Regressing on cell cycle genes in scRNA-Seq

Question

[oriolebaltimore]

Dear group members, While analyzing single cell RNA-Seq data from early stage tumor and advanced stage tumors, is it recommended to normalize the cell cycle genes. If we regress the G1, G2M and S phase genes there are some downstream complications if one wants to find differences between quiescent vs. differentiating cells. I observe many vignettes are normalizing these genes.
For studying tumor cells, does this makes sense. I dont' like to do it for my analysis and I don't know pros of doing cell cycle regression. Any thoughts and suggestions are appreciated. Also are there any publications that discussed this. I might be wrong too as I am new to scRNA-seq of tumors.

Thanks -Adrian.

[igor]

There are many vignettes that show this just to say that it is possible. As you already mentioned, there are potential problems with this approach. This may explain why most publications do not take this approach.