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bio-single-cell-preprocessing

85 / 100 · Low risk

Fine to try.

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

Quality control, ambient-RNA handling, normalization, and feature selection for single-cell RNA-seq using Scanpy (Python) and Seurat (R). Use when filtering low-quality cells with MAD-adaptive thresholds, setting tissue-aware mito cutoffs, removing ambient RNA (SoupX/CellBender/DecontX), choosing a normalization (shifted-log vs scran vs sctransform vs Pearson residuals), selecting highly variable genes, or deciding whether to scale and regress out covariates.

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