RnaSeqGeneEdgeRQL

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5

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

Bioconductor version: Development (3.24)

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")):

Yunshun Chen, Aaron Lun, Gordon Smyth. RnaSeqGeneEdgeRQL: Gene-level RNA-seq differential expression and pathway analysis using Rsubread and the edgeR quasi-likelihood pipeline. doi:10.18129/B9.bioc.RnaSeqGeneEdgeRQL, R package version 1.37.0, https://bioconductor.org/packages/RnaSeqGeneEdgeRQL.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

BiocManager::install("RnaSeqGeneEdgeRQL")

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("RnaSeqGeneEdgeRQL")

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

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R Script

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Details

biocViews	GeneExpressionWorkflow, ImmunoOncologyWorkflow, Workflow
Version	1.37.0
In Bioconductor since	BioC 3.5 (R-3.4) (9.5 years)
License	Artistic-2.0
Depends	R (>= 3.3.0), edgeR (>= 4.3.6), gplots, org.Mm.eg.db, GO.db, BiocStyle
Imports
System Requirements
URL	http://f1000research.com/articles/5-1438/v2

Suggests	knitr, knitcitations, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	RnaSeqGeneEdgeRQL_1.37.0.tar.gz
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)
macOS Binary (sonoma-arm64)
Source Repository	git clone https://git.bioconductor.org/packages/RnaSeqGeneEdgeRQL
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/RnaSeqGeneEdgeRQL
Package Short Url	https://bioconductor.org/packages/RnaSeqGeneEdgeRQL/
Package Downloads Report	Download Stats