bio-chipseq-visualization
Visualize ChIP-seq data using deepTools, Gviz, and ChIPseeker. Create heatmaps, profile plots, and genome browser tracks. Visualize signal around peaks, TSS, or custom regions. Use when visualizing ChIP-seq signal and peaks.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-chipseq-visualization --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+, deepTools 3.5+ 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. # ChIP-seq Visualization **"Create a heatmap of ChIP-seq signal around peaks"** → Generate signal heatmaps, profile plots, and genome browser tracks showing enrichment patterns around genomic features. - CLI: `deeptools computeMatrix reference-point` → `plotHeatmap` - R: `Gviz`, `ChIPseeker::plotAvgProf()` ## deepTools - Compute Matrix **Goal:** Build a signal matrix of ChIP-seq coverage around reference points for downstream heatmaps and profiles. **Approach:** Use computeMatrix to extract bigWig signal values in windows around genomic features like TSS. ```bash # Compute signal matrix around TSS computeMatrix reference-point \ --referencePoint TSS \ -b 3000 -a 3000 \ # 3kb upstream and downstream -R genes.bed \ # Refe
- Version Compatibility
- deepTools - Compute Matrix
- deepTools - Scale-Regions
- deepTools - Heatmap
- deepTools - Profile Plot
- Create BigWig from BAM
- ChIPseeker Profile Heatmap (R)
- Gviz - Genome Browser Tracks (R)
- Multiple Samples in Gviz
- EnrichedHeatmap (R)
- IGV Batch Screenshot
- Key Tools Comparison
- deepTools Key Commands
- Related Skills
Compute signal matrix around TSS computeMatrix reference-point \ Signal across gene bodies computeMatrix scale-regions \ Generate heatmap from matrix plotHeatmap \ With profile on top Average profile plot plotProfile \ Multiple samples comparison
What does the bio-chipseq-visualization skill do?
Visualize ChIP-seq data using deepTools, Gviz, and ChIPseeker. Create heatmaps, profile plots, and genome browser tracks. Visualize signal around peaks, TSS, or custom regions. Use when visualizing ChIP-seq signal and peaks.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-chipseq-visualization --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.