-value (saves ~80% tokens)

Environment Variables