Selecting spots from different sections and performing DEG analysis

[DecodeGenome]

Hi, I am trying to select spots from different sections and do differential gene expression analysis, like your example of Neighborhood analysis, how to perform such analysis within STUtility package?

Your help with detailed script will be highly appreciated.

Thanks,

Wei

[ludvigla]

Hi,

If you wish to manually select spots, you can use the ManualAnnotation function.

se <- ManualAnnotation(se)

This will open up a shiny application where you can select spots and assign different labels in your tissue sections. When you quit the application (quit button), the annotations will be returned to you Seurat object meta data in a column called "labels". With these labels it's pretty straightforward to proceed with differential expression analysis (DEA) using for example FindMarkers. You can just have a look at Seurats tutorials for DEA or the one provided on the STUtility website.

/Ludvig