This is a Shiny App that assists formatting spatial proteomics/transciptomics data into an SPE (SpatialExperiment) object. Accepted data format includes inForm and HALO for spatial proteomics data and Visium, Xenium, MERSCOPE, and CosMX for spatial transcriptomics data. All data format that was not listed here can be read via "general" format.
To use the Shiny App, navigate to your local folder and use git to clone the SPIAT-shiny repo.
git clone https://github.com/TrigosTeam/SPIAT-shiny.git
If using RStudio, open the app.R file and click Run App to start the application;
If using command line, make sure you are in the SPIAT-shiny folder and enter Rscript app.R, and then paste the url into a browser to use the application. You can follow the video here to get started.
More video tutorials: