systemPipeRdata

DOI: 10.18129/B9.bioc.systemPipeRdata    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see systemPipeRdata.

systemPipeRdata: NGS workflow templates and sample data

Bioconductor version: 3.11

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

Details

biocViews Alignment, ChIPSeq, Coverage, DataImport, ExperimentData, GeneExpression, GeneSetEnrichment, Genetics, ImmunoOncology, Infrastructure, MethylSeq, QualityControl, RNASeq, RiboSeq, SNP, Sequencing, WorkflowStep
Version 1.16.2
License Artistic-2.0
Depends methods
Imports BiocGenerics, devtools
LinkingTo
Suggests RUnit, BiocStyle, knitr, rmarkdown, systemPipeR
SystemRequirements
Enhances
URL https://github.com/tgirke/systemPipeRdata
Depends On Me
Imports Me RNASeqR
Suggests Me systemPipeR
Links To Me
Build Report  

Package Archives

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

Source Package systemPipeRdata_1.16.2.tar.gz
Windows Binary
macOS 10.13 (High Sierra)
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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: