CancerSubtypes: an R/Bioconductor package for molecular cancer subtype identification, validation and visualization

TLDR

Identifying molecular cancer subtypes from multi‑omics data is a critical step toward personalized medicine. The authors introduce CancerSubtypes, an R package that identifies cancer subtypes using gene expression, miRNA expression, and DNA methylation data. CancerSubtypes integrates four well‑cited computational methods into a unified framework that standardizes preprocessing, feature selection, result computation, biological validation, and visualization, and provides a consistent input/output format for comparing methods. The package effectively infers cancer subtypes, enables comparison of predictions across methods, and supports testing of new discovery approaches, as demonstrated in multiple application scenarios.

Abstract

Identifying molecular cancer subtypes from multi-omics data is an important step in the personalized medicine. We introduce CancerSubtypes, an R package for identifying cancer subtypes using multi-omics data, including gene expression, miRNA expression and DNA methylation data. CancerSubtypes integrates four main computational methods which are highly cited for cancer subtype identification and provides a standardized framework for data pre-processing, feature selection, and result follow-up analyses, including results computing, biology validation and visualization. The input and output of each step in the framework are packaged in the same data format, making it convenience to compare different methods. The package is useful for inferring cancer subtypes from an input genomic dataset, comparing the predictions from different well-known methods and testing new subtype discovery methods, as shown with different application scenarios in the Supplementary Material.The package is implemented in R and available under GPL-2 license from the Bioconductor website (http://bioconductor.org/packages/CancerSubtypes/)[e-mail] or [e-mail] data are available at Bioinformatics online.