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systemPipeRdata

This is the development version of systemPipeRdata; for the stable release version, see systemPipeRdata.

systemPipeRdata: Workflow templates and sample data


Bioconductor version: Development (3.19)

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 "4.4") and enter:


if (!require("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")
systemPipeRdata: Workflow templates and sample data HTML R Script
WF: Basic Single Cell Template HTML R Script
WF: BLAST Template HTML R Script
WF: Cheminformatics Drug Similarity Template 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 HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Alignment, ChIPSeq, Coverage, DataImport, ExperimentData, GeneExpression, GeneSetEnrichment, Genetics, ImmunoOncology, Infrastructure, MethylSeq, QualityControl, RNASeq, RiboSeq, SNP, Sequencing, WorkflowStep
Version 2.7.0
License Artistic-2.0
Depends
Imports methods, Biostrings, BiocGenerics, jsonlite, remotes
System Requirements
URL https://github.com/tgirke/systemPipeRdata https://systempipe.org/
See More
Suggests GenomicFeatures, GenomicRanges, IRanges, Rsamtools, ShortRead, rtracklayer, RUnit, BiocStyle, knitr, rmarkdown, systemPipeR
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me systemPipeR, systemPipeShiny
Links To Me
Build Report Build Report

Package Archives

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

Source Package systemPipeRdata_2.7.0.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/
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