Arboreto

Overview

Arboreto is a computational library for inferring gene regulatory networks (GRNs) from gene expression data using parallelized algorithms that scale from single machines to multi-node clusters.

Core capability: Identify which transcription factors (TFs) regulate which target genes based on expression patterns across observations (cells, samples, conditions).

When to Use This Skill

Use this skill when the user wants to:

• Infer a TF → target-gene regulatory network from a bulk or single-cell expression matrix.
• Run the GRN-inference step (step 1) of a SCENIC / pySCENIC pipeline.
• Compare GRNBoost2 against GENIE3, or build a consensus network across random seeds.
• Scale GRN inference across cores or a Dask cluster.

Does NOT Trigger