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ENCODE Toolkit MCP Server | MCPpedia
Home / Servers / ENCODE Toolkit E ENCODE Toolkit MCP Server 20 MCP tools + 48 skills for ENCODE Project genomics — search, download, pipelines
41 Fair Install Claude Desktop Claude Code Cursor VS Code Windsurf Zed Cline ChatGPT Goose Continue
~/Library/Application Support/Claude/claude_desktop_config.json Copy
{
"mcpServers": {
"ammawla-encode-toolkit": {
"command": "npx",
"args": [
"-y",
"encode-toolkit@0.3.0-beta.5"
]
}
}
}Related servers F MCP server for Firecrawl — web search, scraping, and biomedical/arXiv paper search.
Environment This server does not declare environment variables.
Tools show up when the registry metadata or the repository README lists them. GitHub enrichment fills this in when a token is configured.
About MCP server and Claude Code plugin for the ENCODE Project: search, download and analyze ChIP-seq, ATAC-seq, RNA-seq, WGBS, Hi-C and CUT&RUN data with 20 tools, 47 skills and 7 Nextflow pipelines
FAQ
What is ENCODE Toolkit? 20 MCP tools + 48 skills for ENCODE Project genomics — search, download, pipelines
How do I install ENCODE Toolkit? Pick a client above and copy the generated config. Cursor and VS Code also have a deep link when the server can run locally or remotely.
Is ENCODE Toolkit official? No. Registry-listed is not the same as vendor-official. Read the methodology for the difference.
How is the trust score calculated? This listing scores 41 (Fair). The formula is published on the methodology page. Reviews 0 published · no average
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Stats
Stars 21
Weekly downloads —
License AGPL-3.0
Language Python
Updated Mar 9, 2026
Last commit Sep 27, 2026 Good
Search, read, annotate, and add to your Zotero research library, local or web.
H Local-first agentic RAG with citations - hybrid search, reranking, multimodal document retrieval
M Local-first, cloud-friendly memory — 100+ tools, 99.2% LongMemEval-S retrieval@8, hybrid search.
D Crawl documentation sites into local corpora agents can search, read, and diff fully offline.
O Secure MCP access to Onyx search, chat, projects, and administration.