encode-database

What problem does it solve?

This Skill allows users to efficiently query the ENCODE Portal REST API to find and download regulatory genomics data, such as TF ChIP-seq experiments, ATAC-seq/DNase-seq peaks, and histone marks across various cell types and tissues.

Core Features & Use Cases

• Experiment Search: Find experiments by assay type, target protein, and biosample.
• File Download: Retrieve peak files (BED, bigWig) for specific experiments.
• cCRE Query: Identify candidate cis-Regulatory Elements (cCREs) in genomic regions or near genes.
• Biosample Browsing: List available cell types and tissues in the ENCODE database.
• Use Case: You need to find all available CTCF ChIP-seq peak files for the K562 cell line to annotate potential regulatory regions near a gene of interest.

Quick Start

Use the encode-database skill to find all CTCF ChIP-seq experiments in the K562 cell line.