v0.3.0-beta.2

ENCODE Toolkit v0.3.0-beta.2

MCP server for the ENCODE Project — 20 tools, 47 skills, 14 database integrations, and 7 analysis pipelines for genomics research in Claude Code.

Highlights

• 20 MCP tools: Search, download, track, compare, and cross-reference ENCODE data
• 47 expert skills: Analysis workflows, pipeline execution, external database integration
• 14 databases: ENCODE, PubMed, bioRxiv, ClinicalTrials.gov, Open Targets, GTEx, ClinVar, GWAS Catalog, JASPAR, gnomAD, Ensembl, UCSC, GEO, CELLxGENE
• 7 Nextflow pipelines: ChIP-seq, ATAC-seq, RNA-seq, WGBS, Hi-C, DNase-seq, CUT&RUN
• Full provenance tracking: SQLite-backed experiment tracking with publications and citations
• MD5 verification: All file downloads verified for integrity

Install

claude mcp add encode -- uvx encode-toolkit

Links

• PyPI
• npm
• Documentation