ammawla/encode-toolkit

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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

Обзор

Search ENCODE, cross-reference 14 databases, run 7 analysis pipelines, and generate publication-ready methods — all from natural language in Claude Code. Start from ENCODE but go everywhere: discover histone peaks, cross-reference with GWAS variants, check ClinVar pathogenicity, pull GTEx expression, analyze TF binding motifs from JASPAR, run pipelines, and generate publication-ready methods with full provenance — in one conversation. Alex M. Mawla. (2026). ENCODE-Toolkit: an MCP server, Claude plugin, and skills suite for ENCODE genomic data access and analysis. Zenodo. https://doi.org/10.5281/zenodo.18917511 Start a new Claude Code session and enter: That's it. All 20 tools, 47 skills, and the MCP connector are now available. MCP-only install (tools only, no skills) If you only need the 20 MCP tools without the 47 workflow skills: Or in MCP client config: { "command": "npx", "args": ["encode-toolkit"] }

README

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ENCODE Toolkit — Genomics Research Infrastructure for Claude

Search ENCODE, cross-reference 14 databases, run 7 analysis pipelines, and generate publication-ready methods — all from natural language in Claude Code.

Start from ENCODE but go everywhere: discover histone peaks, cross-reference with GWAS variants, check ClinVar pathogenicity, pull GTEx expression, analyze TF binding motifs from JASPAR, run pipelines, and generate publication-ready methods with full provenance — in one conversation.

Citation Notes

If you use ENCODE-Toolkit, please cite:

Открыть полный README на GitHub

Установка

npx encode-toolkit

Новичок в MCP? Начните с руководства на mcpskill.org →

Конфигурация

{
  "mcpServers": {
    "encode": {
      "command": "encode-toolkit"
    }
  }
}