systemPipeRdata

DOI: 10.18129/B9.bioc.systemPipeRdata    

systemPipeRdata: Workflow templates and sample data

Bioconductor version: Release (3.15)

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 "4.2") 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 2.0.1
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_2.0.1.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

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