bio-copy-number-hrd-scoring
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, deriving LOH/LST/TAI scars from allele-specific copy number, deciding between scar-based and mutationa
npx skills add BioTender-max/awesome-bio-agent-skills --skill hrd-scoring --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## 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 - Whole-genome: `HRDetect` (weighted multi-sig
- Version Compatibility
- The Three Genomic Scars
- Method Selection
- Computing Genomic Scars with scarHRD
- The Postdoc-Level Caveats
- Failure Modes
- Relative copy number used as input
- LST inflated by uncorrected whole-genome doubling
- Treating a high score as proof of drug response
- Low tumor purity
- Panel HRD score read as a whole-genome score
- Reconciliation
- Quantitative Thresholds
- Common Errors
What does the bio-copy-number-hrd-scoring skill do?
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, deriving LOH/LST/TAI scars from allele-specific copy number, deciding between scar-based and mutationa
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill hrd-scoring --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.