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tooluniverse-epigenomics-chromatin

Analyze histone ChIP-seq, ATAC-seq, chromatin states, and TF binding from ENCODE and GTEx.

1.7k|254|Updated Mar 3, 2025
Search Tags:#chromatin#epigenomics#atac-seq#chip-seq#ENCODE#GTEx#eQTL
One-click install
npx skills add https://github.com/mims-harvard/ToolUniverse --skill tooluniverse-epigenomics-chromatin
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: tooluniverse-epigenomics-chromatin
Source: https://github.com/mims-harvard/ToolUniverse/tree/main/plugins/tooluniverse/skills/tooluniverse-epigenomics-chromatin
Command: npx skills add https://github.com/mims-harvard/ToolUniverse --skill tooluniverse-epigenomics-chromatin

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Interpreting non-coding regulatory elements and variants requires querying many disconnected databases (ENCODE, GTEx, JASPAR, RegulomeDB, UCSC). This Skill orchestrates those queries into a phased workflow so you can answer chromatin and gene-regulation questions with convergent multi-layer evidence instead of isolated lookups.

Core Features & Use Cases

  • Regulatory element mapping: Retrieve ENCODE cCREs, SCREEN classifications, and ChromHMM chromatin states for any genomic locus or gene.
  • Histone and accessibility analysis: Search ENCODE ChIP-seq experiments by histone mark (H3K27ac, H3K4me3, etc.) and ATAC-seq datasets by cell type, with GEO fallbacks.
  • eQTL and variant impact scoring: Combine GTEx eQTLs, RegulomeDB rankings, and JASPAR motif disruption checks to assess whether a variant is regulatory.
  • Use Case: Given rsID rs4994, score it with RegulomeDB, check cCRE overlap via UCSC, pull GTEx eQTL evidence, and test TF motif disruption to build a four-layer regulatory impact assessment.

Quick Start

Ask the agent to find candidate cis-regulatory elements near BRCA1 and check whether any nearby variants are supported eQTLs in breast tissue.

Frequently Asked Questions about tooluniverse-epigenomics-chromatin

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

FAQPage Schema
How do I find regulatory elements near a gene using ENCODE data?▼

Use SCREEN_get_regulatory_elements with the gene name to get PLS, pELS, and dELS classifications, or UCSC_get_encode_cCREs with chromosome coordinates for region-based cCRE retrieval. Confirm with ENCODE_get_chromatin_state for ChromHMM annotations.

How to assess whether a non-coding variant affects gene regulation?▼

Build multi-layer evidence: score the variant with RegulomeDB_query_variant, check cCRE overlap via UCSC_get_encode_cCREs, query GTEx eQTLs for nearby genes, and test TF motif disruption with jaspar_search_matrices. Convergence across three or more layers indicates a high-confidence regulatory variant.

What is the difference between this skill and tooluniverse-epigenomics?▼

This skill covers histone modifications, chromatin accessibility, TF binding, and eQTL analysis. The tooluniverse-epigenomics skill handles DNA methylation array data such as CpG beta values and differential methylation, which this skill explicitly does not cover.

Why does ENCODE_search_histone_experiments return zero results for my tissue?▼

ENCODE uses specific ontology terms for biosamples. Try appending 'tissue', 'epithelium', or 'cell' to the term, for example 'breast epithelium' instead of 'breast', or use the biosample_term_name parameter with the exact ENCODE ontology name.

Can I use GTEx eQTL tools without versioned GENCODE IDs?▼

GTEx_get_expression_summary and GTEx_get_single_tissue_eqtls accept plain gene symbols and auto-resolve versions. GTEx_get_multi_tissue_eqtls and GTEx_calculate_eqtl require exact versioned GENCODE IDs such as ENSG00000012048.20.

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