Skills
.Work. You
Rest

encode-ccres-database

Official

Query cCRE annotations and experiments.

Education & Research#graphql#genomics#gwas#encode#gene expression#regulatory elements#biosample metadata
Authorgoogle-deepmind
Version1.0.0
Installs0

System Documentation

What problem does it solve?

Researchers need a fast way to find and contextualize human regulatory DNA elements (cCREs) and the experimental evidence behind them across assemblies and biosamples.

Core Features & Use Cases

  • cCRE discovery and ranking: Search cCREs by genomic coordinates, accessions, or CTCF signal ranges using the SCREEN GraphQL API.
  • Functional context retrieval: Fetch cCRE details (including max Z-scores across assays) and associated biosample assay information, with support for identifying high-confidence Type A biosamples.
  • Downstream biological linkage: Retrieve nearby genes, orthologous cCREs across assemblies, linked genes, ENTEx allelic imbalance annotations, gene expression (TPM/FPKM), and GWAS-related summaries.
  • Direct ENCODE Portal access: Run custom REST API queries for experiments and downloadable dataset metadata when SCREEN does not cover the needed object type.

Quick Start

Run a coordinate-based search for candidate cis-regulatory elements on chr11 from 5205263 to 5207263 and save the results to a JSON file in /tmp.

Dependency Matrix

Required Modules

None required

Components

scriptsreferences

💻 Claude Code Installation

Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.

Please help me install this Skill:
Name: encode-ccres-database
Download link: https://github.com/google-deepmind/science-skills/archive/main.zip#encode-ccres-database

Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
View Source Repository

Agent Skills Search Helper

Install a tiny helper to your Agent, search and equip skill from 471,000+ vetted skills library on demand.