Introduction

👋🏻 What is this workshop about?

The course will give an overview on how to conceptually approach bioinformatics. During the three days of the course we will dive into a bulk RNA-seq experiment and carry out the main steps of a standard data analysis pipeline.

Program Outline

Day 1 🤓

• Setup RStudio or Posit
• Get familiar with the Posit interface
• Learn about bulk RNA-seq data processing
• Download the data needed for the workshop

Day 2 🧑🏼‍💻

• Learn about data normalization
• Learn about the edgeR package
• Explore different normalization methods
• Normalize the data with functions provided by the edgeR package
• Perform diagnostic and exploratory analysis on the data

Day 3 🧞‍♂️

• Learn about the theory behind differential expression analysis
• Perform differential expression analysis using edgeR
• Visualize the results
• Perform further downstream analysis on interesting gene groups

How To Reach Us

• Jacopo Arrigoni (jacopo.arrigoni@ifom.eu)
• Mattia Toninelli (mattia.toninelli@ifom.eu)

Feel free to drop us an e-mail if you have any curiosity or question!

Credits

Some of the images and inspiration came from other tutorials available online, in particular this work for images and this work for some of the information regarding data normalization. All of the code present within this site was developed and is readily implementable in RStudio using RMarkdown.

License

All of the material in this course is under a Creative Commons Attribution license (CC BY 4.0) which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.