Is the Arboreto skill free?

Yes. The skill itself is free from K-Dense-AI/scientific-agent-skills. SkillProof publishes the install command and an independent test verdict at no cost.

What is the Arboreto SkillProof Score?

8.8/10 — installs cleanly 5/5, triggers reliably 5/5, output vs. baseline 7/10, docs & honesty 5/5.

How do I install Arboreto?

Copy the install command from this page, run it in your terminal, and restart Claude Code. Skills live in ~/.claude/skills/ (global) or .claude/skills/ inside a project.

Can I use Arboreto with Cursor, Copilot, Gemini CLI, Codex or other AI tools?

The SKILL.md format is native to Claude (Claude Code, Desktop, claude.ai). The instructions inside adapt to other assistants: Cursor rules, GitHub Copilot instructions, Windsurf rules, Custom GPTs, AGENTS.md for OpenAI Codex, and GEMINI.md for Google Gemini CLI — our conversion guides cover each, and the free converter on the tools page does the wrapping for you.

Arboreto

Infer gene regulatory networks from expression data with GRNBoost2/GENIE3, scaled via Dask.

by K-Dense-AI · K-Dense-AI/scientific-agent-skills

Tested · Works

Install — copy the command Download source ↗

Test report

Verdict: Tested · Works
Score: 8.8/10
Tested: Jul 14, 2026
Environment: Claude Code 2.x (agent harness)
Upstream re-checked: Aug 10, 2026 · b837e2d

The Quick Start marks the `if __name__ == '__main__':` Dask guard as 'Critical' and repeats it in Troubleshooting; a baseline script assembled from general arboreto knowledge dropped that guard, which is a genuine hang/crash bug on macOS and Windows spawn-based multiprocessing.

Scored on four weighted criteria — install, triggering, output vs. baseline, docs. How scoring works

Installs cleanly 5/5
Triggers reliably 5/5
Output vs. baseline 7/10
Docs & honesty 5/5

What Arboreto does

Guides GRN inference from bulk or single-cell RNA-seq expression data using arboreto's GRNBoost2 and GENIE3 algorithms, including TF filtering, local/cluster Dask scaling, and pySCENIC integration. Triggers when analyzing transcriptomics data to find transcription-factor-to-target-gene regulatory relationships.

How to install Arboreto

git clone https://github.com/K-Dense-AI/scientific-agent-skills
cd scientific-agent-skills
mkdir -p ~/.claude/skills
cp -r skills/arboreto ~/.claude/skills/arboreto

Skills live in ~/.claude/skills/ (global) or .claude/skills/ (per-project). Restart Claude Code after installing.

Commands — how to trigger Arboreto

/arboreto Infer gene regulatory networks from expression data with GRNBoost2/GENIE3, scaled via Dask.

It also activates on plain-language prompts like these:

Infer a gene regulatory network with GRNBoost2
Run GENIE3 GRN inference on my expression matrix
Build a GRN from single-cell data using arboreto

Frequently asked questions

Is the Arboreto skill free?: Yes. The skill itself is free from K-Dense-AI/scientific-agent-skills. SkillProof publishes the install command and an independent test verdict at no cost.
Does Arboreto work with Claude Code?: We tested it with Claude Code 2.x (agent harness) on Jul 14, 2026. Verdict: Tested · Works. The Quick Start marks the `if __name__ == '__main__':` Dask guard as 'Critical' and repeats it in Troubleshooting; a baseline script assembled from general arboreto knowledge dropped that guard, which is a genuine hang/crash bug on macOS and Windows spawn-based multiprocessing.
What is the Arboreto SkillProof Score?: 8.8/10 — installs cleanly 5/5, triggers reliably 5/5, output vs. baseline 7/10, docs & honesty 5/5.
How do I install Arboreto?: Copy the install command from this page, run it in your terminal, and restart Claude Code. Skills live in ~/.claude/skills/ (global) or .claude/skills/ inside a project.
Can I use Arboreto with Cursor, Copilot, Gemini CLI, Codex or other AI tools?: The SKILL.md format is native to Claude (Claude Code, Desktop, claude.ai). The instructions inside adapt to other assistants: Cursor rules, GitHub Copilot instructions, Windsurf rules, Custom GPTs, AGENTS.md for OpenAI Codex, and GEMINI.md for Google Gemini CLI — our conversion guides cover each, and the free converter on the tools page does the wrapping for you.