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

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