Arboreto

Overview

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.

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

Upstream: PyPI 0.1.6 (2021-02-09, latest). Docs: arboreto.readthedocs.io. Primary downstream consumer: pySCENIC.