Setup

Installing Software

R and RStudio

You can download and install R and RStudio through the posit.co website.

Install both R and RStudio

The Posit website should automatically detect your operating system and link to the correct download file.

Mac users

On Mac iOS, the download file should be .tar.gz format

PC users

On windows operating system, the downloaded file should be .exe format

Lockdown Browser

For BIOL90042 Masters Students Only: Install Lockdown Browser using this link https://download.respondus.com/lockdown/download.php?id=113132090

Files and Folders

New Desktop Folder

Create a new folder on your Desktop named BIOL90042_workshops

Download data files

Download the .zip file via this link, and save inside BIOL90042_workshops

Unzip data files

Unzip the data.zip directory. You should see 4 files. Do not unzip any other files at this stage.

RStudio Code

Open RStudio

Create new .R file

File > New File > R Script

Copy & Paste

Copy the code block below and paste into the new file:

Copy icon

Hint - Click the clipboard icon at top right in the code block below!

## Setting up R for workshops 

## Install tidyverse 
install.packages("tidyverse") 

## Install conflicted
install.packages("conflicted") 

## Install readxl & writexl
install.packages("readxl")
install.packages("writexl")

## Install ggrepel  
install.packages("ggrepel") 

## Install tidyrstats 
install.packages("tidyrstats") 

##Install patchwork
install.packages("patchwork") 


## Install and Load packages required for RNAseq 

if (!requireNamespace("BiocManager", quietly = TRUE)) 

  install.packages("BiocManager") 

BiocManager::install("RNAseq123") 


## Install tidyheatmaps 
install.packages("tidyheatmaps") 

## Install tidymodels
install.packages("tidymodels") 

## Install vip
install.packages("vip") 

## Install xgboost
install.packages("xgboost") 

## Install ggridges
install.packages("ggridges")

## Load all libraries

library(tidyverse)
library(conflicted)
library(readxl)
library(writexl)

library(ggrepel) 
library(tidyrstats) 
library(patchwork) 

library(edgeR) 
library(limma) 

library(tidyheatmaps) 

library(tidymodels)
library(vip)
library(xgboost)

library(ggridges)

Save the new file

File > Save the new file inside your BIOL90042_workshops folder, with name setup.R

Run the code

Select all the code with mouse click & drag, or CMD A (mac) / CTRL A (pc), and clicking ‘Run’.

Note this will take some time and there may be errors, so let us know and we can assist.