bio-workflows-causal-genomics-pipeline

bio-workflows-causal-genomics-pipeline is a skill for Claude Code, Codex from BioTender-max/awesome-bio-agent-skills. It costs 173 tokens per session (5,471 once invoked), scanned A, original, no licence file.

A workflow for studying which genetic variants may cause changes in traits or disease after a genome-wide association study (GWAS). It combines several statistical analyses to compare genetic signals, test possible causal links, and prioritize likely genes.

In plain words
What is it for?
Use it to assess heritability, genetic correlation, Mendelian randomization, colocalization, fine-mapping, mediation, and transcriptome-wide association results. It also supports prioritizing genes and evaluating possible drug targets.
Why use it?
Post-GWAS results show associations, but not necessarily which variant or gene is responsible. This workflow helps organize follow-up analyses that investigate those possible causes.

Skill for Claude CodeCodex

Which agent this was written for is unclear — body not stored (licence); the path alone says nothing.

Good fit Use it to assess heritability, genetic correlation, Mendelian randomization, colocalization, fine-mapping, mediation, and transcriptome-wide association results. It also supports prioritizing genes and evaluating possible drug targets.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/biotender-max/awesome-bio-agent-skills/causal-genomics-pipeline
Install

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.

Any agent
npx skills add BioTender-max/awesome-bio-agent-skills --skill causal-genomics-pipeline
Clone the repo
git clone --depth 1 https://github.com/BioTender-max/awesome-bio-agent-skills

Made for: Claude Code, Codex.

Wrote 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.

agentmods badge for bio-workflows-causal-genomics-pipeline

README.md
[![agentmods](https://agentmods.dev/badge/skills/biotender-max/awesome-bio-agent-skills/causal-genomics-pipeline/github.svg)](https://agentmods.dev/skills/biotender-max/awesome-bio-agent-skills/causal-genomics-pipeline)
Your own site
<a href="https://agentmods.dev/skills/biotender-max/awesome-bio-agent-skills/causal-genomics-pipeline"><img src="https://agentmods.dev/badge/skills/biotender-max/awesome-bio-agent-skills/causal-genomics-pipeline/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.

agentmods 80×15 button for bio-workflows-causal-genomics-pipeline

Your own site · 80×15
<a href="https://agentmods.dev/skills/biotender-max/awesome-bio-agent-skills/causal-genomics-pipeline"><img src="https://agentmods.dev/badge/skills/biotender-max/awesome-bio-agent-skills/causal-genomics-pipeline.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 173 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 5,471 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.
Origin unknown No closer match found in the catalogue.
Token cost

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.

ModelPer sessionOnce invoked
Fable 5.1 $0.00173 $0.05471
Opus 5 $0.00086 $0.02736
Sonnet 5 $0.00035 $0.01094
Haiku 4.5 $0.00017 $0.00547

Measured 9d ago against content hash 014996e75383, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-12, from the pricing page.

Security

Grade A, and why

bio-workflows-causal-genomics-pipeline 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 9d 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.

skills/bioskills/causal-genomics-pipeline/SKILL.md · 317 lines

The source is not reproduced here

A licence we could not identify

The repository carries a LICENSE file, but it is custom or dual enough that GitHub cannot name it and neither can this catalogue. Unknown terms are not permission, so the body is not copied here. Read the licence at the source and decide for yourself.

Read it on GitHub

Files

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.

Changes

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.

  1. 9d ago First seen · 317 lines · 173 tokens per session scan A 014996e75383

Subscribe to this mod's changes

bio-workflows-causal-genomics-pipeline is a skill published in the GitHub repository BioTender-max/awesome-bio-agent-skills (178 stars, last pushed 2mo ago), with no licence file. It adds 173 tokens to every session and 5,471 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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