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!
Does anyone has any experience with CDseq? I havent managed yet to perform deconvolution. Could this be to the read depth of my experiment (2-10M Quantseq reads). I have also tried the Monaco et al. approach, which also didnt work.
Any suggestions are welcomed.
Please let me know if you ever had success. I have been able to deconvolve bulk sample using single cell reference, but still have remaining questions regarding results. Also the CDseq github may be a more appropriate place to ask such questions.
Did you manage to run CDSeqR? I am just trying to run it but not sure how? Can you please let me know if the deconvolution worked for you and how did you do it?
Kind Regards, Shweta Johari