systemPipeR Documentation

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The analysis of Next-generation sequencing (NGS) data remains a major obstacle to the efficient utilization of the technology. While substantial effort has been invested on the development of software dedicated to the individual analysis steps of NGS experiments, insufficient resources are currently available for integrating the individual software components within the widely used R/Bioconductor environment into automated workflows capable of running the analysis of most types of NGS applications from start-to-finish in a time-efficient and reproducible manner.


To address this need, we have developed the R/Bioconductor package systemPipeR. It is an extensible environment for both building and running end-to-end analysis workflows with automated report generation for a wide range of NGS applications. Its unique features include a uniform workflow interface across different NGS applications, automated report generation, and support for running both R and command-line software on local computers and computer clusters. A flexible sample annotation infrastructure efficiently handles complex sample sets and experimental designs.

To simplify the analysis of widely used NGS applications, the package provides pre-configured workflows and reporting templates for a wide range of NGS applications that are listed on the Workflow Collection page of this site. Additional workflow templates will be provided in the future. systemPipeR accelerates the extraction of reproducible analysis results from NGS experiments. By combining the capabilities of many R/Bioconductor and command-line tools, it makes efficient use of existing software resources without limiting the user to a set of predefined methods or environments.


systemPipeR is freely available for all common operating systems from Bioconductor. Its GitHub repository is here.


This project is funded by NSF award ABI-1661152.

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