search

sqjin / CellChat

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

Comparison analysis of multiple datasets with different cellular compositions. #220

Open charlesgwellem opened 3 years ago

charlesgwellem commented 3 years ago

Thank you for your very helpful package. A single cell RNA sequencing experiment was done in my lab some 3 years ago on cells that were sorted and treated with a profibrotic agent. I wish to see if these cells sorted 3 years ago play a role in the disease through interaction. I have found another single cell RNA seq data set online of the same disease performed in another lab, in another country but containing all cells of the tissue. Can I run cellchat between my previously sorted and sequenced cells and the new online data set, to see which other cells my previously sorted cells interract with?

sqjin commented 3 years ago

@charlesgwellem yes, you can use the default pipeline to do it.

sqjin commented 3 years ago

@charlesgwellem It is better you can use the same normalization methods for both datasets.

charlesgwellem commented 3 years ago

@sqjin Thank you very much. I also wish to ask if batch effects won't be an issue. Are there methods in cellchatr also robust to batch effects?

sqjin commented 3 years ago

@charlesgwellem CellChat does not have specific functions to address batch effects. I would suggest you to check the expression levels of housekeeping genes. If these genes show similar expression levels across different datasets, then there is only little batch effect.