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bio-pathway-go-enrichment

100 / 100 · Low risk

Fine to try.

By lilinji/GeneTind-Life-Skills (GitHub) · data · 17 stars · scanned at commit 908229c

Runs Gene Ontology over-representation analysis (ORA) on a gene LIST with clusterProfiler enrichGO, the one-sided hypergeometric/Fisher 2x2 test phyper(k-1, M, N-M, n, lower.tail=FALSE). Covers why the BACKGROUND universe (not the gene list) is the null and decides significance, why omitting universe= is a bug, why enrichGO defaults to ont='MF' not 'BP', why pvalueCutoff filters p.adjust not raw p, why ORA discards effect magnitude and inherits GO-DAG true-path redundancy (simplify, topGO), why…

Works with any agent that supports SKILL.md skills.

What this skill can do

We found nothing in the files we read that matches our rules. That does not prove the skill is safe: see the limits of static scanning.

Install

Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.

if [ -e ~/.agents/skills/'bio-pathway-go-enrichment' ] || [ -L ~/.agents/skills/'bio-pathway-go-enrichment' ]; then echo 'A skill folder named bio-pathway-go-enrichment already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/lilinji/GeneTind-Life-Skills' "$d" && git -C "$d" checkout --quiet '908229c955510a1841b216e8bf58f6b22818d4dc' -- 'skills/bio-pathway-go-enrichment' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/bio-pathway-go-enrichment' ~/.agents/skills/'bio-pathway-go-enrichment' && rm -rf "$d"; fi

Codex reads ~/.agents/skills directly. For Claude Code, Cursor, Copilot, Gemini CLI, Antigravity or OpenCode, also link it. For Claude Code: ln -s ~/.agents/skills/'bio-pathway-go-enrichment' ~/.claude/skills/'bio-pathway-go-enrichment' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.

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