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 agentmods add skills/gptomics/bioskills/pleiotropy-detectionnpx skills add GPTomics/bioSkills --skill pleiotropy-detectiongit 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/pleiotropy-detection)<a href="https://agentmods.dev/skills/gptomics/bioskills/pleiotropy-detection"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/pleiotropy-detection.svg" alt="Measured on agentmods" 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 | $0.00137 | $0.09186 |
| Opus 5 | $0.00068 | $0.04593 |
| Sonnet 5 | $0.00027 | $0.01837 |
| Haiku 4.5 | $0.00014 | $0.00919 |
Grade A, and why
bio-causal-genomics-pleiotropy-detection 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 6d 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
2 near-identical copies found in the catalogue:
- bio-causal-genomics-pleiotropy-detection — 98% identical, 12 lines differ
- correct-scientific-figure — 86% identical, 467 lines differ
How it starts
The opening of the file, as written. The whole thing — 437 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: TwoSampleMR 0.5.11+, MendelianRandomization 0.9.0+, MR-PRESSO 1.0+, CAUSE 1.2.0+, MR-Clust 0.1.0+, MRMix 0.1+, mr.raps 0.4.1+ (GitHub), LHC-MR 0.0.0.9000+ (GitHub), LCV (script-based, no version tag), simex 1.8+.
Before using code patterns, verify installed versions match. If versions differ:
- R:
packageVersion('<pkg>')then?function_nameto verify parameters - For GitHub-only packages, check the repo HEAD vs the local install date
If code throws errors, introspect the installed package and adapt the example rather than retrying.
Pleiotropy Detection in Mendelian Randomization
"Validate my MR result against pleiotropic bias" -> Decompose violations of the exclusion-restriction assumption into uncorrelated horizontal pleiotropy (UHP, addressable by Egger / median / mode / MR-PRESSO) and correlated horizontal pleiotropy (CHP, addressable only by CAUSE / LHC-MR / LCV), then run a method battery whose assumptions span both regimes.
- R:
TwoSampleMR::mr()(IVW + Egger + median + mode),mr_pleiotropy_test(),mr_heterogeneity(),mr_leaveoneout(),directionality_test() - R:
MRPRESSO::mr_presso()for UHP outlier removal + distortion test - R:
cause::cause()for CHP-aware estimation;mrclust::mr_clust_em()for mechanism-heterogeneous instruments - R:
MendelianRandomization::mr_conmix()for contamination mixture;MRMix::MRMix()for mixture-of-distributions
UHP vs CHP: The Central Postdoc-Grade Distinction
Horizontal pleiotropy comes in two regimes, and most "standard" MR sensitivity methods address only one of them.
| Regime | Definition | InSIDE assumption | Methods that handle it |
|---|---|---|---|
| UHP (uncorrelated horizontal pleiotropy) | Pleiotropic effect alpha_j independent of instrument-exposure effect gamma_j | Holds | IVW (balanced UHP only), MR-Egger, weighted median, weighted mode, MR-PRESSO, MR-RAPS, MR-Mix, contamination mixture |
| CHP (correlated horizontal pleiotropy) | alpha_j correlates with gamma_j through a shared upstream factor (heritable confounder, network mediator) | Violated | CAUSE, LHC-MR, LCV, MR-Clust (partial), Steiger-filtered MR (partial) |
What ships with it
6 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.
- 6d ago First seen · 437 lines · 137 tokens per session scan A 6ae8fa480d44
bio-causal-genomics-pleiotropy-detection is a skill published in the GitHub repository GPTomics/bioSkills (1,199 stars, last pushed 21d ago), licensed MIT. It adds 137 tokens to every session and 9,186 once invoked, about $0.0007 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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