Enrichr MCP Server
Description
<!-- * @Date: 2025-06-03 14:18:58 * @LastEditors: tianqitang1 Tianqi.Tang@ucsf.edu * @LastEditTime: 2025-06-04 20:43:36 * @FilePath: /enrichr-mcp-server/README.md --> # Enrichr MCP Server <div align="center"> <img src="icon.svg" alt="Enrichr MCP Server Icon" width="128"…
About
<!-- * @Date: 2025-06-03 14:18:58 * @LastEditors: tianqitang1 Tianqi.Tang@ucsf.edu * @LastEditTime: 2025-06-04 20:43:36 * @FilePath: /enrichr-mcp-server/README.md --> # Enrichr MCP Server <div align="center"> <img src="icon.svg" alt="Enrichr MCP Server Icon" width="128" height="128"> </div> A Model Context Protocol…
Details
- Author
- tianqitang1
- Downloads
- 163
- Categories
- Developer Tools, Other
Jump to
- Multi-library enrichment analysis with simultaneous queries
- Significance filtering (adjusted p < 0.05)
- Detailed results with p-values, z-scores, and combined scores
- Hundreds of gene set libraries supported
- Robust error handling with informative messages
- Specialized GO Biological Process tool
Setting up with Highlight
This MCP is not yet compatible with Highlight’s one-click setup. However, you can still use it with Highlight by following these steps:
- Download and install Highlight from highlightai.com/download
- Navigate to the plugins tab and select "Add Custom Plugin"
-
Configure the plugin with the settings below
Plugin Name
Enrichr MCP ServerCommand (node, npx, python, etc.)Please refer to the README for specific instructions on how to obtain API keys or other required environment variables.
- Enable "Start Automatically" if you want the plugin to start when Highlight launches
From the repository
Install globally via npx -y enrichr-mcp-server and configure in your MCP client (e.g., .cursor/mcp.json). Use the enrichr_analysis tool for multi-library enrichment, or the query_enrichr_go_bp_tool / go_enrichment tools for GO Biological Process analysis. Custom default libraries can be set via CLI arguments (--libraries) or the ENRICHR_DEFAULT_LIBRARIES environment variable.
enrichr_analysis
Perform gene set enrichment analysis using Enrichr across multiple gene set libraries. Returns only statistically significant terms (adjusted p < 0.05). Configured default libraries: - GO_Biological_Process_2025: Gene Ontology terms describing biological objectives accomplished by gene products. Any library in Enrichr's live catalog is accepted. Enrichr adds and retires libraries continuously, so do not rely on a memorized list: call suggest_libraries, or read the enrichr://libraries resource, to discover the libraries that currently exist. Pass 'background' to test against a custom background gene set (for example, only the genes expressed in your assay) instead of Enrichr's whole-genome default. This is the statistically correct choice whenever the gene list was drawn from a restricted universe, and it matters: the whole-genome default can overstate significance by many orders of magnitude. Each library's result reports 'backgroundCorrected'. If Enrichr's background service is unavailable the result falls back to uncorrected whole-genome p-values, flagged with a warning — treat those numbers as inflated and re-run rather than reporting them as background-corrected.
suggest_libraries
Suggest relevant Enrichr libraries for a research question. Use this before enrichr_analysis to pick the best libraries for a specific topic.
Claude Desktop / Cursor
Paste into your MCP client config file to install this server.
{
"mcpServers": {
"enrichr mcp server": {
"enrichr-go-only": {
"command": "npx",
"args": [
"-y",
"enrichr-mcp-server",
"--libraries",
"GO_Biological_Process_2025"
]
},
"enrichr-pathways": {
"command": "npx",
"args": [
"-y",
"enrichr-mcp-server",
"-l",
"GO_Biological_Process_2025,KEGG_2021_Human,Reactome_2022"
]
},
"enrichr-disease": {
"command": "npx",
"args": [
"-y",
"enrichr-mcp-server",
"--libraries",
"Human_Phenotype_Ontology,OMIM_Disease,ClinVar_2019"
]
}
}
}
}McpServers
{
"enrichr-go-only": {
"command": "npx",
"args": [
"-y",
"enrichr-mcp-server",
"--libraries",
"GO_Biological_Process_2025"
]
},
"enrichr-pathways": {
"command": "npx",
"args": [
"-y",
"enrichr-mcp-server",
"-l",
"GO_Biological_Process_2025,KEGG_2021_Human,Reactome_2022"
]
},
"enrichr-disease": {
"command": "npx",
"args": [
"-y",
"enrichr-mcp-server",
"--libraries",
"Human_Phenotype_Ontology,OMIM_Disease,ClinVar_2019"
]
}
}Enrichr MCP Server
<div align="center">
</div>
A Model Context Protocol (MCP) server that provides gene set enrichment analysis using the Enrichr API. This server supports multiple gene set libraries from Enrichr and returns only statistically significant results (p < 0.05) to reduce context usage.
Use the button below to install the MCP server to Cursor with default settings (GO Biological Process only).
Features
- Multi-Library Enrichment Analysis: Query multiple Enrichr libraries simultaneously (GO, pathways, diseases, tissues, drugs, etc.)
- GO Enrichment Analysis: Specialized tools for GO Biological Process enrichment analysis
- Comprehensive Library Support: Access to hundreds of gene set libraries including:
- Gene Ontology (Biological Process, Molecular Function, Cellular Component)
- Pathway databases (KEGG, Reactome, WikiPathways, BioCarta, MSigDB)
- Disease/Phenotype databases (Human Phenotype Ontology, GWAS Catalog)
- Tissue/Cell type libraries (GTEx, Human Cell Atlas, ARCHS4)
- Drug/Chemical libraries (DrugMatrix, L1000, TG-GATEs)
- Transcription Factor targets (ChEA, ENCODE)
- MicroRNA targets (TargetScan, miRTarBase)
- Significance Filtering: Returns only terms with adjusted p < 0.05 to reduce noise
- Detailed Results: Provides p-values, z-scores, combined scores, and overlapping genes
- Error Handling: Robust error handling with informative messages
Configuration
MCP Client Configuration
Add this server to your MCP client configuration (e.g., .cursor/mcp.json):
Basic Configuration (GO Biological Process only)
{
"mcpServers": {
"enrichr-server": {
"command": "npx",
"args": ["-y", "enrichr-mcp-server"]
}
}
}
Custom Default Libraries Configuration
You can configure default libraries using CLI arguments in your MCP configuration:
{
"mcpServers": {
"enrichr-go-only": {
"command": "npx",
"args": ["-y", "enrichr-mcp-server", "--libraries", "GO_Biological_Process_2025"]
},
"enrichr-pathways": {
"command": "npx",
"args": ["-y", "enrichr-mcp-server", "-l", "GO_Biological_Process_2025,KEGG_2021_Human,Reactome_2022"]
},
"enrichr-disease": {
"command": "npx",
"args": ["-y", "enrichr-mcp-server", "--libraries", "Human_Phenotype_Ontology,OMIM_Disease,ClinVar_2019"]
}
}
}
Environment Variables Configuration
Alternatively, use environment variables:
{
"mcpServers": {
"enrichr-server": {
"command": "npx",
"args": ["-y", "enrichr-mcp-server"],
"env": {
"ENRICHR_DEFAULT_LIBRARIES": "GO_Biological_Process_2025,KEGG_2021_Human",
"ENRICHR_SERVER_NAME": "my-enrichr-server"
}
}
}
}
Command Line Options
```bash
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