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bio-workflows-spatial-pipeline

85 / 100 · Low risk

Fine to try.

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

Orchestrates the end-to-end spatial transcriptomics pipeline from Space Ranger / vendor output to spatial domains and statistics, branching FIRST on platform class (imaging in-situ Xenium/MERFISH/CosMx vs sequencing/capture Visium/Visium HD/Slide-seq). Use when deciding segmentation-vs-deconvolution and the QC floors from the platform class, committing the coordinate/image-registration frame and panel identity, deconvolving multi-cell spots against an annotated scRNA reference (never relabeling…

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