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alterlab-arboreto

80 / 100 · Low risk

Fine to try.

By AlterLab-IEU/AlterLab-Academic-Skills (GitHub) · research · 87 stars · scanned at commit 3ab6d03

Infer gene regulatory networks (GRNs) from expression matrices using arboreto's scalable GRNBoost2 and GENIE3 tree-ensemble algorithms with Dask-distributed computation. Use when analyzing bulk or single-cell RNA-seq transcriptomics to map transcription-factor-to-target-gene regulatory interactions, build adjacency networks, or run the GRN-inference step of a SCENIC pipeline on large datasets. Part of the AlterLab Academic Skills suite.

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/'alterlab-arboreto' ] || [ -L ~/.agents/skills/'alterlab-arboreto' ]; then echo 'A skill folder named alterlab-arboreto already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/AlterLab-IEU/AlterLab-Academic-Skills' "$d" && git -C "$d" checkout --quiet '3ab6d034385ec4fedc3f6f4099292d4e91f60300' -- 'skills/bioinformatics/alterlab-arboreto' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/bioinformatics/alterlab-arboreto' ~/.agents/skills/'alterlab-arboreto' && 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/'alterlab-arboreto' ~/.claude/skills/'alterlab-arboreto' (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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