bio-chipseq-visualization SKILL.md skillA
bio-chipseq-visualization 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-visualization@git:20260517.81511a7Pins git:20260517.81511a7 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- fridrichmethod/awesome-skills
- Path
skills/bio-chipseq-visualization/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260517.81511a7, committed May 17, 2026
- Size
- 8,310 bytes
- Repository stars
- 15
- License
- a license file GitHub does not identify
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.
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+, 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 \
…Read the whole file at its exact version.
How to install
mdr add fridrichmethod/awesome-skills/bio-chipseq-visualization@sha256:fa7b84ccb8318653The 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_5r5jn4dx3gsau32d)
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Versions
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_5r5jn4dx3gsau32d GET https://markdownregistry.com/api/v1/resolve?ref=fridrichmethod/awesome-skills/bio-chipseq-visualization GET https://markdownregistry.com/api/v1/blob/fa7b84ccb83186536b3255515bdc61a9693e49ad3dbd0f3c5bc6bd61301c1c72
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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