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 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 log normalized data directly.  

To run CellPhoneDB task, 

• Click a Normalized counts data node
• Click the Exploratory analysis section in the toolbox
• Click CellPhoneDB

The GUI is simple and easy to understand. The SVD dialog is only asking to select the number of singular values to compute (Figure 2).  By default 100 singular values will be computed if users don't want to compute all of them.  However, the number could be adjusted manually or typed in directly.  Simply click the Finish button if you want to run the task as default.

Figure 1. Interface of SVD task in Partek Flow.

The task report for SVD is similar to PCA. Its output will be used for downstream analysis and visualization, including Harmony (Figure 3).

Figure 2. Example workflows to demonstrate downstream analysis and visualization of SVD output for scATAC-seq data.

References

1. Cusanovich, D., Reddington, J., Garfield, D. et al. The cis-regulatory dynamics of embryonic development at single-cell resolution. Nature 555, 538–542 (2018). https://doi.org/10.1038/nature25981

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