HTGAnalyzer: An accessible R package with a web interface for enhanced transcriptomic analysis in precision medicine

Transcriptomics generates promising data for personalized medicine, but its clinical utility is hindered by technical barriers associated with formalin-fixed, paraffin-embedded samples. Advances in automation and simplified workflows are key for integrating these technologies into routine care. We have developed HTGAnalyzer, an R package that enables bulk transcriptomics analysis from multiple data sources, such as HTG EdgeSeq and RNA-seq. Designed with clinical and molecular diagnostics in mind, HTGAnalyzer includes a fully automatic pipeline that performs sample quality control, data normalization, and a set of transcriptomic and clinical analyses. Importantly, HTGAnalyzer provides quality control and analysis tailored for HTG data, filling the gap left by HTG closure with no alternative solutions. Designed for ease of use without knowledge of bioinformatics, it features a user-friendly Shiny app, standardized functions for easy Docker setup, and enhanced connectivity to clinical data management systems. It delivers a complete analytical workflow in less than 20 min on a standard PC (Intel i7-7500U, 16 GB RAM). We applied HTGAnalyzer to diverse datasets, including a new vulvar cancer cohort, and generated interpretable reports with rich visual outputs. In summary, HTGAnalyzer offers robust quality control and advanced analytics in a single, unified tool, supporting the clinical use of transcriptomics in precision medicine.