systemPipe Workflow Environment

systemPipeR and systemPipeShiny full documentation!

systemPipe (SP) is a generic toolkit for designing and running reproducible data analysis workflows. The environment consists of three major modules implemented as R/Bioconductor packages.

  • systemPipeR (SPR) provides core functionalities for defining workflows, interacting with command-line software, and executing both R and/or command-line software, as well as generating publication-quality analysis reports.

  • systemPipeShiny (SPS) integrates a graphical user interface for managing workflows and visualizing results interactively.

  • systemPipeWorkflow (SPW) offers a collection of pre-configured workflow templates.


All the packages are freely available for all common operating systems from Bioconductor.


This project is funded by NSF award ABI-1661152.

Last modified 2021-10-10: Bot build site (d0c34823)