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To explore more, the task of Explore CellPhoneDB results allows users to filter CellPhoneDB results by specifying the cell type pairs and genes of interest.  See Figure 4 on how to run the task. Its GUI is simple and easy to understand. For each option, the grey colored description explains more details (Figure 2).  If the dataset working on is single cell RNA-Seq, no Micro environment file is needed. However, if the dataset is spatial, most likely you would like to provide the Micro environment file because of its spatial contents. By default 0.10 will be used as threshold to select which cells are used for the analysis in the cluster. 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.

Double click the CellPhoneDB result data node will open the task report in Data Viewer. It is a heatmap that summarizes how many significant interactions identified in the cell type pairs (Figure 3).

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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