bio-chipseq-super-enhancers
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.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-chipseq-super-enhancers --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## 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 ``` ### Input Requir
- Version Compatibility
- Background
- ROSE (Rank Ordering of Super-Enhancers)
- Installation
- Input Requirements
- Run ROSE
- Key Parameters
- Output Files
- Prepare Input Files
- Convert BED to GFF
- Filter Peaks for Enhancers
- Alternative: HOMER Super-Enhancers
- Alternative: SEanalysis
- Custom Hockey Stick Analysis (R)
git clone https://github.com/stjude/ROSE.git
cd ROSE
Requires samtools, R, bedtools
Basic usage
python ROSE_main.py \
With control/input
ROSE requires GFF format for peaks
awk 'BEGIN{OFS="\t"} {print $1,"peaks","enhancer",$2,$3,".",$6,".","ID="NR}' \
peaks.bed > peaks.gff
Remove promoter peaks (within 2.5kb of TSS)What does the bio-chipseq-super-enhancers skill do?
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.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-chipseq-super-enhancers --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.