bio-copy-number-hrd-scoring SKILL.md skillA
bio-copy-number-hrd-scoring 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-hrd-scoring@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-hrd-scoring/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 12,148 bytes
- Repository stars
- 662
- License
- MIT
Quantify homologous recombination deficiency (HRD) from tumor copy number using the three genomic-scar metrics — loss of heterozygosity (LOH), large-scale state transitions (LST), and telomeric allelic imbalance (TAI) — with scarHRD, and via the whole-genome HRDetect and CHORD models. Covers the genomic instability score, the PARP-inhibitor clinical context, whole-genome-doubling correction, and the scar-versus-state distinction. Use when computing an HRD score for PARP-inhibitor eligibility…
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: R 4.3+ with scarHRD 0.1.1+, sequenza 3.0+ (allele-specific input); HRDetect / CHORD as their respective R packages where whole-genome data is available.
Before using code patterns, verify installed versions match. If versions differ:
- R: `packageVersion('scarHRD')` then `?scar_score` to confirm arguments
- scarHRD is GitHub-only (`sztup/scarHRD`); install with `remotes::install_github`
scarHRD consumes allele-specific copy number — a Sequenza `.seqz` file or an ASCAT/allele-specific segment table. It cannot run on relative log2 copy ratio.
# HRD Scoring
**"Is this tumor homologous-recombination deficient"** -> HRD leaves characteristic copy-number scars. Three are quantified and summed into an HRD score: loss of heterozygosity (LOH), large-scale state transitions (LST), and telomeric allelic imbalance (TAI). A high score predicts response to platinum chemotherapy and PARP inhibitors. The scar score is a *consequence* of past HR deficiency — which is both its strength (it integrates over tumor history) and its key limitation.
- R: `scarHRD` — the three genomic scars and their sum
…Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-copy-number-hrd-scoring@sha256:a1435e802e26d487The 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_jbryklziv52yvs7e)
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Versions
The registry has recorded 1 version of this file, committed on Aug 21, 2026.
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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_jbryklziv52yvs7e GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-copy-number-hrd-scoring GET https://markdownregistry.com/api/v1/blob/a1435e802e26d4874dc461d952c80e99348f75ed07378ef7376c9de360396a12
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.