systemPipeRdata

DOI: 10.18129/B9.bioc.systemPipeRdata    

This is the development version of systemPipeRdata; to use it, please install the devel version of Bioconductor.

systemPipeRdata: NGS workflow templates and sample data

Bioconductor version: Development (3.10)

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>

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

Installation

To install this package, start R (version "3.6") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.13.1
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_1.13.1.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

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