CRUX, a platform for visualising, exploring and analysing cancer genome cohort data

• Published in: NAR genomics and bioinformatics Vol. 6; no. 1; p. lqae003
• Main Authors: El-Kamand, Sam, Quinn, Julian M W, Sareen, Heena, Becker, Therese M, Wong-Erasmus, Marie, Cowley, Mark J
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.03.2024
• Subjects: Biomarkers; Cancer; Genomes; Genomic analysis; Survival analysis
• ISSN: 2631-9268; 2631-9268
• DOI: 10.1093/nargab/lqae003

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).