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encode-database

Query the ENCODE Portal REST API for regulatory genomics data and peak files.

298|27|Updated Feb 18, 2026
Search Tags:#genomics#data retrieval#encode#atac-seq#chip-seq#regulatory elements
One-click install
npx skills add https://github.com/jaechang-hits/SciAgent-Skills --skill encode-database
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: encode-database
Source: https://github.com/jaechang-hits/SciAgent-Skills/tree/main/skills/genomics-bioinformatics/encode-database
Command: npx skills add https://github.com/jaechang-hits/SciAgent-Skills --skill encode-database

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires requests, pandas, matplotlib, urllib.parse, gzip, io, and includes scripts (resource) and references (resource) components.

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.

Frequently Asked Questions about encode-database

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I find ChIP-seq experiments for a specific cell line in the ENCODE database?▼

You can query the ENCODE Portal REST API to find ChIP-seq experiments by filtering for specific assay types, target proteins like TFs, and biosamples such as the K562 cell line to retrieve relevant functional genomics data.

What is the best way to retrieve candidate cis-Regulatory Elements (cCREs) near a gene of interest?▼

Querying the SCREEN API allows you to identify candidate cis-Regulatory Elements (cCREs) by searching for regulatory elements within specific genomic regions or located near a target gene of interest.

Can I download ATAC-seq peak files in BED or bigWig formats directly through the ENCODE API?▼

Yes, querying the ENCODE Portal REST API facilitates the discovery and direct download of regulatory genomics peak files, including ATAC-seq and DNase-seq peaks, in formats such as BED and bigWig.

How do I list available cell types and tissues in the ENCODE database for comparative genomics?▼

You can browse and list available biosamples by querying the ENCODE Portal REST API, which supports listing diverse cell types and tissues for comparative genomics across different experiments.

Do I need pandas and matplotlib to query ENCODE regulatory genomics data?▼

The skill utilizes pandas and matplotlib as dependencies to process and visualize the retrieved regulatory genomics data, alongside requests and urllib.parse for interacting with the ENCODE REST API.

What types of regulatory genomics data can I retrieve for variant annotation?▼

You can retrieve TF ChIP-seq experiments, ATAC-seq and DNase-seq peaks, and histone mark tracks from the ENCODE database to facilitate variant annotation and regulatory element analysis.

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