Before performing RNA-Seq exercises, you'll need the following software and packages on your device

Get base R

https://mirrors.nics.utk.edu/cran/

Install RStudio Desktop (posit) from this link

https://posit.co/downloads/

From an interactive R session or RStudio, install the following packages

if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")

BiocManager::install("AnnotationForge")
BiocManager::install("apeglm")
BiocManager::install("org.At.tair.db", character.only = TRUE)
BiocManager::install("clusterProfiler")
BiocManager::install("DESeq2")
BiocManager::install("EnhancedVolcano")
BiocManager::install("enrichplot")
BiocManager::install("GenomicFeatures")
BiocManager::install("GO.db")
BiocManager::install("pathview")
BiocManager::install("tximport")

install.packages("ggpubr")
install.packages("pheatmap")
install.packages("RSQLite")
install.packages("tidyverse")

It is recommended to check that these installs work by attempting to load each package using library(), for example:

library(AnnotationForge)
library(apeglm)
library("org.At.tair.db", character.only = TRUE)
library(clusterProfiler)
library(DESeq2)
library(EnhancedVolcano)
library(enrichplot)
library(GenomicFeatures)
library(GO.db)
library(pathview)
library(tximport)

library(ggpubr)
library(pheatmap)
library(RSQLite)
library(tidyverse)