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.
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References in zbMATH (referenced in 3 articles )
Showing results 1 to 3 of 3.
- Akalin, Altuna: Computational genomics with R. With the assistance of Verdan Franke, Bora Uyar and Jonathan Ronen (2021)
- Kuan-Hao Chao, Yi-Wen Hsiao, Yi-Fang Lee, Chien-Yueh Lee, Liang-Chuan Lai, Mong-Hsun Tsai, Tzu-Pin Lu, Eric Y. Chuang: RNASeqR: an R package for automated two-group RNA-Seq analysis workflow (2019) arXiv
- Sanguinetti, Guido (ed.); Huynh-Thu, Vân Anh (ed.): Gene regulatory networks. Methods and protocols (2019)