Prerequisites and Installation

To get started, you will need to install the required software and download the necessary data. It is important to install R before installing RStudio so that RStudio can automatically detect your R installation.

• Download R first from the CRAN website (version 4.2 or higher is recommended) here. Be sure to pick the R version specific to your operating system (Windows, macOS, or Linux), and install the software in the default directories prompted by the installer.

• Download RStudio Desktop only after R is fully installed here. Again, pick the RStudio version specific to your operating system, and install it in the default directory.

• Ensure your system has at least 8GB of memory, though 16GB or more is highly recommended.

• Download the required UBC data objects (.rds files) from this OSF link under the Data folder here. Unzip these files in your downloads folder.

---

Overview

Repository structure:

└── xenium_demo/
    ├── Readme.md  # Current file  
    ├── scripts/ 
    │   ├── Walkthrough.md
    │   ├── 0_Load_Packages.R
    |   ├── 1_Single_file_Demo.R
    │   ├── 2_Merging_Demo.R
    │   ├── 3_SingleR_lavel_transfer.R
    │   ├── 4_Differential_expression.R
    |

---

Open in Rstudio

To download and open the repo in Rstudio, do the following:

First download the repository:

• Click on the green button saying "code" at the top of this page
• Then Click on Download Zip
• In your downloads folder, unzip the file in the downloads folder itself (Note: Macs automatically unzip these files.)

Then Open Rstudio and:

• Click on file (top-left)
• Click on new project, then existing directory
• Navigate to your downloads folder and select the unzipped directory

Then, to begin demo:

• Navigate to the scripts folder
• Follow the scripts in numbered order (0 to 4)

NOTE: Make sure to run 0_Load_Packages.R and download the data before the workshop begins.