Hello, I need to know if CEMiTool is suitable for the analysis of single cell data, as far as I understand it is primarily designed for bulk RNA Seq data. If I can use it, what are the required pre-processing steps on my single cell data with huge number of samples/cells?

At a high level, differential expression analysis of single cell data proceeds through the usual pre-processing steps, to clustering and identification of cell types, and then to comparisons between cells of the same type in different groups using pseudo-bulk data. According to the CEMiTool vignette you just need a matrix or data.frame containing your data, which is what the pseudo-bulk data will be, so presumably it's fine.