ENCODE Toolkit MCP Server: Install & Setup

Install ENCODE Toolkit in Claude Code

npm

Claude Code

claude mcp add encode-toolkit -- npx -y encode-toolkit

mcp.json (Claude Desktop, Cursor, VS Code, Windsurf)

{
  "mcpServers": {
    "encode-toolkit": {
      "command": "npx",
      "args": [
        "-y",
        "encode-toolkit"
      ]
    }
  }
}

PyPI (uv)

Claude Code

claude mcp add encode-toolkit -- uvx encode-toolkit

mcp.json (Claude Desktop, Cursor, VS Code, Windsurf)

{
  "mcpServers": {
    "encode-toolkit": {
      "command": "uvx",
      "args": [
        "encode-toolkit"
      ]
    }
  }
}

Frequently asked questions

What does the ENCODE Toolkit MCP server do?

Search, download, track and analyze functional genomics experiments from the ENCODE Project.

Is the ENCODE Toolkit MCP server free?

Yes, most likely. Open source and no paid account or API key is mentioned in the listing. Check the provider for current pricing.

Does ENCODE Toolkit run locally or remotely?

Local. Runs on your machine (stdio). You install it with npx, uvx, Docker or from source.

How do I add ENCODE Toolkit to Claude Code?

Run: claude mcp add encode-toolkit -- npx -y encode-toolkit

More science & research MCP servers

View all

Opengenes

longevity-genie/opengenes-mcp

Query the OpenGenes database for aging and longevity research.

LocalAccount neededPython

Databnf

0674

smeet666/mcp-databnf

Search the open catalogue of the Bibliothèque nationale de France for authors, their works and the editions held.

LocalAccount neededTypeScript

LastSearch

201.1k

LastSearch-HQ/lastsearch

Verified web research for AI agents (formerly BrowseAI Dev). Real-time search with cited claims, confidence scores, live citation-health checks, and signed evidence records. MCP server, REST API, and Python SDK.

LocalAccount neededTypeScript

Semantic Scholar

smaniches/semantic-scholar-mcp

Semantic Scholar academic papers: search, paper and author retrieval, citation-graph traversal and recommendations.

LocalAccount neededPython

viznoir

kimimgo/viznoir

Scientific visualization for CFD, FEA and SPH: render, slice, contour, volume-render and animate OpenFOAM, VTK and CGNS data headlessly.

LocalFreePython

Libraryofcongress

0704

smeet666/mcp-libraryofcongress

Full-text search of the Library of Congress's digitised American newspapers, plus catalogue search by media type and curated collections.

LocalAccount neededTypeScript