tgirke/systemPipeR: 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.

Getting started

Package details

AuthorThomas Girke
Bioconductor views Alignment ChIPSeq Coverage DataImport GeneExpression GeneSetEnrichment Genetics ImmunoOncology Infrastructure MethylSeq QualityControl RNASeq ReportWriting RiboSeq SNP Sequencing Workflow
MaintainerThomas Girke <>
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
tgirke/systemPipeR documentation built on May 23, 2023, 1:37 p.m.