I am analysing a 10x Visium spatial dataset than contains 4 images and the corresponding outputs from Space Ranger. I would like to analyse and compare the DE genes from 2 areas of the same image. The data is a slice from mouse colon and some of the colon is tumour and some not - based on the pathologists drawing (see below the area labelled ‘T’). What package or method would be best suited to this task? Thanks
