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BlishLab / scriabin

Analysis of cell-cell communication at single-cell resolution
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Usable for mouse datasets? #1

Closed bhavyaac closed 2 years ago

bhavyaac commented 2 years ago

Hello! This is a very exciting project, thank you for your hard work. I wanted to ask you here since I wasn't able to find this information in the manuscript: is Scriabin usable with mouse scRNA-seq datasets?

ajwilk commented 2 years ago

Hi there! Good question--yes, Scriabin can be used with any ligand-receptor pair database, and functions that require a ligand-receptor pair database (eg. GenerateCCIM) will take a custom list of ligand-receptor pairs by setting database = "custom" and passing character vectors of ligands and corresponding receptors to arguments ligands and recepts, respectively.

Ultimately, I have plans to automatically support standard mouse ligand-receptor databases in the package but haven't implemented this quite yet. In the meantime the approach I described above will work. I will also make sure this gets documented appropriately.

Do be aware there are caveats with using non-human data in the ligand activity predictions run by NicheNet (see https://github.com/saeyslab/nichenetr/issues/104)

I'll leave this open for the time being and circle back once I've documented as described

bhavyaac commented 2 years ago

Thank you for the information!

ajwilk commented 2 years ago

Mouse datasets are now usable by setting species="mouse" in the core functions that require a ligand-receptor database (eg. GenerateCCIM). Please re-install and let me know if you run into any issues!