The systemPipeR package provides a suite of R/Bioconductor for designing, building and running end-to-end analysis workflows on local machines, HPC clusters and cloud systems, while generating at the same time publication quality analysis reports.

For detailed information on usage, see the package vignette, by typing vignette("systemPipeR"), or more information on the project here:

All software-related questions should be posted to the Bioconductor Support Site:

The code can be viewed at the GitHub repository:


Backman TWH, Girke T (2016) systemPipeR: NGS workflow and report generation environment. BMC Bioinformatics 17 (1).


Daniela Cassol, Tyler Backman, Thomas Girke