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systemPipeR: NGS workflow and report generation environment

Bioconductor version: Release (3.1)

R package for building end-to-end analysis pipelines with automated report generation for next generation sequence (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq. An important feature is support for running command-line software, such as NGS aligners, on both single machines or compute clusters. 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>

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PDF R Script ChIP-Seq Report Template
PDF R Script RNA-Seq Report Template
PDF R Script VAR-Seq Report Template
HTML R Script Overview Vignette
PDF   Reference Manual


biocViews Alignment, ChIPSeq, Coverage, DataImport, GeneExpression, GeneSetEnrichment, Genetics, Infrastructure, MethylSeq, QualityControl, RNASeq, SNP, Sequencing, Software
Version 1.2.23
In Bioconductor since BioC 3.0 (R-3.1) (1 year)
License Artistic-2.0
Depends Rsamtools, Biostrings, ShortRead, methods
Imports BiocGenerics, GenomicRanges, GenomicAlignments, VariantAnnotation, rjson, grid, ggplot2, limma, edgeR, DESeq2, GOstats, GO.db, annotate, pheatmap, BatchJobs
Suggests ape, RUnit, BiocStyle, knitr, rmarkdown, biomaRt, GenomicFeatures, BiocParallel
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
Suggests Me
Build Report  

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Package Source systemPipeR_1.2.23.tar.gz
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Mac OS X 10.6 (Snow Leopard) systemPipeR_1.2.23.tgz
Mac OS X 10.9 (Mavericks) systemPipeR_1.2.23.tgz
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