El-Kamand Sam, Quinn Julian M W, Sareen Heena, Becker Therese M, Wong-Erasmus Marie, Cowley Mark J
Children's Cancer Institute, Randwick, NSW 2031, Australia.
Centre for Circulating Tumour Cell Diagnostics and Research, Ingham Institute for Applied Medical Research, 1 Campbell St, Liverpool, NSW 2170, Australia.
NAR Genom Bioinform. 2024 Feb 1;6(1):lqae003. doi: 10.1093/nargab/lqae003. eCollection 2024 Mar.
To better understand how tumours develop, identify prognostic biomarkers and find new treatments, researchers have generated vast catalogues of cancer genome data. However, these datasets are complex, so interpreting their important features requires specialized computational skills and analytical tools, which presents a significant technical challenge. To address this, we developed CRUX, a platform for exploring genomic data from cancer cohorts. CRUX enables researchers to perform common analyses including cohort comparisons, biomarker discovery, survival analysis, and to create visualisations including oncoplots and lollipop charts. CRUX simplifies cancer genome analysis in several ways: (i) it has an easy-to-use graphical interface; (ii) it enables users to create custom cohorts, as well as analyse precompiled public and private user-created datasets; (iii) it allows analyses to be run locally to address data privacy concerns (though an online version is also available) and (iv) it makes it easy to use additional specialized tools by exporting data in the correct formats. We showcase CRUX's capabilities with case studies employing different types of cancer genome analysis, demonstrating how it can be used flexibly to generate valuable insights into cancer biology. CRUX is freely available at https://github.com/CCICB/CRUX and https://ccicb.shinyapps.io/crux (DOI: 10.5281/zenodo.8015714).
为了更好地理解肿瘤的发展过程、识别预后生物标志物并寻找新的治疗方法，研究人员已经生成了大量的癌症基因组数据目录。然而，这些数据集非常复杂，因此解读其重要特征需要专业的计算技能和分析工具，这带来了重大的技术挑战。为了解决这个问题，我们开发了CRUX，一个用于探索癌症队列基因组数据的平台。CRUX使研究人员能够进行常见的分析，包括队列比较、生物标志物发现、生存分析，并创建可视化图表，如肿瘤图谱和棒棒糖图。CRUX在几个方面简化了癌症基因组分析：（i）它有一个易于使用的图形界面；（ii）它允许用户创建自定义队列，以及分析预编译的公共和私人用户创建的数据集；（iii）它允许在本地运行分析以解决数据隐私问题（尽管也有在线版本），以及（iv）它通过以正确的格式导出数据，使使用其他专业工具变得容易。我们通过采用不同类型癌症基因组分析的案例研究展示了CRUX的功能，证明了它如何可以灵活地用于生成对癌症生物学的有价值见解。CRUX可在https://github.com/CCICB/CRUX和https://ccicb.shinyapps.io/crux免费获取（DOI：10.5281/zenodo.8015714）。
