Hello, I hope you are doing well. First of all, thank you for developing NicheNet. I find it to be a very useful and impressive framework for studying cell communication, and I have been exploring it for a project I am currently working on.
I have a methodological question regarding this project, and I wanted to ask for your opinion.
I am interested in studying organ-to-organ communication between two tissues. My idea is to identify ligands expressed in organ 1 using bulk RNA-seq data, and then study receptor expression (and potentially downstream effects) in organ 2 using single-cell RNA-seq /CITE-seq data.
I have been considering using NicheNet because, conceptually, it seems very relevant for ligand–target inference. However, I am unsure whether this framework can properly handle this type of setup, since the sender side would come from bulk RNA-seq while the receiver side comes from single-cell data.
Do you think NicheNet could be applied in this scenario? If yes, how would you approach the analysis? Or would you recommend another strategy better suited for studying inter-organ communication when integrating bulk RNA-seq with single-cell/CITE-seq data?
I would really appreciate your thoughts.
Thank you very much for your time.
Hello, I hope you are doing well. First of all, thank you for developing NicheNet. I find it to be a very useful and impressive framework for studying cell communication, and I have been exploring it for a project I am currently working on.
I have a methodological question regarding this project, and I wanted to ask for your opinion.
I am interested in studying organ-to-organ communication between two tissues. My idea is to identify ligands expressed in organ 1 using bulk RNA-seq data, and then study receptor expression (and potentially downstream effects) in organ 2 using single-cell RNA-seq /CITE-seq data.
I have been considering using NicheNet because, conceptually, it seems very relevant for ligand–target inference. However, I am unsure whether this framework can properly handle this type of setup, since the sender side would come from bulk RNA-seq while the receiver side comes from single-cell data.
Do you think NicheNet could be applied in this scenario? If yes, how would you approach the analysis? Or would you recommend another strategy better suited for studying inter-organ communication when integrating bulk RNA-seq with single-cell/CITE-seq data?
I would really appreciate your thoughts.
Thank you very much for your time.