systemPipeShiny Documentation

systemPipeShiny (SPS) extends the widely used systemPipeR (SPR) workflow environment with a versatile graphical user interface provided by a Shiny App. This allows non-R users, such as experimentalists, to run many systemPipeR’s workflow designs, control, and visualization functionalities interactively without requiring knowledge of R. Most importantly, SPS has been designed as a general purpose framework for interacting with other R packages in an intuitive manner. Like most Shiny Apps, SPS can be used on both local computers as well as centralized server-based deployments that can be accessed remotely as a public web service for using SPR’s functionalities with community and/or private data. The framework can integrate many core packages from the R/Bioconductor ecosystem. Examples of SPS' current functionalities include:

  • A default interactive workflow module to create experimental designs, visualize and customize workflow topologies with previews, and programming free workflow execution within the application.
  • An interactive module with extensive plot options to visualize downstream analysis of a RNA-Seq workflow.
  • A quick ggplot module to make all variety of scientific plots from any user defined tabular data.
  • An extendable set of visualization functionalities makes it easy to design custom Shiny Apps under SPS framework without any knowledge of Shiny.
  • A ‘Canvas Workbench’ to manage complex visual results. It allows users to organize and to compare plots in an efficient manner combined with a session screenshot feature to edit scientific and publishable figures.
  • Three other supporting packages to help all users from beginners and advanced developers to extend under current SPS framework or on their own visualization apps.

Demos demos

View our online demo app:

Type and link option changed notes
Default full installation{blk} See installation full app
Minimum installation{blk} See installation no modules installed
Login enabled{blk} login_screen = TRUE; login_theme = "empty" no modules installed
Login and login themes{blk} login_screen = TRUE; login_theme = "random" no modules installed
App admin page{blk} admin_page = TRUE or simply add “?admin” to the end of URL of demos

For the login required demos, the app account name is “user” password “user”.

For the admin panel login, account name “admin”, password “admin”.

Please DO NOT delete or change password when you are using the admin features. will reset the app once a while, but this will affect other people who are trying the demo simultaneously.

Rstudio Cloud demo

There is an Rstudio Cloud project instance that you can also play with. You need to create a free new account. Two Bioconductor related modules - workflow & RNAseq are not installed. They require more than 1GB RAM to install and to run which is beyond the limit of a free account.


Use systempipe_docker for instructions.

Other packages in systemPipeShiny

Package Description Documents Function reference Demo
systemPipeShiny{blk} SPS main package website link demo{blk}
spsComps{blk} SPS UI and server components website link demo{blk}
drawer{blk} SPS interactive image editing tool website link demo{blk}
spsUtil{blk} SPS utility functions website link NA
Last modified 2022-11-03 : Update (e7d389ce)