Can be used to integrate massive bioinformatics resources, such as tool/script and database. It provides the R functions and Shiny web application. Hundreds of bioinformatics tool/script and database have been included.
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('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)
Alignment and Assembly:
You can use the BioInstaller in Docker since v0.3.0. Shiny application was supported since v0.3.5.
docker pull bioinstaller/bioinstallerdocker run -it -p 80:80 -p 8004:8004 -v /tmp/download:/tmp/download bioinstaller/bioinstaller
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.
Related Other Resources
Shiny application supported
Numbers increased of included items, especialy the databases
Use github forum
Add Opencpu, Shiny and Rstudio service in Docker container
Use 'Setting' module in Shiny application to manage the variables
Multiple resources file be supported
Adjust and set db, github, nongithub, web and docker in inst/extdata/config
Meta information of software and database be added in newly supported items
Decompress can be auto-recognized
change.info default is to write tempfile() now
Fixed a bug when set save.to.db to FALSE. It can raise installed fail
ANNOVAR databases can be download using inst/extdata/databases/ANNOVAR.toml
Move databases toml file to inst/extdata/databases/
local.source be supported (Don't need download the source code again when it were download already)
docker.search be added to download and search docker repo
craw.all.versions be added to crawl source code of all version (Sotwares or databases)
#R# CMD #R# marked the R CMD need to be runed
glue parse be supported
Softwares versions of github.cfg be fetched from github API
destdir and download.dir can be setted respectively
verbose default is TRUE, show log infomation
unlink()clean tests files fail on windows (force = TRUE)