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- Title
CancerSubtypes: an R/Bioconductor package for molecular cancer subtype identification, validation and visualization.
- Authors
Taosheng Xu; Thuc Duy Le; Lin Liu; Ning Su; Rujing Wang; Bingyu Sun; Colaprico, Antonio; Bontempi, Gianluca; Jiuyong Li
- 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.
- Subjects
CANCER diagnosis; GENE expression; MICRORNA; DNA methylation; DATA visualization; INDIVIDUALIZED medicine; GENOMICS; CANCER genetics
- Publication
Bioinformatics, 2017, Vol 33, Issue 19, p3131
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/btx378