ENCODE Toolkit

This connects Claude to the ENCODE Project's genomics data repository and chains together 13 additional databases including GTEx, ClinVar, GWAS Catalog, JASPAR, and gnomAD. The 20 MCP tools handle search, metadata retrieval, and file downloads from ENCODE's REST API. The 48 skills are workflow recipes that guide Claude through multi-step analysis patterns like ChIP-seq peak calling, cross-referencing variants with regulatory elements, pulling tissue expression profiles, and generating methods sections with full provenance tracking. Built for researchers who need to move from "find all H3K27ac ChIP-seq in pancreas" to downloaded BEDfiles, overlap analysis with GWAS hits, motif scanning, and a citable audit trail without leaving the conversation. Ships as a Claude Code plugin or standalone MCP server with 98% test coverage and no telemetry.