DOI: 10.18129/B9.bioc.systemPipeR    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see systemPipeR.

systemPipeR: NGS workflow and report generation environment

Bioconductor version: 3.8

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.

Author: Thomas Girke

Maintainer: Thomas Girke <thomas.girke at>

Citation (from within R, enter citation("systemPipeR")):


To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))

For older versions of R, please refer to the appropriate Bioconductor release.


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PDF R Script ChIP-Seq Workflow Template
HTML R Script Overview Vignette
PDF R Script Ribo-Seq Workflow Template
PDF R Script RNA-Seq Workflow Template
PDF R Script VAR-Seq Workflow Template
PDF   Reference Manual
Text   NEWS


biocViews Alignment, ChIPSeq, Coverage, DataImport, GeneExpression, GeneSetEnrichment, Genetics, ImmunoOncology, Infrastructure, MethylSeq, QualityControl, RNASeq, RiboSeq, SNP, Sequencing, Software
Version 1.16.1
In Bioconductor since BioC 3.0 (R-3.1) (4.5 years)
License Artistic-2.0
Depends Rsamtools(>= 1.31.2), Biostrings, ShortRead(>= 1.37.1), methods
Imports BiocGenerics, GenomicRanges, GenomicFeatures(>= 1.31.3), SummarizedExperiment, VariantAnnotation(>= 1.25.11), rjson, ggplot2, grid, limma, edgeR, DESeq2, GOstats, GO.db, annotate, pheatmap, BatchJobs
Suggests ape, RUnit, BiocStyle, knitr, rmarkdown, biomaRt, BiocParallel, BiocManager
SystemRequirements systemPipeR can be used to run external command-line software (e.g. short read aligners), but the corresponding tool needs to be installed on a system.
Depends On Me
Imports Me DiffBind, RNASeqR
Suggests Me systemPipeRdata
Links To Me
Build Report  

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Source Package systemPipeR_1.16.1.tar.gz
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Mac OS X 10.11 (El Capitan) systemPipeR_1.16.1.tgz
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