Comparing cell populations with different amounts of cell

sqjin / CellChat

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data

GNU General Public License v3.0

639 stars 146 forks source link

Comparing cell populations with different amounts of cell #229

Open michaelkutza opened 3 years ago

michaelkutza commented 3 years ago

Hi there,

I currently analyzing a dataset with the same cell types in two conditions. Unfortunately most cells belong to one condition. Does cellchat have a way to 'regress' that out in the compared analysis?

Thanks for developing such a lovely tool!

sqjin commented 3 years ago

@michaelkutza Why not remove these cell groups before running cellchat? You can also use the subsetCellChat function or define sources.use and targets.use in certain functions.

michaelkutza commented 3 years ago

@sqjin I want to compare the two conditions. Is it be feasible if 60-80% of all cells belong to one condition?

sqjin commented 3 years ago

@michaelkutza Based on my experience, this is unexpected.