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.
Feature:
Field
#You can install this package directly from CRAN by running (from within R):
install.packages('BioInstaller')
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)
Quality Control:
Alignment and Assembly:
Variant Detection:
Variant Annotation:
Utils:
Genome:
Others:
Databases:
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:
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.
R package:
Related Other Resources
Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License