Development of interactive biological web applications with R/Shiny

• Published in: Briefings in bioinformatics Vol. 23; no. 1
• Main Authors: Jia, Lihua, Yao, Wen, Jiang, Yingru, Li, Yang, Wang, Zhizhan, Li, Haoran, Huang, Fangfang, Li, Jiaming, Chen, Tiantian, Zhang, Huiyong
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 17.01.2022; Oxford Publishing Limited (England)
• Subjects: Applications programs; Bioinformatics; Computational Biology; Data analysis; Data science; Internet resources; Programming Languages; Software; biological database; R; data analysis; biological web application development; Shiny; web server
• ISSN: 1467-5463; 1477-4054; 1477-4054
• DOI: 10.1093/bib/bbab415

Abstract Development of interactive web applications to deposit, visualize and analyze biological datasets is a major subject of bioinformatics. R is a programming language for data science, which is also one of the most popular languages used in biological data analysis and bioinformatics. However, building interactive web applications was a great challenge for R users before the Shiny package was developed by the RStudio company in 2012. By compiling R code into HTML, CSS and JavaScript code, Shiny has made it incredibly easy to build web applications for the large R community in bioinformatics and for even non-programmers. Over 470 biological web applications have been developed with R/Shiny up to now. To further promote the utilization of R/Shiny, we reviewed the development of biological web applications with R/Shiny, including eminent biological web applications built with R/Shiny, basic steps to build an R/Shiny application, commonly used R packages to build the interface and server of R/Shiny applications, deployment of R/Shiny applications in the cloud and online resources for R/Shiny.