Workflow Package: rnaseqGene

RNA-seq workflow: gene-level exploratory analysis and differential expression

Bioconductor version: Release (3.8)

Here we walk through an end-to-end gene-level RNA-seq differential expression workflow using Bioconductor packages. We will start from the FASTQ files, show how these were aligned to the reference genome, and prepare a count matrix which tallies the number of RNA-seq reads/fragments within each gene for each sample. We will perform exploratory data analysis (EDA) for quality assessment and to explore the relationship between samples, perform differential gene expression analysis, and visually explore the results.

Author: Michael Love [aut, cre]

Maintainer: Michael Love <michaelisaiahlove at>

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


To install this package, start R and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
BiocManager::install("rnaseqGene", version = "3.8")


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



HTML R Script RNA-seq workflow at the gene level


biocViews GeneExpressionWorkflow, Workflow
Version 1.4.0
License Artistic-2.0
Depends R (>= 3.3.0), BiocStyle, airway, Rsamtools, GenomicFeatures, GenomicAlignments, BiocParallel, magrittr, DESeq2, apeglm, vsn, dplyr, ggplot2, pheatmap, RColorBrewer, PoiClaClu, ggbeeswarm, genefilter, AnnotationDbi,, ReportingTools, Gviz, sva, RUVSeq, fission
Suggests knitr, rmarkdown
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: