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

doi:10.7717/peerj.5853

PeerJ (Oct 2018)

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

DOI: https://doi.org/10.7717/peerj.5853
Journal volume & issue: Vol. 6
p. e5853

Abstract

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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).

Published in PeerJ

ISSN: 2167-8359 (Online)
Publisher: PeerJ Inc.
Country of publisher: United States
LCC subjects: Medicine; Science: Biology (General)
Website: https://peerj.com/

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