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Download R and R Studio

  1. Go to the CRAN website and follow the instructions to download and install R.
  2. Download and install RStudio.

Installing additional packages

Open RStudio and install the following packages.

## To install needed CRAN packages:
install.packages("tidyverse")
install.packages("GGally")
install.packages("caret")
install.packages("gmodels")
install.packages("rpart")
install.packages("rpart.plot")
install.packages("dendextend")
install.packages("randomForest")
install.packages("mlr3")
install.packages("devtools")

## To install needed Bioconductor packages:
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install()
BiocManager::install(c("limma", "edgeR"))

# To install libraries from GitHub source
library(devtools)
install_github("vqv/ggbiplot")

In case you encounter issues with ggbiplot, please have a look at this GitHub issue.

Load them to make sure they were successfully installed.

# Load packages
library(ggbiplot)

library(tidyverse) # working with data frames, plotting
library(GGally)
library(caret)
library(gmodels)
library(rpart)
library(rpart.plot)
library(randomForest)

library(dendextend)
library(mlr3)


library(edgeR)      # cpm, etc -- RNA-Seq normalization
library(limma)      # lmFit, etc -- fitting many models