Arboreto

--- name: arboreto description: 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. --- # 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). ## Quick Start Install arboreto: ```bash uv pip install arboreto ``` Basic GRN inference: ```python import pandas as pd from arboreto.algo import grnboost2 if __name__ == '__main__': # Load expression data (genes as columns) e