HTGAnalyzer : An accessible R package with a web interface for enhanced transcriptomic analysis in precision medicine
Díez-Ahijado, Laia (Universitat de Barcelona)
del Rincón, Aarón Marcén (Institut d'investigacions biomèdiques August Pi i Sunyer)
Marimón, Lorena (Hospital Clínic i Provincial de Barcelona)
Saco, Adela (Hospital Clínic i Provincial de Barcelona)
del Pino, Marta (Hospital Clínic i Provincial de Barcelona)
Torné, Aureli (Hospital Clínic i Provincial de Barcelona)
Darecka, Katarzyna (Hospital Clínic i Provincial de Barcelona)
Sisuashvili, Lia (Hospital Clínic i Provincial de Barcelona)
Peñuelas, Núria (Facultat de Medicina i Ciències de la Salut. Universitat de Barcelona (UB))
Pascual-Mas, Pau (ISGlobal)
Carreras-Dieguez, Núria (Hospital Clínic i Provincial de Barcelona)
Ordi, Oriol (Instituto de Salud Carlos III)
Rakislova, Natalia (Instituto de Salud Carlos III)
Albero, Robert (Institut d'investigacions biomèdiques August Pi i Sunyer)

Date:	2025
Abstract:	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.
Grants:	Instituto de Salud Carlos III PI23/00494 Generalitat de Catalunya Program\u201D
Rights:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, sempre que no sigui amb finalitats comercials, i sempre que es reconegui l'autoria de l'obra original.
Language:	Anglès
Document:	Article ; recerca ; Versió publicada
Published in:	Computers in Biology and Medicine, Vol. 196 (september 2025) , p. 110772, ISSN 1879-0534

DOI: 10.1016/j.compbiomed.2025.110772

10 p, 6.4 MB

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