bio-copy-number-allele-specific-copy-number SKILL.md skillA
bio-copy-number-allele-specific-copy-number 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-copy-number-allele-specific-copy-number@git:20260726.5bc48c3Pins git:20260726.5bc48c3 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/allele-specific-copy-number/SKILL.md- Versions recorded
- 3
- Latest version
- git:20260726.5bc48c3, committed Jul 26, 2026
- First version recorded
- May 24, 2026
- Size
- 16,136 bytes
- Repository stars
- 15
- License
- a license file GitHub does not identify
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 fridrichmethod/awesome-skills/bio-copy-number-allele-specific-copy-number@sha256:ee43e209b5e8c195The line at the top of this page pins the label git:20260726.5bc48c3, 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_gjqfscktj5deskwn)
2 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 3 versions of this file, between May 24, 2026 and Jul 26, 2026, about one every 31 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260726.5bc48c3 latest | 2026-07-26 | 5bc48c3 | 16,136 B | A | view · diff |
| git:20260531.6e617c4 | 2026-05-31 | 6e617c4 | 16,140 B | A | view · diff |
| git:20260524.1fee1b9 | 2026-05-24 | 1fee1b9 | 16,140 B | A | view |
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 (16136 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
fridrichmethod/awesome-skills · 15 stars · license a license file GitHub does not identify · pushed 2026-10-18 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_gjqfscktj5deskwn GET https://markdownregistry.com/api/v1/resolve?ref=fridrichmethod/awesome-skills/bio-copy-number-allele-specific-copy-number GET https://markdownregistry.com/api/v1/blob/ee43e209b5e8c195ac2f4370915504d47a5b7a9f08e281cfa91c755a93d0cf85
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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