Arboreto Bioinformatics Analysis

소개

Arboreto provides a high-performance framework for reconstructing gene regulatory networks (GRNs) from gene expression data. By identifying transcription factor-target gene relationships, it helps researchers uncover the underlying regulatory logic in biological systems. It is specifically designed to handle the scale of modern transcriptomics, supporting both bulk and single-cell RNA-seq datasets. With built-in support for Dask, Arboreto scales seamlessly from local multi-core machines to distributed computing clusters, making it an essential tool for systems biology and complex genomic analysis.

주요 기능

• High-speed GRN inference using GRNBoost2 and GENIE3 algorithms
• Scalable distributed computing integration via Dask
• 0 GitHub stars
• Support for large-scale single-cell and bulk RNA-seq datasets
• Core integration capability with the pySCENIC analysis pipeline
• Transcription factor filtering for focused regulatory analysis

사용 사례

• Comparing gene network topology across different experimental conditions
• Mapping transcription factor interactions in high-throughput genomic studies
• Identifying cell-type-specific regulatory links in single-cell datasets