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bio-workflows-atacseq-pipeline

80 / 100 · Low risk

Fine to try.

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

Orchestrates the end-to-end bulk ATAC-seq pipeline from FASTQ to differential accessibility and TF footprints, chaining Nextera-aware fastp QC, Bowtie2 alignment, chrM removal, dedup, a single Tn5 +4/-5 shift, MACS3 peak calling, Corces fixed-width consensus, DiffBind/csaw differential accessibility, and TOBIAS footprinting. Use when committing the reference build + blacklist once, recognizing ATAC has NO input control (the shift-extend model IS the background), applying the Tn5 shift exactly o…

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