Add ENCODE Toolkit MCP server

[ammawla]

Summary

Add ENCODE Toolkit as an MCP server to the Life Sciences Marketplace. This is an MCP server for the ENCODE Project (encodeproject.org), the largest public catalog of functional genomic elements.

What It Provides

• 20 MCP tools for searching experiments, downloading files with MD5 verification, tracking provenance, and managing citations
• 48 expert skills covering 15 assay types (ChIP-seq, ATAC-seq, RNA-seq, WGBS, Hi-C, CUT&RUN, CUT&Tag, CRISPR screens, STARR-seq, MPRA, eCLIP, and more)
• 7 Nextflow pipelines for ChIP-seq, ATAC-seq, RNA-seq, WGBS, Hi-C, DNase-seq, and CUT&RUN
• 14 database cross-references including PubMed, GTEx, ClinVar, GWAS Catalog, gnomAD, Ensembl, UCSC, JASPAR, GEO, and CellxGene

Installation

Installs via npx (stdio transport):

npx encode-toolkit@latest

Published on both npm and PyPI as encode-toolkit.

Files Changed

• encode-toolkit/.claude-plugin/plugin.json — Plugin manifest with MCP server config
• .claude-plugin/marketplace.json — Added entry to plugins array
• README.md — Added to Quick Start and Available Plugins sections

Requirements

• Python 3.10+ and Node.js 16+
• No authentication required for public ENCODE data
• No telemetry

Repository

https://github.com/ammawla/encode-toolkit