My lab does a lot of single cell RNAseq of samples that include tumor cells. I have a pipeline in place that reduces dimension, clusters cells, and automatically assigns cell type labels to those clusters (mostly using
SingleR). However, I do not currently have a way to differentiate tumor cells from normal cells, which would allow me to perform other downstream analyses such as copy number variation using
inferCNV. Are there any tools in R/Python/Bash etc. that would allow me to differentiate between those two cell types, or is doing so manually using biomarkers the best option? I'd like for the process to be as objective / reproducible as possible.