Workflow Package: RnaSeqGeneEdgeRQL

Gene-level RNA-seq differential expression and pathway analysis using Rsubread and the edgeR quasi-likelihood pipeline

Bioconductor version: 3.7

This workflow package provides, through its vignette, a complete case study analysis of an RNA-Seq experiment using the Rsubread and edgeR packages. The workflow starts from read alignment and continues on to data exploration, to differential expression and, finally, to pathway analysis. The analysis includes publication quality plots, GO and KEGG analyses, and the analysis of a expression signature as generated by a prior experiment.

Author: Yunshun Chen, Aaron Lun, Gordon Smyth

Maintainer: Yunshun Chen <yuchen at wehi.edu.au>, Gordon Smyth <smyth at wehi.edu.au>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("RnaSeqGeneEdgeRQL")

Documentation

To view available workflows for the version of this package installed in your system, start R and enter:

browseVignettes("RnaSeqGeneEdgeRQL")

 

HTML

R Script

From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline

Details

biocViews	GeneExpressionWorkflow, Workflow
Version	1.2.3
License	Artistic-2.0
Depends	R (>= 3.3.0), edgeR, gplots, org.Mm.eg.db, GO.db
Imports
LinkingTo
Suggests	knitr, knitcitations
SystemRequirements
Enhances
URL	http://f1000research.com/articles/5-1438
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Suggests Me
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Build Report