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bio-pathway-reactome

100 / 100 · Low risk

Fine to try.

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

Tests a gene list or ranked gene vector for over-representation or coordinated shifts in Reactome's curated, peer-reviewed, reaction-level pathways using ReactomePA's enrichPathway (ORA) and gsePathway (GSEA), reading the local reactome.db so a run is reproducible given the Bioconductor release. Covers why Reactome's atomic unit is the REACTION and pathways are nested containers so a parent and child enrich on the same genes and double-count one signal, why only human is curated and every other…

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-reactome' ] || [ -L ~/.agents/skills/'bio-pathway-reactome' ]; then echo 'A skill folder named bio-pathway-reactome 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 "$d" checkout --quiet '908229c955510a1841b216e8bf58f6b22818d4dc' -- 'skills/bio-pathway-reactome' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/bio-pathway-reactome' ~/.agents/skills/'bio-pathway-reactome' && 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-reactome' ~/.claude/skills/'bio-pathway-reactome' (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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