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.
Demo
View our online demo app:
Other packages in systemPipeShiny
Package | Description | Documents | Function reference | Demo |
---|---|---|---|---|
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SPS main package | website | link | demo |
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SPS UI and server components | website | link | demo |
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SPS interactive image editing tool | website | link | demo |
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SPS utility functions | website | link | NA |