Analysis of Differential Gene Expression of bulk RNA-seq data using “DESeq2” in RStudio
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RNA-Seq is a high-throughput sequencing method used for unbiased detection and quantification of messenger RNA molecules, allowing the identification of genes and pathways underlying normal and pathological conditions. RNA-seq sequencing services are increasingly affordable which has led to the proliferation of published data available in public repositories accessible for everyone’s use and reanalysis. Therefore, the knowledge on how to analyze this type of data is becoming an increasingly valuable skill.
Join us in learning how to perform some basic differential gene expression of bulk RNA-seq data available on GREIN - GEO RNA-seq Experiments Interactive Navigator. We will use RStudio, a free and open-source software that provides a friendly environment to run R packages such as “DESEq2”, which is one of the methods used to analyze bulk RNA-seq data and find differentially expressed (DEX) genes.
This workshop is designed for: biomedical researchers with none to minimal knowledge of command language or R programming. Limited to 10 seats.
You will learn how to:
- Import data files into RStudio
- Load R packages
- Run “DESeq2”
- Save processed data files into your computer (e.g. normalized counts, DEX genes table)
- Perform basic data visualization (e.g. PCA plot, MA plot)
- Bring a laptop with R and RStudio installed and running.
- Prework documentation with instructions on how to install R and RStudio will be sent to you a week prior to the workshop to help you get ready.
- We will also provide you with the files of an RNA-seq dataset publicly available on NCBI’s GEO Datasets
Attendees to this workshop may be interested in attending the following: