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. And run the installer.

• Download RStudio Desktop only after R is fully installed here. And run the installer.

• 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. And place it in the directory of your choice.

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Overview

TODO: The goal is not just to run code, but to explain why each step exists and what decisions users should think about during analysis.

└── xenium_demo/
    ├── Readme.md  # Current file  
    ├── scripts/ 
    │   ├── Walkthrough.md
    │   ├── 0_Load_Packages.R
    |   ├── 1_Single_file_Demo.R
    │   ├── Merging_raw.R
    │   ├── merging_harmony.R
    |

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Open in Rstudio

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

First download the repository:

• Click on the green button with "code"
• Then Click on Download Zip
• In your downloads folder, unzip the file to your desired directory

Then Open Rstudio and:

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

Then, to begin demo:

• Navigate to the scripts directory
• Follow the scripts in numbered order

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