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.