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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
One-click install
npx skills add https://github.com/nahisaho/satori --skill scientific-encode-screen
Or copy as Structured Prompt for Agent▼
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.

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