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:
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
BibTeX
@software{mawla_2026_encode_toolkit,
author = {Mawla, Alex M.},
title = {ENCODE-Toolkit: an MCP server, Claude plugin, and skills suite for ENCODE genomic data access and analysis},
year = {2026},
publisher = {Zenodo},
doi = {10.5281/zenodo.18917511},
url = {https://doi.org/10.5281/zenodo.18917511}
}
