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BioInstaller: a comprehensive R package to integrate bioinformatics resources

, , , ,
1 State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, China
2 School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
3 State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
DOI
10.7287/peerj.preprints.27221v1
Published
Accepted
Subject Areas
Bioinformatics, Statistics
Keywords
R package, integrate bioinformatics resources, Shiny application
Copyright
© 2018 Li et al.
Licence
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
Cite this article
Li J, Cui B, Dai Y, Bai L, Huang J. 2018. BioInstaller: a comprehensive R package to integrate bioinformatics resources. PeerJ Preprints 6:e27221v1

Abstract

The number of bioinformatics resources, such as tools/scripts and databases are growing exponentially. This poses a great challenge for users to access, manage, and integrate the corresponding bioinformatics resources. To facilitate the request, we proposed a comprehensive R package, BioInstaller, which includes the R functions, Shiny application, and the HTTP representational state transfer (REST) application programming interfaces (APIs). We also established a community-based configuration pool to collect, access and share bioinformatics resources. The source code of BioInstaller is freely available at our lab website http://bioinfo.rjh.com.cn/labs/jhuang/tools/bioinstaller or popular package host GitHub at: https://github.com/JhuangLab/BioInstaller. Also, a docker image can be downloaded from DockerHub (https://hub.docker.com/r/bioinstaller).

Author Comment

This is a submission to PeerJ for review.

Supplemental Information

List of BioInstaller included tools/scripts

DOI: 10.7287/peerj.preprints.27221v1/supp-1

List of BioInstaller supported databases

DOI: 10.7287/peerj.preprints.27221v1/supp-2

Demo functions and configuration item to query versions in BioInstaller

(A) GitHub APIs integrated in R function can access GitHub projects meta information, including branches, tags and releases versions. (B) The demo function shows how to get the versions of the sequence alignment tool GMAP. (C) The demo configuration item shows how to download and install miniconda2 using mirror URL.

DOI: 10.7287/peerj.preprints.27221v1/supp-3

Shiny application basic modules: introduction, dashboard and uploading

(A) Overview of Shiny navigation bar tab items and the introduction module page. (B) Dashboard module page contains system monitor, task queue monitor, query system, and others. (C) Output table in dashboard module shows all files in ‘PATH’ directory’s environment variable. It also includes search and export functions. (D) UI of upload module contains extra fields, including file type, genome version, and description, to describe the information of the files. (E) Save button was used to save uploaded file and update the related database. (F) Preview box was used to view uploaded files before confirming uploading.

DOI: 10.7287/peerj.preprints.27221v1/supp-4

More examples of dashboard module boxes

(A) The example of R session information of host running Shiny application. (B) Installed R package of the host running Shiny application. (C) Output table of all environment variables and its value. (D)(E)(F)Output table and text of installed items via BioInstaller, conda, and spack.

DOI: 10.7287/peerj.preprints.27221v1/supp-5

Shiny application 'Installer' module

(A)(B) Using the download of ‘db_ucsc_refgene’ shows how it works of Shiny 'Installer' module. Dynamic and interactive manipulations are supported. Log information of submitted download/install job can be recalled using given random characters. (C)(D) The input box and output log to create a new softwares environment using the conda plugin of 'Installer' module. (E)(F) The input box and output log to install 'zlib' using the spack plugin of 'Installer' module.

DOI: 10.7287/peerj.preprints.27221v1/supp-6

Shiny application 'Setting' module

(A) Rendered UI from the YAML format configuration file. (B) YAML editor allows users to add and modify variables used in the Shiny application. This can real-time update the UI of panel (A).

DOI: 10.7287/peerj.preprints.27221v1/supp-7

Github forum of BioInstaller

(A) Search the keyword on the github website with the the autosuggestor autocompletion functionality (B) Demo output of github search using 'RNA'. Key word was colored yellow. (C) Demo posts of forum of BioInstaller.

DOI: 10.7287/peerj.preprints.27221v1/supp-8

R functions pool of version query from original website (non-github)

DOI: 10.7287/peerj.preprints.27221v1/supp-9

Summary of UCSC sequence and annotation data which BioInstaller supported

DOI: 10.7287/peerj.preprints.27221v1/supp-10

Demo plugin (easy_project) of 'Pipeline' module

DOI: 10.7287/peerj.preprints.27221v1/supp-11

Demo plugin (maftools) of Shiny application 'Instant' module

DOI: 10.7287/peerj.preprints.27221v1/supp-12

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Jianfeng Li conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Bowen Cui conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Yuting Dai contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.

Ling Bai contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.

Jinyan Huang conceived and designed the experiments, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.

Data Deposition

The following information was supplied regarding data availability:

Project name: BioInstaller

Project home page - Package: http://bioinfo.rjh.com.cn/labs/jhuang/tools/bioinstaller

Project home page - Package (CRAN): https://CRAN.R-project.org/package=BioInstaller

Project source code - Package: https://github.com/JhuangLab/BioInstaller.

Project docker image: https://hub.docker.com/r/bioinstaller.

Operating system(s): Platform independent

Tested Operating system(s): MAC OS 10.13.6, Centos 7.1, Ubuntu 16.04, and Windows 10 (limited functions)

Tested browsers: Google Chrome (v68), Safari (v11.1.2), and Firefox (v61.0.2)

Programming languages: R, HTML, CSS and JavaScript

Requirements: R (> 3.3.0), Shiny (R package), Opencpu (R package), and a web browser

Optional functions: Maftools (R package), conda (Python package), spack (Python package), and docker

License: MIT

Funding

This work was supported by the National Natural Science Foundation of China (No. 81570122, 81770205), the National Key Research and Development Program (No. 2016YFC0902800), the Shanghai Municipal Education Commission-Gaofeng Clinical Medicine Grant Support (20161303). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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