search

sqjin / CellChat

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data
GNU General Public License v3.0
613 stars 140 forks source link

Doing stats across two datasets in merged CellChat #453

Open bayankizil opened 1 year ago

bayankizil commented 1 year ago

Hello!

Thank you so much for developing this incredibly useful tool! I merged two datasets with the same cell types to compare signaling from cell type 1 (het) to cell type 2 and cell type 1 (wt) to cell type 2. In netVisualBubble, I can set the threshold of the p-value to identify significant interactions. However, can I do a statistical test using this tool to see whether there is a significant difference between the strength of a certain signaling communication across the two datasets?

sqjin commented 1 year ago

@bayankizil You can check the tutorial and there is one part we combine the differential expression analysis. The rankNet function also implement a statistical test by setting 'do.stat = TRUE'.