systemPipeRdata

DOI: 10.18129/B9.bioc.systemPipeRdata    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see systemPipeRdata.

systemPipeRdata: NGS workflow templates and sample data

Bioconductor version: 3.9

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 "3.6") 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	ChIP-Seq Workflow Template
HTML	R Script	RIBO-Seq Workflow Template
HTML	R Script	RNA-Seq Workflow Template
HTML	R Script	systemPipeRdata: NGS workflow templates and sample data
HTML	R Script	VAR-Seq Workflow Template
PDF		Reference Manual
Text		README
Text		NEWS

Details

biocViews	Alignment, ChIPSeq, Coverage, DataImport, ExperimentData, GeneExpression, GeneSetEnrichment, Genetics, ImmunoOncology, Infrastructure, MethylSeq, QualityControl, RNASeq, SNP, Sequencing
Version	1.12.0
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_1.12.0.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	https://bioconductor.org/packages/systemPipeRdata/
Package Downloads Report	Download Stats