(SPS) extends the widely used systemPipeR
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
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.
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.shinyapp.io 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.