This workshop will provide an introduction to statistical methods and software for differential expression analysis based on RNA-seq read counts. All of the methods considered involve a negative binomial distribution for the counts as a starting point. In addition, the statistical methods all utilize some form of empirical Bayes analysis by which gene-specific error variances are ‘shrunk’ towards a common value or a trend obtained by fitting a smooth to a mean-variance plot. Analysis using the open source R packages, limma, edgeR and DESeq2, will be illustrated and compared. All three packages are available in Bioconductor, an open source project focused on the analysis of data from emerging biological assays.
RNA-Seq Analysis in R with DESeq2, edgeR, and limma
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Monday
October
27
2025
Type of Workshop:
Lecture
Time:
10:00am –
12:00pm
Workshop Location:
Zoom
Files for this workshop are available in Box.
Access FilesA video of this workshop is available at Cornell’s Video on Demand site.
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