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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. These data were published and shared by M. Kapustina, details here

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.