I want to define two clusters of cells in my dataset and find marker genes that are specific to one and the other. Is there a way to do this in Seurat? Say, if I produce two subsets by the SubsetData function, is there a way to feed them into some other function that would calculate marker genes? If not, what other packages would you recommend for doing that?

If you look here:

https://satijalab.org/seurat/seurat_clustering_tutorial_part2.html

I just need a way to define ident myself, the number of levels (2) and assign numbers to each cell (0, 1), and then run DE between 0 and 1 clusters which is obvious how to do afterwards.