systemPipeR: NGS workflow and report generation environment

systemPipeR is an R/Bioconductor package for building end-to-end analysis pipelines with automated report generation for next generation sequence (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and many others. An important feature is support for running command-line software, such as NGS aligners, on both single machines or compute clusters. This includes both interactive job submissions or batch submissions to queuing systems of clusters. Efficient handling of complex sample sets and experimental designs is facilitated by a well-defined sample annotation infrastructure which improves reproducibility and user-friendliness of many typical analysis workflows in the NGS area.

Installation

To install the package, please use the biocLite method as instructed here.

Usage

Instructions for running systemPipeR are given in its vignette (manual). The sample data set used in the vignette can be downloaded here. The expected format to define NGS samples (e.g. FASTQ files) and their labels are given in targets.txt and targetsPE.txt (latter is for PE reads). The run parameters of command-line software are defined by param files that have a simplified JSON-like name/value structure. Here is a sample param file for Tophat2: tophat.param. Templates for setting up custom project reports are provided as *.Rnw files in the vignettes subdirectory of this package. The corresponding PDFs of these report templates are linked here: systemPipeRNAseq, systemPipeChIPseq and systemPipeVARseq.