systemPipeRdata

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see systemPipeRdata.

systemPipeRdata: Workflow templates and sample data

Bioconductor version: 3.13

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 "4.1") 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")

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 HTML R Script

Reference Manual PDF

README Text

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Alignment, ChIPSeq, Coverage, DataImport, ExperimentData, GeneExpression, GeneSetEnrichment, Genetics, ImmunoOncology, Infrastructure, MethylSeq, QualityControl, RNASeq, RiboSeq, SNP, Sequencing, WorkflowStep

Version 1.20.0

License Artistic-2.0

Depends methods

Imports BiocGenerics, jsonlite, remotes, GenomicFeatures, GenomicRanges, IRanges, Rsamtools, ShortRead, rtracklayer

System Requirements

URL https://github.com/tgirke/systemPipeRdata

Suggests RUnit, BiocStyle, knitr, rmarkdown, systemPipeR

Linking To

Enhances

Depends On Me

Imports Me RNASeqR

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_1.20.0.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/

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