Data & ReproClinical MedicineFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction

bio-chipseq-super-enhancers

Maintainer FreedomIntelligence · Last updated April 1, 2026

Identifies super-enhancers from H3K27ac ChIP-seq data using ROSE and related tools. Use when studying cell identity genes, cancer-associated regulatory elements, or master transcription factor binding regions that cluster into large enhancer domains.

OpenClawNanoClawAnalysisReproductionbio-chipseq-super-enhancers🧬 bioinformatics (gptomics bio-* suite)bioinformatics — epigenomics & chromatinidentifies

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-chipseq-super-enhancers

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

CLI: ROSE_main.py -g hg38 -i peaks.gff -r chip.bam -c input.bam.
Identify super-enhancers from H3K27ac ChIP-seq" → Stitch nearby enhancer peaks and rank by signal to find large regulatory domains controlling cell identity genes. CLI: ROSE_main.py -g hg38 -i peaks.gff -r chip.bam -c input.bam.
Identify super-enhancers (SEs) - large clusters of enhancers that control cell identity genes.
Large clusters of enhancer regions.
Marked by H3K27ac, Med1, BRD4.

Source Doc

Excerpt From SKILL.md

Installation

git clone https://github.com/stjude/ROSE.git
cd ROSE

## Input Requirements

1. **BAM file** - H3K27ac ChIP-seq aligned reads
2. **Peak file** - Called peaks (BED or GFF)
3. **Genome annotation** - TSS annotations

## Run ROSE

**Goal:** Identify super-enhancers by stitching nearby enhancer peaks and ranking by H3K27ac signal.

**Approach:** Run ROSE_main.py with a GFF peak file, ChIP-seq BAM, and optional input control to stitch enhancers within 12.5 kb, rank by signal, and identify the inflection point separating super-enhancers from typical enhancers.

```bash

Use cases

Use when studying cell identity genes, cancer-associated regulatory elements, or master transcription factor binding regions that cluster into large enhancer domains.