I have scRNA-seq data from two species, human and mouse, for the same tissues at several developmental time points. I am interested to compare the data between the species to identify common (and different) cell-types and lineages etc. Are there any best practise guidelines or advice on how to use scanpy for this?
Naively, I imagine running the analysis separately on the human and mouse matrixes, rather than treating them as batches within the same analysis (because of the heterogeneity). Then later, one could compare the annotated cell populations and expressed genes (via mapping the human-mouse orthologs) and somehow ‘align’ the cell-lineages. I expect this to be non-trivial, given the divergence of the species and the not direct equivalence of different tissues and developmental time points.
I hope this isn’t too broad to ask here and thank you for any help!