Comments (1)
Hi @yankeqiang,
This sounds really interesting. I think conceptually NicheNet can be used on quantitative proteomics data as well. The ligand-target matrix indicates the potential that a certain ligands regulates the expression of a certain gene. Since proteomics gives you the expression at the protein level, I think there is no problem in using NicheNet on it. I just never had done it myself.
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Related Issues (20)
- Is there a helper function to draw the plot in the description ? HOT 1
- Inquiry about Signaling and Gene Regulatory Networks Data in Omnipath and NicheNet HOT 1
- Query: AUPR HOT 1
- Error while plotting a ligand-receptor interaction network
- Error running nichenet_seuratobj_aggregate on v5 Seurat obj HOT 7
- Assistance Needed: nichenetr Package Installation Error in R
- Zenodo Data Inquiry HOT 1
- Identifying bonafide ligand-receptor pairs in the updated ligand-receptor database (V2)
- SeuratV5 HOT 4
- Error finding log fold change information of ligands from sender cells (Seurat V5 object) HOT 6
- How exactly the ligand activity were calculate? HOT 1
- I cannot run the "get_weighted_ligand_receptor_links" and "prepare_ligand_receptor_visualization" while I have nichnetr installed HOT 2
- Preferable metric to infer cell-to-cell communication HOT 1
- what is ligand_tf_matrix for?? HOT 1
- `get_exprs_avg` changes underscore to hyphen in cell type names
- How to choose the best ligand to continue analysis with the potential ligand?
- How should I assign a pathway/pathways to the target genes when running nichenetr? HOT 3
- cannot complete assign_ligands_to_celltype HOT 1
- missing function for circos plot visualization HOT 2
- I can't install nichenet HOT 1
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