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How to obtain cell-cell interaction list

Hi,

im doing Ligand-receptor interaction analysis with single cell data. I have two questions.

1) there are several ligand-receptor databases. How can i combine these databases and use that for LR interaction?

2) after cell-cell interaction analysis, how to obtain final results including the interacting cell types, ligands,receptors,potential targets in signal receiver cell type, etc?

any answer would be much appreciated.

Thank you

seurat scrna-seq lr-interaction cellphonedb cellchat
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written by Song • Song

2 answers

Hi miyeok, For your first question, the answer is yes. If I remember correctly, both cellphone DB and cellchat integrate several databases together when doing analysis. As for getting the final interacting celltypes/ligands/etc, different software has different criteria. For example, CellphoneDB provides a interaction P value for you to select the candidates.

Good luck

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written by shiyang_bio • shiyang_bio

Thank you so much!!

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written by Song • Song

I often use LIANA, which is a framework that combines 7 methods and 16 different databases for ligand-receptor analysis. You can either run each method/resource indipendently or you can combine multiple into one final result.

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written by fracarb8 fracarb8

Thank you so much. i'll check :)

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written by Song • Song

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