BioInstaller: a comprehensive R package to construct interactive and reproducible biological data analysis applications based on the R platform
Jianfeng Li,
Bowen Cui,
Yuting Dai,
Ling Bai,
Jinyan Huang
Affiliations
Jianfeng Li
State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, China
Bowen Cui
State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, China
Yuting Dai
State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, China
Ling Bai
State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, China
Jinyan Huang
State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, China
The increase in bioinformatics resources such as tools/scripts and databases poses a great challenge for users seeking to construct interactive and reproducible biological data analysis applications. Here, we propose an open-source, comprehensive, flexible R package named BioInstaller that consists of the R functions, Shiny application, the HTTP representational state transfer application programming interfaces, and a docker image. BioInstaller can be used to collect, manage and share various types of bioinformatics resources and perform interactive and reproducible data analyses based on the extendible Shiny application with Tom’s Obvious, Minimal Language and SQLite format databases. The source code of BioInstaller is freely available at our lab website, http://bioinfo.rjh.com.cn/labs/jhuang/tools/bioinstaller, the popular package host GitHub, https://github.com/JhuangLab/BioInstaller, and the Comprehensive R Archive Network, https://CRAN.R-project.org/package=BioInstaller. In addition, a docker image can be downloaded from DockerHub (https://hub.docker.com/r/bioinstaller/bioinstaller).
