TRIAGE: an R package for regulatory gene analysis

Area of Science:

• Genomics
• Computational Biology
• Molecular Biology

Background:

• Standard RNA sequencing (RNA-seq) analysis struggles to fully elucidate the regulatory basis of cellular identity and function.
• Identifying regulatory elements is crucial for understanding cellular responses in development and disease.

Purpose of the Study:

• To introduce the TRIAGE R package, a novel toolkit for analyzing regulatory elements in bulk and single-cell RNA-seq data.
• To provide an efficient and adaptable pipeline for transcriptomic data analysis and visualization, focusing on regulatory gene networks.

Main Methods:

• The TRIAGE R package utilizes TRIAGE methods, integrating consortium-level H3K27me3 data to enrich for cell-type-specific regulatory regions.
• The package facilitates the construction of analysis and visualization pipelines for transcriptomic data.

Main Results:

• The TRIAGE R package effectively analyzes regulatory elements in RNA-seq datasets, going beyond standard differential expression analysis.
• Demonstrated utility across three independent transcriptomic datasets, showcasing integration into standard workflows for regulatory mechanism examination.

Conclusions:

• The TRIAGE R package offers a powerful solution for uncovering regulatory gene networks and understanding cell identity.
• This toolkit enhances the analysis of transcriptomic data, providing deeper insights into regulatory mechanisms in various biological contexts.