Workflow Package: RnaSeqGeneEdgeRQL

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

Bioconductor version: Release (3.8)

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>

Citation (from within R, enter citation("RnaSeqGeneEdgeRQL")):

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("RnaSeqGeneEdgeRQL", version = "3.8")

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 1.4.0
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
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

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