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

Bioconductor version: Release (3.19)

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>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


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

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


biocViews GeneExpressionWorkflow, ImmunoOncologyWorkflow, Workflow
Version 1.28.0
License Artistic-2.0
Depends R (>= 3.3.0), edgeR, gplots,, GO.db, BiocStyle
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Suggests knitr, knitcitations, rmarkdown
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Follow Installation instructions to use this package in your R session.

Source Package RnaSeqGeneEdgeRQL_1.28.0.tar.gz
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