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 is the development version of systemPipeR; for the stable release version, see systemPipeR.

systemPipeR: NGS workflow and report generation environment

Bioconductor version: Development (3.4)

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

Details

biocViews Alignment, ChIPSeq, Coverage, DataImport, GeneExpression, GeneSetEnrichment, Genetics, Infrastructure, MethylSeq, QualityControl, RNASeq, RiboSeq, SNP, Sequencing, Software
Version 1.7.2
In Bioconductor since BioC 3.0 (R-3.1) (1.5 years)
License Artistic-2.0
Depends Rsamtools, Biostrings, ShortRead, methods
Imports BiocGenerics, GenomicRanges, GenomicFeatures, SummarizedExperiment, VariantAnnotation, rjson, ggplot2, grid, limma, edgeR, DESeq2, GOstats, GO.db, annotate, pheatmap, BatchJobs
LinkingTo
Suggests ape, RUnit, BiocStyle, knitr, rmarkdown, biomaRt, 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 DiffBind
Suggests Me
Build Report  

Package Archives

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

Package Source systemPipeR_1.7.2.tar.gz
Windows Binary systemPipeR_1.7.2.zip
Mac OS X 10.9 (Mavericks) systemPipeR_1.7.2.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/systemPipeR
Package Short Url http://bioconductor.org/packages/systemPipeR/
Package Downloads Report Download Stats

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