Xenium_DataAnalysis_Input

[RViuj]

Hi,
As part of a research study, I received the following outputs from our Spatial Research facility to work with. I am not sure what kind of downstream analysis I could do using the files I received. However, I want to analyse cell clustering, neighbourhood, cell cell interaction and gene of interest specific analysis. The study includes data from treated and untreated cancer tissue samples.

In the analysis folder, I could find clustering, diffexp, pca and umap subfolders with csv files. May I know how I could combine gene expression data from the individual treated and untreated samples to compare and get results or use individual sample data to generate plots to show inter tumour heterogeneity between the individual samples?
I did go through Seurat's informative link below.
https://satijalab.org/seurat/articles/seurat5_spatial_vignette_2#mouse-brain-10x-genomics-xenium-in-situ
However, I was unable to figure out the input data file I could use to start the analysis. Any potential Seurat tutorial web links to use and learn to do the analysis will be very much appreciated. I am a beginner and I hope you don't mind helping/guiding me with the questions above or anything you consider could be useful !
Thank you,
RV.