Arboreto - Gene Regulatory Network Inference

Overview

Arboreto is a Python library for inferring gene regulatory networks (GRNs) from gene expression data using machine learning algorithms. It enables scalable GRN inference from single machines to multi-node clusters using Dask for distributed computing. The skill provides comprehensive support for both GRNBoost2 (fast gradient boosting) and GENIE3 (Random Forest) algorithms.

When to Use This Skill

This skill should be used when:

• Inferring regulatory relationships between genes from expression data
• Analyzing single-cell or bulk RNA-seq data to identify transcription factor targets
• Building the GRN inference component of a pySCENIC pipeline
• Comparing GRNBoost2 and GENIE3 algorithm performance
• Setting up distributed computing for large-scale genomic analyses
• Troubleshooting arboreto installation or runtime issues

Core Capabilities

1. Basic GRN Inference