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bio-workflows-chipseq-pipeline

95 / 100 · Low risk

Fine to try.

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

Orchestrates the end-to-end ChIP-seq pipeline from FASTQ to blacklist-filtered, annotated peaks, chaining fastp QC, Bowtie2 alignment, pre-dedup library-complexity QC (NRF/PBC), duplicate removal, chrM + ENCODE-blacklist filtering, MACS3 peak calling against a matched input, IDR/consensus reproducibility, deepTools signal tracks, and ChIPseeker annotation. Use when committing the reference build + blacklist version + effective genome size once, pairing each IP with its matched control, computin…

Works with any agent that supports SKILL.md skills.

What this skill can do

Install

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

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