mouse support?

[betoCRUKScot]

Dear starCAT developers,

Does starCAT supports mouse cell annotation?

I had a look at the supplementary table 2 from the paper (an excel file).
Kotliar, Dylan et al. “Reproducible single-cell annotation of programs underlying T cell subsets, activation states and functions.” Nature methods, 10.1038/s41592-025-02793-1. 3 Sep. 2025, doi:10.1038/s41592-025-02793-1

I noticed that the genes are for human.

Is there an equivalent table for mouse?

Kind regards

[dylkot]

Hi @betoCRUKScot, currently the GEP catalog was derived only from human datasets. Ideally someone should do a similar analysis of mouse datasets but it hasn't been done yet to date. Sorry about that!

[betoCRUKScot]

Hi Dylan @dylkot, thank you for your answer.
Is building this GEP catalog something that I could do? :) if so, are there some steps to follow or recommendations?
Or would this imply generating new sequencing data (which is something that I can't do).
Kind regards,
Beto

[dylkot]

Hi, yes absolutely. You can follow the single dataset example for a reference built from one dataset or the multi dataset example for building a reference from multiple mouse datasets. The core of it is to run cNMF on at least one mouse dataset. Then one of the outputs will have ".starcat_spectra" in the file name and that is the catalog that can be passed as an input to starCAT. If you want to combine GEPs from multiple mouse T cell datsets then you would use the BuildConsensusReference class in this package