Zhao Qiongyi, Shim Woo Jun, Sun Yuliangzi, Sinniah Enakshi, Shen Sophie, Boden Mikael, Palpant Nathan J
Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, St Lucia, Brisbane, QLD 4072, Australia.
School of Chemistry and Molecular Biosciences, The University of Queensland, 68 Cooper Rd, St Lucia, Brisbane, QLD 4072, Australia.
Brief Bioinform. 2025 Jan 12;26(1). doi: 10.1093/bib/bbaf004.
Regulatory genes are critical determinants of cellular responses in development and disease, but standard RNA sequencing (RNA-seq) analysis workflows, such as differential expression analysis, have significant limitations in revealing the regulatory basis of cell identity and function. To address this challenge, we present the TRIAGE R package, a toolkit specifically designed to analyze regulatory elements in both bulk and single-cell RNA-seq datasets. The package is built upon TRIAGE methods, which leverage consortium-level H3K27me3 data to enrich for cell-type-specific regulatory regions. It facilitates the construction of efficient and adaptable pipelines for transcriptomic data analysis and visualization, with a focus on revealing regulatory gene networks. We demonstrate the utility of the TRIAGE R package using three independent transcriptomic datasets, showcasing its integration into standard analysis workflows for examining regulatory mechanisms across diverse biological contexts. The TRIAGE R package is available on GitHub at https://github.com/palpant-comp/TRIAGE_R_Package.
调控基因是发育和疾病中细胞反应的关键决定因素，但标准的RNA测序（RNA-seq）分析工作流程，如差异表达分析，在揭示细胞身份和功能的调控基础方面存在重大局限性。为应对这一挑战，我们推出了TRIAGE R软件包，这是一个专门设计用于分析批量和单细胞RNA-seq数据集中调控元件的工具包。该软件包基于TRIAGE方法构建，该方法利用联盟级别的H3K27me3数据来富集细胞类型特异性调控区域。它有助于构建高效且适应性强的转录组数据分析和可视化管道，重点是揭示调控基因网络。我们使用三个独立的转录组数据集展示了TRIAGE R软件包的实用性，展示了其如何融入标准分析工作流程以检查不同生物学背景下的调控机制。TRIAGE R软件包可在GitHub上获取，网址为https://github.com/palpant-comp/TRIAGE_R_Package。
