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deseq2-differential-expression

100 / 100 · Low risk

Fine to try.

By BioTender-max/awesome-bio-agent-skills (GitHub) · coding · 219 stars · scanned at commit 8cbdd18

Bulk RNA-seq DE with R/Bioconductor DESeq2. Negative binomial GLM, empirical Bayes shrinkage, Wald/LRT tests, multi-factor designs, Salmon tximeta import, apeglm LFC shrinkage, MA/volcano/heatmap viz. R gold standard. Use pydeseq2-differential-expression for Python; use edgeR for TMM normalization.

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/'deseq2-differential-expression' ] || [ -L ~/.agents/skills/'deseq2-differential-expression' ]; then echo 'A skill folder named deseq2-differential-expression already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/BioTender-max/awesome-bio-agent-skills' "$d" && git -C "$d" checkout --quiet '8cbdd18837aa6296c4e77616a03b323bd69b57b1' -- 'skills/sciagent/deseq2-differential-expression' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/sciagent/deseq2-differential-expression' ~/.agents/skills/'deseq2-differential-expression' && 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/'deseq2-differential-expression' ~/.claude/skills/'deseq2-differential-expression' (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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