ENCODE Genomics Toolkit
๐ง - MCP server and Claude Plugin for a full ENCODE Project genomic data and analysis toolkit โ s
What is ENCODE Genomics Toolkit?
ENCODE Genomics Toolkit is a Model Context Protocol (MCP) server that allows AI assistants like Claude, Cursor, and VS Code to ๐ง - mcp server and claude plugin for a full encode project genomic data and analysis toolkit โ s
๐ง - MCP server and Claude Plugin for a full ENCODE Project genomic data and analysis toolkit โ s
This server falls under the Data Science & ML category on MCPgee, the world's largest MCP server directory with 33,000+ servers.
Features
- MCP protocol support
Use Cases
Maintainer
Works with
Installation
NPM
npx -y encode-toolkitPIP
pip install encode-toolkitManual Installation
npx -y encode-toolkitConfiguration
Configuration Details
claude_desktop_config.json
Performance
Response Metrics
Resource Usage
How to Set Up and Use ENCODE Genomics Toolkit
The ENCODE Toolkit MCP server is a comprehensive bioinformatics platform that connects Claude and other AI assistants to the ENCODE Project's genomic data repository along with 13 additional integrated databases including GTEx, ClinVar, GWAS Catalog, JASPAR, gnomAD, Ensembl, and GEO. It exposes 20 tools for searching experiments, downloading files with MD5 verification, tracking data provenance, running seven pre-built analysis pipelines (ChIP-seq, ATAC-seq, RNA-seq, WGBS, Hi-C, DNase-seq, CUT&RUN), and exporting publication-ready citations. Researchers can query millions of functional genomics datasets and execute complex analyses entirely through natural language.
Prerequisites
- Python 3.10 or later installed
- uv package manager installed (recommended) or pip
- Claude Code or Claude Desktop as the MCP client
- Optional: ENCODE access key and secret key from your ENCODE user profile for restricted data access
Install the encode-toolkit package
Install encode-toolkit using uvx (recommended) or pip. uvx requires no virtual environment management.
# With uvx (recommended):
uvx encode-toolkit
# With pip:
pip install encode-toolkitAdd the server to Claude Desktop config
Add the encode entry to your Claude Desktop claude_desktop_config.json using the uvx command.
{
"mcpServers": {
"encode": {
"command": "uvx",
"args": ["encode-toolkit"]
}
}
}Or install as a Claude Code plugin
If you use Claude Code, install the toolkit as a plugin directly from the marketplace for the best integration experience.
/plugin marketplace add ammawla/encode-toolkit
/plugin install encode-toolkitRegister ENCODE credentials for restricted data (optional)
For accessing restricted ENCODE datasets, store your access key and secret using the encode_manage_credentials tool within Claude after the server is running.
Restart Claude Desktop and run a test search
Restart Claude Desktop and ask it to search for ENCODE experiments to confirm the server is working.
ENCODE Genomics Toolkit Examples
Client configuration
Claude Desktop JSON config for the ENCODE Toolkit MCP server.
{
"mcpServers": {
"encode": {
"command": "uvx",
"args": ["encode-toolkit"]
}
}
}Prompts to try
Example prompts for genomic data search, download, analysis, and cross-database queries.
- "Find all histone ChIP-seq experiments for human pancreas tissue in ENCODE"
- "Download all BED narrowPeak files from experiment ENCSR133RZO to ~/data/encode"
- "What GWAS variants overlap islet enhancers identified in ENCODE?"
- "Run a ChIP-seq analysis pipeline on my uploaded FASTQ files"
- "Get citations for the ENCODE experiments I downloaded today in BibTeX format"
- "Show me the provenance of the derived BigWig file from ENCSR456ABC"Troubleshooting ENCODE Genomics Toolkit
uvx command not found
Install uv by running: curl -LsSf https://astral.sh/uv/install.sh | sh โ then reopen your terminal. uvx is included with uv.
Access denied when downloading restricted ENCODE files
Use the encode_manage_credentials tool inside Claude to store your ENCODE access key and secret key obtained from your ENCODE user profile at encodeproject.org. These are stored securely in the OS keyring.
Pipeline execution fails or returns incomplete results
Ensure you have sufficient disk space and memory for the pipeline. Large genomics pipelines (RNA-seq, Hi-C) can require significant resources. Check the encode-toolkit GitHub issues page for known pipeline-specific requirements.
Frequently Asked Questions about ENCODE Genomics Toolkit
What is ENCODE Genomics Toolkit?
ENCODE Genomics Toolkit is a Model Context Protocol (MCP) server that ๐ง - mcp server and claude plugin for a full encode project genomic data and analysis toolkit โ s It connects AI assistants to external tools and data sources through a standardized interface.
How do I install ENCODE Genomics Toolkit?
Install via npm with the command: npx -y encode-toolkit. Then add the server configuration to your AI client's JSON config file (e.g., claude_desktop_config.json or .cursor/mcp.json).
Which AI clients work with ENCODE Genomics Toolkit?
ENCODE Genomics Toolkit works with all major MCP-compatible AI clients including Claude Desktop, Claude Code, Cursor, VS Code (GitHub Copilot), Windsurf, and Cline.
Is ENCODE Genomics Toolkit free to use?
Yes, ENCODE Genomics Toolkit is open source and available under the AGPL 3.0 license. You can use it freely in both personal and commercial projects.
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Quick Config Preview
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