CancerSubtypes: an R/Bioconductor package for molecular cancer subtype identification, validation and visualization
CancerSubtypes: an R/Bioconductor package for molecular cancer subtype identification, validation and visualization
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CancerSubtypes：用于分子癌症亚型识别、验证和可视化的 R/Bioconductor 软件包
DOI：
10.1093/bioinformatics/btx378
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发表时间：
2017-10-01
期刊：
影响因子：
5.8
通讯作者：
Li, Jiuyong
中科院分区：
文献类型：
--
作者：
Xu, Taosheng;Thuc Duy Le;Li, Jiuyong
从多组学数据中识别癌症分子亚型是个体化医疗的重要一步。我们介绍了CancerSubtypes，一个使用多组学数据识别癌症亚型的R软件包，包括基因表达，miRNA表达和DNA甲基化数据。CancerSubtypes集成了四种主要的计算方法，这些方法被高度引用用于癌症亚型识别，并为数据预处理，特征选择和结果跟踪分析提供了标准化框架，包括结果计算，生物学验证和可视化。框架中每一步的输入和输出都以相同的数据格式打包，便于比较不同的方法。该软件包可用于从输入基因组数据集推断癌症亚型，比较来自不同已知方法的预测，并测试新的亚型发现方法，如补充材料中的不同应用场景所示。可用性和实现：该软件包以R实现，并可在GPL-2许可下从Bioconductor网站（http：//bioconductor.org/packages/CancerSubtypes/）获得。
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.Availability and implementation: The package is implemented in R and available under GPL-2 license from the Bioconductor website (http://bioconductor.org/packages/CancerSubtypes/).