bio-copy-number-cnv-visualization SKILL.md skillA
bio-copy-number-cnv-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-copy-number-cnv-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-copy-number-cnv-visualization/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 13,315 bytes
- Repository stars
- 662
- License
- MIT
Visualize copy number profiles, segments, allele-specific tracks, and cohort patterns from CNVkit, GATK, ASCAT, FACETS, Sequenza, and other callers. Covers genome-wide and per-chromosome log2 scatter plots, B-allele-frequency/minor-allele-fraction tracks, ideograms, cohort heatmaps, circos views, and caller-native plots. Use when creating publication CNV figures, choosing which plot answers a given question, diagnosing a wrong diploid baseline visually, displaying loss of heterozygosity, or…
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: matplotlib 3.8+, pandas 2.2+, numpy 1.26+, seaborn 0.13+, CNVkit 0.9.10+, GATK 4.5+; R 4.3+ with ggplot2 3.5+.
Before using code patterns, verify installed versions match. If versions differ:
- Python: `pip show matplotlib pandas` then `help(function)` for signatures
- R: `packageVersion('ggplot2')` then `?function_name`
- CLI: `cnvkit.py version`, `gatk --version`
If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example rather than retrying.
# CNV Visualization
**"Plot my copy number profile"** -> A CNV figure is an argument, not a picture. The plot type, the y-axis quantity, and where the diploid baseline sits all determine what the reader can conclude. The single most important rule: a depth-only log2 plot cannot show loss of heterozygosity, cannot show tumor purity, and silently misleads if the diploid baseline is centered on a non-diploid mode.
- CLI: `cnvkit.py scatter` / `diagram` / `heatmap`; `gatk PlotModeledSegments`
- Python: `matplotlib` for custom genome-wide and allele-specific tracks
- R: `ggplot2`, `karyoploteR` for publication ideograms
…Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-copy-number-cnv-visualization@sha256:70a3e9801eb9fb0fThe 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_mhink3m7ymgc4phk)
2 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 1 version of this file, committed on Aug 21, 2026.
Audit of the latest version
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- pass: No zero-width or bidi control characters
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- 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
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Source
pku-yuangroup/openai4s · 662 stars · license MIT · pushed 2026-11-03 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_mhink3m7ymgc4phk GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-copy-number-cnv-visualization GET https://markdownregistry.com/api/v1/blob/70a3e9801eb9fb0f0c00a30ddbc5bdc6f04c717e155850f7bd4c502bd7e41159
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.