systemPipeShiny(SPS) a Shiny-based R/Bioconductor package that extends the widely used systemPipeR workflow environment and data visualization with a versatile graphical user interface.

There is an online demo of systempipeShiny. This application is hosted by a small server. Do not use it for production activities. Heavy tasks will crash it and disconnect you from it.


To install the package, please use the BiocManager::install command:

if (!requireNamespace("BiocManager", quietly=TRUE))
BiocManager::install("systemPipeShiny", build_vignettes=TRUE, dependencies=TRUE)

To obtain the most recent updates immediately, one can install it directly from GitHub as follow:

if (!requireNamespace("BiocManager", quietly=TRUE))
BiocManager::install("systemPipeR/systemPipeShiny", build_vignettes=TRUE, dependencies=TRUE)

If you are on Linux, you may also need the following libraries. Different distributions may have different commands, but the following commands are examples for Ubuntu:

sudo apt-get install libcurl4-openssl-dev
sudo apt-get install libv8-dev
sudo apt-get install libxm12-dev
sudo apt-get install libssl-dev

Quick start

This is a basic example which shows how to use systempipeShiny package:

## Imports the library
## Creates the project directory

By default, a project folder is created and named as SPS_+DATE. This project folder provides all the necessary files to launch the application. If you are using Rstudio, global.R file will be opened automatically and this is the only file you may need to make custom changes if there is any.

## Launching the interface


For additional details regarding the functions of systempipeShiny, please consult the vignette available here.

Please use for reporting bugs, issues or for suggesting new features to be implemented.


Click to expand the list of internal notes.

Run to update the website (./docs/ folder)


Running roxygen



See github projects

Try the systemPipeShiny package in your browser

Any scripts or data that you put into this service are public.

systemPipeShiny documentation built on March 16, 2021, 6:01 p.m.