Workflow from Scientific Research

Overview of niche-DE Ligand-Receptor pipeline: We aim to determine which ligand-receptor pairs are active between the ligand expressing niche cell type n and the receptor expressing index cell type i . (1): Using the ligand-target potential matrix from niche-net, we extract the top K downstream genes for each ligand. (2): Using these downstream genes, we calculate a ligand activity score using the niche-DE T-statistic vector between index-niche pair (i,n) for the top K downstream genes. (3): Ligands with an activity score greater than a threshold value and their corresponding receptor(s) are screened for expression in the niche cell type.

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