Type Package Title systemPipeR: NGS workflow and report generation environment Version 1.0.11 Date 2015-07-02

Description R package for building end-to-end analysis pipelines with automated report genera-tion for next generation sequence (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq. An important feature is support for running command-line soft-ware, such as NGS aligners, on both single machines or compute clusters. Instructions for us-ing systemPipeR are given in the Overview Vignette (PDF). The remaining Vignettes, linked be-low, are workflow templates for common NGS use cases