bio-chipseq-visualization SKILL.md skillA
bio-chipseq-visualization from pku-yuangroup/openai4s is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add pku-yuangroup/openai4s/bio-chipseq-visualization@git:20260821.2d1b678Pins git:20260821.2d1b678 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- pku-yuangroup/openai4s
- Path
skills/bioskills/bio-chip-seq-chipseq-visualization/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 14,519 bytes
- Repository stars
- 662
- License
- MIT
Visualizes ChIP-seq data using deepTools (computeMatrix, plotHeatmap, plotProfile, bamCoverage, bamCompare), pyGenomeTracks (modern INI-driven track plots), Gviz (R browser-style), EnrichedHeatmap (ComplexHeatmap-based), ChIPseeker tag heatmaps, and IGV batch screenshots. Handles bigWig normalization choices (CPM, BPM, RPGC, spike-in scaled), bamCompare operations (log2 ratio, subtract) with SES scaling, k-means clustering of heatmaps for biological subgrouping, and spike-in-scaled tracks for…
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: deepTools 3.5+, pyGenomeTracks 3.9+, Gviz 1.46+, EnrichedHeatmap 1.32+, ChIPseeker 1.38+, IGV 2.17+, samtools 1.19+, bedtools 2.31+. # ChIP-seq Visualization **"Visualize ChIP-seq signal around features of interest"** -> Generate normalized signal tracks (bigWig), heatmaps centered on TSS/peaks, average profile plots, and genome-browser views — with normalization that supports the biological claim (within-sample vs cross-sample vs spike-in scaled). - CLI (production): deepTools `bamCoverage` -> `computeMatrix` -> `plotHeatmap` / `plotProfile` - CLI (config-driven tracks): pyGenomeTracks (replaces Gviz for many use cases) - R (publication): Gviz, EnrichedHeatmap, ChIPseeker tag heatmaps - GUI: IGV with batch scripts for reproducible screenshots The single most consequential choice is **bigWig normalization** — it determines whether visual comparison reflects biology. Get this right before generating any heatmap or browser view. ## bigWig Normalization Decision Tree | Goal | Method | When to use | |------|--------|------------| …
Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-chipseq-visualization@sha256:8f92b756a38a1adaThe line at the top of this page pins the label git:20260821.2d1b678, 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_4vpw5jputvbl6vom)
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Versions
The registry has recorded 1 version of this file, committed on Aug 21, 2026.
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (14519 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
pku-yuangroup/openai4s · 662 stars · license MIT · pushed 2026-11-03 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_4vpw5jputvbl6vom GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-chipseq-visualization GET https://markdownregistry.com/api/v1/blob/8f92b756a38a1adad67223370f8efae0d4a5b06b1f5ad2c20d6e56feebe05f62
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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