Tutorial to perform Differential Gene Expression Analysis with R and RStudio.
Download and install R : https://cran.r-project.org/bin/windows/base/
Download and install RStudio : https://www.rstudio.com/products/rstudio/download/#download
In RStudio Console type the following commands to install the libraries needed by FastTrack:
Install Bioconductor
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(version = "3.13")Install DESeq2 and hgu133plus2.db from Bioconductor
BiocManager::install("DESeq2")
BiocManager::install("hgu133plus2.db")Install all other libraries
install.packages("pheatmap")
install.packages("ggplot2")
install.packages("readxl")
install.packages("writexl")
install.packages("tibble")
install.packages("scales")
install.packages("viridis")
install.packages("tidyr")Download the repository and open the file UserGuide.nb.html (or AdvancedUserGuide.nb.html) with your browser and follow the instructions.
Part of the code comes from :
https://genviz.org/module-04-expression/0004/02/01/DifferentialExpression/
https://bioconductor.org/packages/devel/workflows/vignettes/maEndToEnd/inst/doc/MA-Workflow.html