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bio-workflows-multiome-pipeline

100 / 100 · Low risk

Fine to try.

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

Orchestrates the end-to-end 10x Multiome (paired scRNA + scATAC) pipeline from Cell Ranger ARC output to a jointly-embedded, annotated object, chaining per-modality QC, AMULET fragment-based ATAC doublet detection, per-modality normalization (RNA SCT/PCA; ATAC TF-IDF/LSI), WNN (or MultiVI) integration, joint clustering, RNA-based annotation, and LinkPeaks peak-to-gene linking. Use when enforcing the shared cell-barcode intersection between modalities (cellranger-ARC not -atac), keeping per-moda…

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