Introduction

During the workshop, we will be using the statistical computing software called R to perform calculations and produce data visualisations.

Fortunately, we have a cloud-based version of R available to us at the following website: R Studio Cloud.

Please follow the steps below to:

  1. Create Account

  2. Create Project

  3. R Markdown

  4. Install Packages

Create Account

Navigate to the R Studio Cloud website and click on the GET STARTED FOR FREE button.

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Select a free acount. This will provide us with enough resources for the workshop (1 GB RAM, 1 CPU and 25 hours per month). In reality this is a tiny resource allocation - many computational operations in genomics require exponentially more resources which are performed on high performance compute (HPC) clusters or more recently, on the cloud.

../../_images/r_cloud_2.png

Enter a valid email address and fill out the rest of the information (password, name). R Studio Cloud will send you an email with a link to verify your email address. Click on the link to verify your email address - you should now be able to log into R Studio Cloud.

Select R Studio Cloud from the options listed below:

../../_images/r_cloud_3.png

Create Project

Once your account has been created, you need to create a project for the workshop. This is to let R Studio Cloud know what type of environment you want to work in, and allows them to track your resource usage.

Select New Project > New R Studio Project.

../../_images/r_cloud_4.png

R Markdown

During the workshop we want to be able to create PDF or HTML documents containing our code and code outputs. To do this, we will be using the R Markdown document type.

In your project workspace, select File > New File > R Markdown…

You will be prompted to install packages, select yes.

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You can now make R Markdown documents, which we will return to later in the workshop.

Install Packages

In your project workspace, you have some very basic packages that come pre-installed. We will need to install more packages for the workshop.

Installing packages to your workspace is analogous to installing apps on your phone via the App Store / Google Play except we are installing packages from Bioconductor - a home for open source bioinformatics software.

In the console, please insert the following lines of code to install the required packages:

install.packages("ggplot2")
install.packages("pheatmap")
install.packages("ggpubr")
install.packages("rcolorbrewer")
install.packages("cluster")
install.packages("gplots")
install.packages("caret")
install.packages("e1071")