To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("systemPipeR")

In most cases, you don't need to download the package archive at all.

systemPipeR

   

This package is for version 3.0 of Bioconductor; for the stable, up-to-date release version, see systemPipeR.

systemPipeR: NGS workflow and report generation environment

Bioconductor version: 3.0

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 (PDF). The remaining Vignettes, linked below, are workflow templates for common NGS use cases.

Author: Thomas Girke

Maintainer: Thomas Girke <thomas.girke at ucr.edu>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("systemPipeR")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("systemPipeR")

 

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

Details

biocViews Alignment, ChIPSeq, Coverage, DataImport, GeneExpression, GeneSetEnrichment, Genetics, Infrastructure, MethylSeq, QualityControl, RNASeq, SNP, Sequencing, Software
Version 1.0.12
In Bioconductor since BioC 3.0 (R-3.1) (1.5 years)
License Artistic-2.0
Depends Rsamtools, Biostrings, ShortRead, methods
Imports BiocGenerics, rjson, grid, ggplot2, limma, edgeR, DESeq2, GOstats, GO.db, annotate, pheatmap, BatchJobs
LinkingTo
Suggests ape, RUnit, BiocStyle, 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.
Enhances
URL https://github.com/tgirke/systemPipeR
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source systemPipeR_1.0.12.tar.gz
Windows Binary systemPipeR_1.0.12.zip
Mac OS X 10.6 (Snow Leopard) systemPipeR_1.0.12.tgz
Mac OS X 10.9 (Mavericks) systemPipeR_1.0.12.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/systemPipeR/tree/release-3.0
Package Short Url http://bioconductor.org/packages/systemPipeR/
Package Downloads Report Download Stats

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