bio-chipseq-super-enhancers SKILL.md skillA
bio-chipseq-super-enhancers from fridrichmethod/awesome-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add fridrichmethod/awesome-skills/bio-chipseq-super-enhancers@git:20260517.81511a7Pins git:20260517.81511a7 in mdr.lock. Pin the fingerprint instead.
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- SKILL.md skill
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- fridrichmethod/awesome-skills
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skills/bio-chipseq-super-enhancers/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260517.81511a7, committed May 17, 2026
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- a license file GitHub does not identify
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.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
## Version Compatibility
Reference examples tested with: GenomicRanges 1.54+, bedtools 2.31+, ggplot2 3.5+, samtools 1.19+
Before using code patterns, verify installed versions match. If versions differ:
- R: `packageVersion('<pkg>')` then `?function_name` to verify parameters
- CLI: `<tool> --version` then `<tool> --help` to confirm flags
If code throws ImportError, AttributeError, or TypeError, introspect the installed
package and adapt the example to match the actual API rather than retrying.
# Super-Enhancer Calling
**"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.
## Background
Super-enhancers are:
- Large clusters of enhancer regions
- Marked by H3K27ac, Med1, BRD4
- Control cell identity genes
- Often altered in disease/cancer
## ROSE (Rank Ordering of Super-Enhancers)
### Installation
```bash
git clone https://github.com/stjude/ROSE.git
cd ROSE
# Requires samtools, R, bedtools
```
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How to install
mdr add fridrichmethod/awesome-skills/bio-chipseq-super-enhancers@sha256:f66158435cfed9ebThe line at the top of this page pins the label git:20260517.81511a7, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_vjrxqysgsxjpvse3)
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The registry has recorded 1 version of this file, committed on May 17, 2026.
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Source
fridrichmethod/awesome-skills · 15 stars · license a license file GitHub does not identify · pushed 2026-11-02 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_vjrxqysgsxjpvse3 GET https://markdownregistry.com/api/v1/resolve?ref=fridrichmethod/awesome-skills/bio-chipseq-super-enhancers GET https://markdownregistry.com/api/v1/blob/f66158435cfed9ebbf49ae10c9e536e426f09269739b796b67e3cb945fe74561
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.
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