Encode Ccres Database

If you're working with genomic data and need to identify regulatory elements in non-coding DNA, this skill queries the ENCODE Registry through their SCREEN GraphQL API. It pulls data on candidate cis-Regulatory Elements like promoters, enhancers, and insulators based on biochemical signatures. Part of Google DeepMind's science-skills collection, it's been installed over 900 times and has passed multiple security audits. The setup requires uv and prompts you to review ENCODE's API terms before use. This is specialized tooling, so you'll know if you need it. If you're analyzing chromatin accessibility or histone modifications to understand gene regulation, it saves you from writing GraphQL queries by hand.

skills.sh installs: 2.2K
GitHub stars: 3.4K
last updated: Aug 21, 2026

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Install

$ npx -y skills add google-deepmind/science-skills --skill encode-ccres-database --agent claude-code

Installs into .claude/skills of the current project.

Files

ENCODE Database Skill

This skill allows you to query the ENCODE Registry of cCREs (candidate cis-Regulatory Elements) via the SCREEN GraphQL API. It helps identify functional non-coding DNA elements (like Promoters, Enhancers, and insulators) by analyzing biochemical signatures (DNase, H3K4me3, H3K27ac, CTCF).

Prerequisites

uv: Read the uv skill and follow its Setup instructions to ensure uv is installed and on PATH.
User Notification: If .licenses/encode_ccres_database_LICENSE.txt does not already exist in the workspace root directory then (1) prominently notify the user to check the terms at https://www.encodeproject.org/help/rest-api/, then (2) create the file recording the notification text and timestamp.