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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.

R language, as the most popular programming language for statistics, biological data analysis, and big data, has enabled diverse and free R packages (>14000) for different types of applications. However, due to the lack of high-performance and open-source cloud platforms based on R (e.g., Galaxy for Python users), it is still difficult for R users, especially those without web development skills, to construct interactive and reproducible biological data analysis applications supporting the upload and management of files, long-time computation, task submission, tracking of output files, exception handling, logging, export of plots and tables, and extendible plugin systems.

The collection, management, and share of various bioinformatics tools/scripts and databases are also essential for almost all bioinformatics analysis projects.

Here, we established a new platform to construct interactive and reproducible biological data analysis applications based on R language. This platform contains diverse user interfaces, including the R functions and R Shiny application, REST APIs, and support for collecting, managing, sharing, and utilizing massive bioinformatics tools/scripts and databases.





#You can install this package directly from CRAN by running (from within R):


# install.packages("devtools")

Shiny UI overview

Note, the Shiny application of BioInstaller was migrated to bioshiny project. All shiny files in this package will deprecated soon.

In the new project, we will provides one-click method (command line and Shiny UI) to create bioshiny application and its plugins. We are also developing more free plugins of bioshiny for various bioinformatics data analysis.

# Start the standalone Shiny application
BioInstaller::web(auto_create = TRUE)

Contributed Resources

Support Summary

Quality Control:

Alignment and Assembly:

Variant Detection:

Variant Annotation:






You can use the BioInstaller in Docker since v0.3.0. Shiny application was supported since v0.3.5.

docker pull bioinstaller/bioinstaller
docker run -it -p 80:80 -p 8004:8004 -v /tmp/download:/tmp/download bioinstaller/bioinstaller

Service list:


How to contribute?

Please fork the GitHub BioInstaller repository, modify it, and submit a pull request to us. Especialy, the files list in contributed section should be modified when you see a tool or database that not be included in the other software warehouse.


Jianfeng Li


R package:


Related Other Resources

Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License