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veltenlab / rnamagnet

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How to use this tool for human data? #1

Closed YiweiNiu closed 3 years ago

YiweiNiu commented 4 years ago

Hi,

Thanks for developing this nice tool!

I found that the ligand-receptor data in this package are for mice. I wonder if we could use this package along with interaction data from cellphonedb.

If the answer is yes, are there anything I should notice?

Any help would be appreciated.

velten-lab commented 3 years ago

Sorry for the delayed reply. Actually the evidence underlying these interactions is not really species specific, neither in our case, nor for cellphonedb as far as I understand. You can just translate the gene ids in the ligand-receptor table to human using biomart. Or you can download the cellphonedb interaction data and transform it to the format we were using. I hope that helps!

YiweiNiu commented 3 years ago

Thank you for your reply. It's not late at all. I would try it in our data.