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.
Keywords: RNA sequencing data analysis; TRIAGE R package; regulatory elements; regulatory gene analysis; single-cell RNA sequencing data analysis.
© The Author(s) 2025. Published by Oxford University Press.