.___        __                    .___             __  .__                  __          
|   | _____/  |________  ____   __| _/_ __   _____/  |_|__| ____   ____   _/  |_  ____  
|   |/    \   __\_  __ \/  _ \ / __ |  |  \_/ ___\   __\  |/  _ \ /    \  \   __\/  _ \ 
|   |   |  \  |  |  | \(  <_> ) /_/ |  |  /\  \___|  | |  (  <_> )   |  \  |  | (  <_> )
|___|___|  /__|  |__|   \____/\____ |____/  \___  >__| |__|\____/|___|  /  |__|  \____/ 
         \/                        \/           \/                    \/                
__________.__       .__        _____                            __  .__                 
\______   \__| ____ |__| _____/ ____\___________  _____ _____ _/  |_|__| ____   ______  
 |    |  _/  |/  _ \|  |/    \   __\/  _ \_  __ \/     \\__  \\   __\  |/ ___\ /  ___/  
 |    |   \  (  <_> )  |   |  \  | (  <_> )  | \/  Y Y  \/ __ \|  | |  \  \___ \___ \   
 |______  /__|\____/|__|___|  /__|  \____/|__|  |__|_|  (____  /__| |__|\___  >____  >  
        \/                  \/                        \/     \/             \/     \/   

Machine Learning Introduction 2023

By Gustaw Eriksson, gustaw.eriksson@ki.se

A quick and dirty run of the DESeq2 vignette on the parsilla dataset. Please download the DESeq2_workshop.Rmd and open it in RStudio. If you do not want to run the code, you can download either the .html or .pdf file to see the code and output without running it yourself.

If R and Rstudio is not installed, you can install R from here; https://www.r-project.org/ and RStudio from here; https://posit.co/download/rstudio-desktop/

After opening DESeq2_workshop.Rmd install BiocManager (done automatically) and the required packages by changing the install.packages.flag from TRUE to FALSE.

Thereafter, run all the code section to generate output.

The tutorial is fully based on DESeq2 vignette by Love et al. found here: http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#data-quality-assessment-by-sample-clustering-and-visualization

Enjoy!