systemPipeRdata

DOI: 10.18129/B9.bioc.systemPipeRdata  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see systemPipeRdata.

systemPipeRdata: Workflow templates and sample data

Bioconductor version: 3.16

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 "4.2") and enter:

if (!require("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		NEWS

Details

biocViews	Alignment, ChIPSeq, Coverage, DataImport, ExperimentData, GeneExpression, GeneSetEnrichment, Genetics, ImmunoOncology, Infrastructure, MethylSeq, QualityControl, RNASeq, RiboSeq, SNP, Sequencing, WorkflowStep
Version	2.2.0
License	Artistic-2.0
Depends
Imports	methods, Biostrings, BiocGenerics, jsonlite, remotes
LinkingTo
Suggests	GenomicFeatures, GenomicRanges, IRanges, Rsamtools, ShortRead, rtracklayer, RUnit, BiocStyle, knitr, rmarkdown, systemPipeR
SystemRequirements
Enhances
URL	https://github.com/tgirke/systemPipeRdata https://systempipe.org/
Depends On Me
Imports Me	RNASeqR
Suggests Me	systemPipeR, systemPipeShiny
Links To Me
Build Report

Package Archives

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

Source Package	systemPipeRdata_2.2.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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