scientific-encode-screen

Query ENCODE, SCREEN, and ChIP-Atlas APIs to map regulatory elements for a gene.

3|1|Updated Feb 11, 2026

Search Tags:#genomics #regulatory #data-integration #screen #encode #epigenome #chipatlas

Ready to run

npx skills add https://github.com/nahisaho/satori --skill scientific-encode-screen

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: scientific-encode-screen
Source: https://github.com/nahisaho/satori/tree/main/src/.github/skills/scientific-encode-screen
Command: npx skills add https://github.com/nahisaho/satori --skill scientific-encode-screen

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

This integration pipeline consolidates ENCODE REST API, SCREEN, and ChIP-Atlas queries to create a cohesive epigenome atlas for a gene or region, reducing manual cross-resource analysis.

Core Features & Use Cases

ENCODE search: Query experiments, biosamples, and files to assemble relevant datasets.
SCREEN cCREs: Retrieve candidate cis-regulatory elements and associated signals.
ChIP-Atlas enrichment: Compute TF/histone enrichment for gene lists.
End-to-end pipeline: Integrate results into a unified workflow for regulatory genomics analyses.

Quick Start

Call the encode_epigenome_pipeline with a gene name and biosample to generate integrated epigenome results.

Frequently Asked Questions about scientific-encode-screen

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

FAQPage Schema

How do I integrate ENCODE and ChIP-Atlas epigenome data for a specific gene?▼

To integrate epigenome data, query the ENCODE REST API, SCREEN, and ChIP-Atlas to consolidate experiments, candidate cis-regulatory elements, and transcription factor enrichment into a unified output for your target gene.

What is the best way to map candidate cis-regulatory elements across different cell types?▼

Mapping candidate cis-regulatory elements involves retrieving SCREEN cCREs and associated signals, then aggregating the epigenomic landscapes across your queried tissues or biosamples to identify regulatory regions.

Can I compute transcription factor enrichment for a gene list using ChIP-Atlas data?▼

Yes, you can compute transcription factor and histone enrichment for gene lists by leveraging the ChIP-Atlas integration, which aggregates queried datasets into a standardized regulatory genomics output.

How do I query ENCODE experiments and biosamples programmatically for regulatory genomics analyses?▼

Querying ENCODE experiments and biosamples programmatically requires calling the ENCODE REST API to assemble relevant datasets, which are then integrated with SCREEN and ChIP-Atlas results.

Does this epigenome data integration pipeline require manually cross-referencing multiple genomic resources?▼

No, this integration pipeline consolidates ENCODE, SCREEN, and ChIP-Atlas queries to create a cohesive epigenome atlas, effectively reducing the need for manual cross-resource analysis during regulatory genomics workflows.