The systemPipeR project provides a suite of R/Bioconductor packages for designing, building, and executing end-to-end data analysis workflows on local machines and high-performance computing (HPC) systems, while simultaneously generating publication-quality analysis reports.
For additional information, please visit the project site here.
If you use systemPipeR in published research, please cite:
- Zhang L, Cassol D, Gongol B, Girke T (2026). systemPipeR: a multipurpose workflow management system for reproducible data analysis. NAR Genomics and Bioinformatics, 8(2), lqag032. doi:10.1093/nargab/lqag032
- Backman TWH, Girke T (2016). systemPipeR: NGS workflow and report generation environment. BMC Bioinformatics, 17(1), 388. doi:10.1186/s12859-016-1241-0
Or run citation("systemPipeR") in R.