CellPhoneDB [1] addresses the challenges of studying cell-cell communication in scRNA-seq and spatial data. It allows researchers to move beyond just measuring gene expression and delve into the complicated cellular communication world. By analyzing the scRNA-seq or spatial data through the lens of CellPhoneDB, researchers can identify potential signaling pathways and communication networks between different cell types within the tissue sample. Partek^® Flow^® wrapped the statistical analysis pipeline (method 2) from CellPhoneDB v5[1] for the purpose. 

CellPhoneDB task in Flow can be invoked in Exploratory analysis section by clicking the normalized counts data node (Figure 1). We recommend running CellPhoneDB on the normalized data directly, particularly the log normalized data.  

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Double click the Output matrix data node will open the task report in Data Viewer. It is another variant of heatmap that displays how  how genes of your interest interact with each other in the defined cell type pairs (Figure 5). The exampled plot also indicates the data are from two environments. For instructions on setting up the Micro environment file for your spatial study, refer to Figure 2. CellPhoneDB analysis classifies signaling pathways for genes of interest. These classifications are then used to annotate the heatmap within the task report. 

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