Overview
arboreto is an open-source data skill for Claude Code and compatible agents, published by K-Dense-AI. Its author describes it as: “Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription fact…”. The project has 46k stars on GitHub and is available under the MIT license. Add it to your setup with `git clone https://github.com/K-Dense-AI/scientific-agent-skills ~/.claude/skills/arboreto`.
What arboreto does
Arboreto is a Python library from Aerts Lab for inferring gene regulatory networks (GRNs) from gene expression data. It parallelizes tree-based ensemble regression (GRNBoost2, GENIE3) with Dask across local cores or remote clusters.
What’s inside
The SKILL.md for arboreto is organised into these sections:
- Overview
- Quick Start
- Core Capabilities
- 1. Basic GRN Inference
- 2. Algorithm Selection
- 3. Distributed Computing
- Installation
- Common Use Cases
- Single-Cell RNA-seq Analysis
- Bulk RNA-seq with TF Filtering
- Comparative Analysis (Multiple Conditions)
- Output Interpretation
Installation
Add arboreto to your agent with:
git clone https://github.com/K-Dense-AI/scientific-agent-skills ~/.claude/skills/arboretoReview a skill’s source before installing it — skills can instruct your agent to run commands. This command comes from the skill’s public repository, which is the source of truth for setup steps. New to skills? Read how to install Claude Code skills.
Supported agents
Neither the skill nor its repository names a specific agent. It uses the SKILL.md format, which several agents can load — check the repository for any agent-specific requirements.
License
arboreto is published under the MIT license.
Strengths
- Clear MIT license — safe to read and adapt within its terms
- Ships in K-Dense-AI/scientific-agent-skills, an established project with 45,887 GitHub stars
- Actively maintained — repository updated in the last 30 days
- Its repository gained 12,066 GitHub stars over the last 34 days
Author
Topics
Frequently asked questions
- What does arboreto do?
- Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets.
- How do I install arboreto?
- Run git clone https://github.com/K-Dense-AI/scientific-agent-skills ~/.claude/skills/arboreto in your agent, then reload your skills. Review the source at https://github.com/K-Dense-AI/scientific-agent-skills before installing.
- Is arboreto free to use?
- Yes. arboreto is free and open source under the MIT license, so you can read, run, and adapt it within that license's terms.
- Where does arboreto come from?
- arboreto ships inside K-Dense-AI/scientific-agent-skills, a repository that contains 42 catalogued skills in total. The repository's 45,887 GitHub stars apply to that whole collection, not to this skill on its own.