I have a CropSeq dataset to analyze, and I am confused on whether I should regress out cell cycle or not for downstream identification of clusters, differentially expressed genes, and gene set enrichment analysis.
According to Seurat's standard single-cell analysis, it is advisable to use SCtransorm and regress out the cell cycle effects in order to proceed with downstream analysis (https://satijalab.org/seurat/archive/v3.1/cell_cycle_vignette.html)
However, according to the paper which pioneered CropSeq data analysis https://www.sciencedirect.com/science/article/pii/S0092867416316609, and the respective github repository https://github.com/mhorlbeck/ScreenProcessing, the authors just identify the cell cycle phase of each cell, but they don't regress out the cell cycle effect when normalizing the data.
So my question is: Should I regress out cell cycle effects in my CropSeq data analysis or not?
Thank you very much in advance. Eleni