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sciagent-harmony-batch-correction

85 / 100 · Low risk

Fine to try.

By ai4nucleome/BioMaster (GitHub) · coding · 118 stars · scanned at commit 6f98a63

Harmony batch correction for scRNA-seq and other omics. Removes batch effects from PCA embeddings while preserving biology. Run after PCA, before UMAP. Scales to millions of cells. Python (harmonypy, scanpy) and R (Seurat).

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/'sciagent-harmony-batch-correction' ] || [ -L ~/.agents/skills/'sciagent-harmony-batch-correction' ]; then echo 'A skill folder named sciagent-harmony-batch-correction already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/ai4nucleome/BioMaster' "$d" && git -C "$d" checkout --quiet '6f98a63aa1823304403475b1929424ccf9d4ec46' -- '.opencode/bioskills/sciagent-harmony-batch-correction' && mkdir -p ~/.agents/skills && cp -R "$d"/'.opencode/bioskills/sciagent-harmony-batch-correction' ~/.agents/skills/'sciagent-harmony-batch-correction' && 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/'sciagent-harmony-batch-correction' ~/.claude/skills/'sciagent-harmony-batch-correction' (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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