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encode-ccres-database

Query the ENCODE Registry of cis-Regulatory Elements (cCREs) via the SCREEN GraphQL API, or make custom queries to the ENCODE Portal REST API for experiments and files (ChIP-seq peaks, etc.). Use when you want to query regulatory annotations or raw experimental data across human cell types.

skills/encode_ccres_database/SKILL.md

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# 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

1.  **`uv`**: Read the `uv` skill and follow its Setup instructions to ensure
    `uv` is installed and on PATH.
2.  **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