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 TianGzlab/OmicsClaw --skill polygenic-risk-score-prs-cataloggit clone --depth 1 https://github.com/TianGzlab/OmicsClawWrote 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/tiangzlab/omicsclaw/polygenic-risk-score-prs-catalog)<a href="https://agentmods.dev/skills/tiangzlab/omicsclaw/polygenic-risk-score-prs-catalog"><img src="https://agentmods.dev/badge/skills/tiangzlab/omicsclaw/polygenic-risk-score-prs-catalog/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/tiangzlab/omicsclaw/polygenic-risk-score-prs-catalog"><img src="https://agentmods.dev/badge/skills/tiangzlab/omicsclaw/polygenic-risk-score-prs-catalog.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- NVIDIA SkillSpector pass
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 | $0.00009 | $0.02621 |
| Opus 5 | $0.00005 | $0.01311 |
| Sonnet 5 | $0.00002 | $0.00524 |
| Haiku 4.5 | $0.00001 | $0.00262 |
Grade A, and why
Polygenic Risk Score (PGS Catalog) 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 12d 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.
How it starts
The opening of the file, as written. The whole thing — 201 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Polygenic Risk Score (PGS Catalog)
When to Use This Skill
- You have a trait of interest and want to calculate PRS using published, peer-reviewed weights
- Multi-trait risk profiling (e.g., cardiometabolic panel: CAD, T2D, LDL, BMI, blood pressure)
- Population comparisons of genetic risk across ancestry groups
- No GWAS summary statistics needed — uses pre-computed weights from PGS Catalog
- Quick PRS — minutes per trait (download + score), no LD computation required
For de novo PRS from raw GWAS summary statistics, use the polygenic-risk-score skill (LDpred2-auto) instead.
Installation
install.packages(c("data.table", "ggplot2", "ggprism", "dplyr", "R.utils", "jsonlite", "remotes"))
remotes::install_github("privefl/bigsnpr")
| Software | Version | License | Commercial Use | Install |
|---|---|---|---|---|
| bigsnpr | ≥1.12 | GPL-3 | ✅ Permitted | remotes::install_github("privefl/bigsnpr") |
| data.table | ≥1.14 | MPL-2.0 | ✅ Permitted | install.packages('data.table') |
| ggplot2 | ≥3.4 | MIT | ✅ Permitted | install.packages('ggplot2') |
| ggprism | ≥1.0.3 | GPL (≥3) | ✅ Permitted | install.packages('ggprism') |
| dplyr | ≥1.1 | MIT | ✅ Permitted | install.packages('dplyr') |
| jsonlite | ≥1.8 | MIT | ✅ Permitted | install.packages('jsonlite') |
| R.utils | ≥2.12 | LGPL (≥2.1) | ✅ Permitted | install.packages('R.utils') |
Inputs
- Target genotypes: PLINK binary format (.bed/.bim/.fam) — or use 1000 Genomes Phase 3 example data (2,490 individuals, 5 super-populations)
- PGS Catalog score IDs: One or more PGS IDs (e.g.,
PGS000018for CAD) — usesearch_pgs_catalog()to discover available scores - Genome build: GRCh37 (default, matches 1000 Genomes) or GRCh38
Outputs
Per-trait files:
prs_scores_<trait>.csv— Individual PRS (z-scores, percentiles, population labels)distribution_<trait>.png/svg— PRS distribution histogrampopulation_<trait>.png/svg— PRS by super-population boxplot
What ships with it
7 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.
- 12d ago First seen · 201 lines · 9 tokens per session scan A 4953877fe00d
Polygenic Risk Score (PGS Catalog) is a skill published in the GitHub repository TianGzlab/OmicsClaw (160 stars, last pushed 1mo ago), licensed Apache-2.0. It adds 9 tokens to every session and 2,621 once invoked, about $0.0000 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 2026-08-30.
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