systemPipeRdata

DOI: 10.18129/B9.bioc.systemPipeRdata    

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

systemPipeRdata: NGS workflow templates and sample data

Bioconductor version: 3.8

systemPipeRdata is a helper package to generate with a single command NGS workflow templates that are intended to be used by its parent package systemPipeR. The latter is an environment for building end-to-end analysis pipelines with automated report generation for next generation sequence (NGS) applications such as RNA-Seq, RIBO-Seq, ChIP-Seq, VAR-Seq and many others. Detailed examples for using systemPipeRdata are given in systemPipeR's overview vignette.

Author: Thomas Girke

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

Installation

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

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("systemPipeRdata")

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

Documentation

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

browseVignettes("systemPipeRdata")

 

HTML	R Script	Overview Vignette
PDF		Reference Manual
Text		README
Text		NEWS

Details

biocViews	Alignment, ChIPSeq, Coverage, DataImport, ExperimentData, GeneExpression, GeneSetEnrichment, Genetics, Infrastructure, MethylSeq, QualityControl, RNASeq, SNP, Sequencing
Version	1.10.0
License	Artistic-2.0
Depends	methods
Imports	BiocGenerics
LinkingTo
Suggests	RUnit, BiocStyle, knitr, rmarkdown, systemPipeR
SystemRequirements
Enhances
URL	https://github.com/tgirke/systemPipeRdata
Depends On Me
Imports Me	RNASeqR
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	systemPipeRdata_1.10.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan)
Source Repository	git clone https://git.bioconductor.org/packages/systemPipeRdata
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/systemPipeRdata
Package Short Url	http://bioconductor.org/packages/systemPipeRdata/
Package Downloads Report	Download Stats