13 Analysis example

• Differential expression example

• Info on other tests

Link out directly? https://swbioinf.github.io/spatialsnippets/e_DEPseudobulk_insitu.html

NB: I’ll probably update that material to include some spatial plots.

• Code to load whole dataset

13.1 Spatially informed differntial expression

This particular tests is quite simple - and doesn’t use spatial information. However, if we define some groups in a spatial way, we can use the same approach to test spatial hypotheses;

e.g. Given some cancer samples, identify cancer and stroma microenviromnemt. (NB: How to do that? Potentially with the ‘BuildNicheAssay’ functionality see here)

• Expression in T cells within tumour regions vs normal tissue:
  • (T cells within tumour niche) - (T cells in stromal niche)
• Cancer cell expression in immune hot vs cold region
  • (Cancer cells near T-cells) - (Cancer cells not near T-cells)