systemPipeRdata

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see systemPipeRdata.

systemPipeRdata: NGS workflow templates and sample data


Bioconductor version: 3.9

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 "3.6") 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")
ChIP-Seq Workflow Template HTML R Script
RIBO-Seq Workflow Template HTML R Script
RNA-Seq Workflow Template HTML R Script
systemPipeRdata: NGS workflow templates and sample data HTML R Script
VAR-Seq Workflow Template HTML R Script
Reference Manual PDF
README Text
NEWS Text

Details

biocViews Alignment, ChIPSeq, Coverage, DataImport, ExperimentData, GeneExpression, GeneSetEnrichment, Genetics, ImmunoOncology, Infrastructure, MethylSeq, QualityControl, RNASeq, SNP, Sequencing
Version 1.12.0
License Artistic-2.0
Depends methods
Imports BiocGenerics
System Requirements
URL https://github.com/tgirke/systemPipeRdata
See More
Suggests RUnit, BiocStyle, knitr, rmarkdown, systemPipeR
Linking To
Enhances
Depends On Me
Imports Me RNASeqR
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package systemPipeRdata_1.12.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan)
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