I am trying to infer the different cell types of my whole blood RNAseq experiment, as I can see there are a lot of tools available. I struggled past CDSeqR, which seems to be a new approach for the deconvolution of tissues and I was wondering if anyone has experience with CDSeq and if you think it is recommenable? If not, is there any other tool you can recommend? In my opinion CDSeqR has the advantage of not having to provide a reference dataset and it can estimate the amount of different celltypes as well as their proportions.
Furthermore, in the best case scenario I would like to deconvolute my dataset to specific (immuno) celltypes. Is this possible without a reference dataset or are there any online reference datasets (scRNAseq) that I can use to determine the celltypes? And would if not, would you just use the values provided in the cdseq result to correct in EdgeR analysis?
Thanks for any help!