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saezlab / liana

LIANA: a LIgand-receptor ANalysis frAmework
https://saezlab.github.io/liana/
GNU General Public License v3.0
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LIANA for bulk RNA seq? #64

Closed alhadjil closed 1 year ago

alhadjil commented 1 year ago

Hi,

thanks for this nice package, which works smoothly on scRNASeq datasets. Is it possible to use LIANA for two (or more) bulk RNASeq datasets for CCC?

Thanks!

dbdimitrov commented 1 year ago

Hi @alhadjil,

Thanks. LIANA does not currently support bulk RNA-seq.

An easy way to apply it to bulk would be to use the stats from your DE contrasts join them to known LR interactions (coming e.g. from LIANA's databases), and simply calculate a mean between ligand and receptor stats.

Daniel