systemPipeR swMATH ID: 28861 Software Authors: Backman, T.W.H; Girke, T. Description: systemPipeR: NGS workflow and report generation environment. R package for building and running automated end-to-end analysis workflows for a wide range of next generation sequence (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq. Important features include a uniform workflow interface across different NGS applications, automated report generation, and support for running both R and command-line software, such as NGS aligners or peak/variant callers, on local computers or compute clusters. Efficient handling of complex sample sets and experimental designs is facilitated by a consistently implemented sample annotation infrastructure. Instructions for using systemPipeR are given in the Overview Vignette (HTML). The remaining Vignettes, linked below, are workflow templates for common NGS use cases. Homepage: http://bioconductor.org/packages/devel/bioc/html/systemPipeR.html Dependencies: R Related Software: KEGG; R; STAR; TopHat; FactoMineR; ggplot2; edgeR; HISAT; Bioconductor; sva; JASPAR; TRAPLINE; bcbio-nextgen; CIPHER; Snakemake; Taverna; Galaxy; OLego; Bioconda; pathview Cited in: 2 Publications all top 5 Cited by 6 Authors 1 Akalin, Altuna 1 Franke, Verdan 1 Huynh-Thu, Vân Anh 1 Ronen, Jonathan 1 Sanguinetti, Guido 1 Uyar, Bora Cited in 2 Serials 1 Methods in Molecular Biology 1 Chapman & Hall/CRC Computational Biology Series Cited in 2 Fields 2 Biology and other natural sciences (92-XX) 1 Statistics (62-XX) Citations by Year