BreastSubtypeR: a unified R/Bioconductor package for intrinsic molecular subtyping in breast cancer research.

ABSTRACT: Intrinsic molecular subtyping (IS) of breast cancer is fundamental for understanding disease biology and guiding personalized treatment. While IS methods are standardized in clinical practice, their research implementations vary, leading to inconsistencies and reduced reproducibility. We introduce BreastSubtypeR, an R/Bioconductor package that unifies multiple published IS classifiers into a single, reproducible framework, enabling systematic cross-method comparison and robust cohort-aware selection. Its core feature, AUTO mode, quantitatively evaluates cohort composition and selectively activates classifiers whose assumptions are met, reducing user bias and improving robustness across skewed or subtype-specific cohorts. The package also provides a unified, method-specific normalization pi

SUBMITTER: Yang Q 

PROVIDER: S-EPMC12501779 | biostudies-literature | 2025 Dec

REPOSITORIES: biostudies-literature