I’ve been trying to look into receptor ligand interactions in my mouse datasets, but some of the tools like CellPhoneDB don’t work with mouse genes and require conversion to human orthologs. Is there any way in scanpy to convert mouse genes to human orthologs?
oh sweet, didn’t know squidpy had ligand receptor analysis part. Thanks a lot, I’ll try it out!
I tried running squidpy but moment I try to calculate permutations with sq.gr.ligrec it crashes the Kernel without any error message and restarts it. Not sure if my h5ad file is an issue, it’s a 20755 × 14644 matrix.
*Edit: size of the matrix was an issue and kernel was running out of memory, subsetting the data helped!