Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add GPTomics/bioSkills --skill hrd-scoringgit clone --depth 1 https://github.com/GPTomics/bioSkillsWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/gptomics/bioskills/hrd-scoring)<a href="https://agentmods.dev/skills/gptomics/bioskills/hrd-scoring"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/hrd-scoring/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/gptomics/bioskills/hrd-scoring"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/hrd-scoring.svg" alt="Reviewed on agentmods" width="80" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00172 | $0.02932 |
| Opus 5 | $0.00086 | $0.01466 |
| Sonnet 5 | $0.00034 | $0.00586 |
| Haiku 4.5 | $0.00017 | $0.00293 |
Grade A, and why
bio-copy-number-hrd-scoring scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 7d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
Copies of this mod
1 near-identical copy found in the catalogue:
- bio-copy-number-hrd-scoring — 95% identical, 12 lines differ
How it starts
The opening of the file, as written. The whole thing — 177 lines — stays where its author put it; the contents beside it link to each section on GitHub.
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_scoreto confirm arguments - scarHRD is GitHub-only (
sztup/scarHRD); install withremotes::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-signature model),CHORD(random forest) - Input: allele-specific copy number from Sequenza or ASCAT (see allele-specific-copy-number)
The Three Genomic Scars
| Scar | Definition | Captures |
|---|---|---|
| HRD-LOH | Number of LOH segments > 15 Mb but shorter than a whole chromosome | Large interstitial allelic loss |
| LST | Chromosomal breaks between adjacent segments each >= 10 Mb, separated by < 3 Mb | Large-scale rearrangement burden |
| TAI | Number of subtelomeric regions with allelic imbalance not crossing the centromere | Telomere-bounded allelic imbalance |
The HRD score is the sum of the three (the "genomic instability score", GIS). Each component has a precise size rule — these thresholds (15 Mb, 10 Mb, 3 Mb) are not arbitrary; they were selected to correlate with BRCA1/BRCA2/RAD51C deficiency (Abkevich 2012, Popova 2012, Birkbak 2012).
What ships with it
2 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 7d ago First seen · 177 lines · 172 tokens per session scan A 58e9657864e8
bio-copy-number-hrd-scoring is a skill published in the GitHub repository GPTomics/bioSkills (1,199 stars, last pushed 26d ago), licensed MIT. It adds 172 tokens to every session and 2,932 once invoked, about $0.0009 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.
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