bio-copy-number-allele-specific-copy-number SKILL.md skillA
bio-copy-number-allele-specific-copy-number 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-allele-specific-copy-number@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-allele-specific-copy-number/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 16,367 bytes
- Repository stars
- 638
- License
- MIT
Infer integer allele-specific copy number, tumor purity, and ploidy from tumor sequencing by jointly modeling read depth (logR) and B-allele frequency (BAF) with ASCAT, Sequenza, FACETS, PURPLE, and PureCN (tumor-only). Covers the purity-ploidy identifiability problem, the diploid-baseline (dipLogR) anchor, major/minor copy number, loss of heterozygosity, sunrise/contour fit diagnostics, and reconciliation of conflicting fits. Use when tumor analysis needs absolute copy number rather than…
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: ASCAT 3.1+, Sequenza 3.0+ (sequenza-utils 3.0+), FACETS 0.6+ (snp-pileup), PureCN 2.6+, R 4.3+, Python 3.10+.
Before using code patterns, verify installed versions match. If versions differ:
- R: `packageVersion('ASCAT')` / `'sequenza'` / `'facets'` / `'PureCN'`, then `?function`
- CLI: `sequenza-utils --version`, `snp-pileup --help`
Sequenza 3.0 depends on the `copynumber` Bioconductor package, REMOVED from Bioconductor 3.18+ (2023). Install a maintained fork (`ShixiangWang/copynumber` or `igordot/copynumber`) before Sequenza will load. ASCAT's GC-correction function was renamed across 2.x->3.x (`ascat.GCcorrect` -> `ascat.correctLogR`) — verify against the installed version.
# Allele-Specific Copy Number
…Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-copy-number-allele-specific-copy-number@sha256:86960e9d7c761eb0The 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_vh6re35mojyvpkyx)
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Versions
The registry has recorded 1 version of this file, committed on Aug 21, 2026.
Audit of the latest version
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Source
pku-yuangroup/openai4s · 638 stars · license MIT · pushed 2026-10-21 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_vh6re35mojyvpkyx GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-copy-number-allele-specific-copy-number GET https://markdownregistry.com/api/v1/blob/86960e9d7c761eb0584ddebab48e42c38db43cd59e6c76eeb7a8346df027ec76
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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