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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.<\/jats:p>","DOI":"10.1093\/bib\/bbaf004","type":"journal-article","created":{"date-parts":[[2025,1,13]],"date-time":"2025-01-13T03:35:42Z","timestamp":1736739342000},"source":"Crossref","is-referenced-by-count":3,"title":["TRIAGE: an R package for regulatory gene analysis"],"prefix":"10.1093","volume":"26","author":[{"given":"Qiongyi","family":"Zhao","sequence":"first","affiliation":[{"name":"Institute for Molecular Bioscience, The University of Queensland , 306 Carmody Road, St Lucia, Brisbane, QLD 4072 ,","place":["Australia"]}]},{"given":"Woo Jun","family":"Shim","sequence":"additional","affiliation":[{"name":"Institute for Molecular Bioscience, The University of Queensland , 306 Carmody Road, St Lucia, Brisbane, QLD 4072 ,","place":["Australia"]}]},{"given":"Yuliangzi","family":"Sun","sequence":"additional","affiliation":[{"name":"Institute for Molecular Bioscience, The University 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