ClustAll: An R package for patient stratification in complex diseases

by Asier Ortega-Legarreta, Sara Palomino-Echeverria, Estefania Huergo, Vincenzo Lagani, Narsis A. Kiani, Pierre-Emmanuel Rautou, Nuria Planell Picola, Jesper Tegner, David Gomez-Cabrero

In the era of precision medicine, it is necessary to understand heterogeneity among patients with complex diseases to improve personalized prevention and management strategies. Here, we introduce ClustAll, a Bioconductor package designed for unsupervised patient stratification using clinical data. ClustAll is based on the previously validated methodology ClustAll, a clustering framework that effectively handles intricacies in clinical data, including mixed data types, missing values, and collinearity. Additionally, ClustAll stands out in its ability to identify multiple patient stratifications within the same population while ensuring their robustness. The updated implementation of ClustAll features S4 classes, parallel computing for enhanced computational efficiency, and user-friendly tools for exploring and comparing stratifications against clinical phenotypes. The performance of ClustAll has been validated using two public clinical datasets, confirming its effectiveness in patient stratification and highlighting its potential impact on clinical management. In summary, ClustAll is a powerful tool for patient stratification in personalized medicine.