search

sqjin / CellChat

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data
GNU General Public License v3.0
632 stars 144 forks source link

using cellchat with Xenium data #652

Open GhobrialMoheb opened 1 year ago

GhobrialMoheb commented 1 year ago

Hi @sqjin Just wanted to ask, if it is possible to use cellchat with Xenium data

Thanks

sqjin commented 1 year ago

@GhobrialMoheb How many genes do you have in this data? For the imaging-based spatial data, one challenging is the few number of sequenced genes, which leads to very few number of signaling genes for cell cell communication analysis.

hchoiHiLung commented 11 months ago

For example, if there are only 20 genes (10 L-R pairs) from the gene panel of the Xenium dataset that can also be found in the CellChat database, will this small number make the analysis using CellChat invalid (e.g. will this violate some statistical assumptions etc.)?

sqjin commented 10 months ago

@hchoiHiLung I just updated identifyOverExpressedGenes to allow the identification of over-expressed genes without performing DE. And thus you can perform the analysis using only a few number of L-R pairs.