Entering edit mode
18 months ago
angus.j.g.campbell
▴
10
Hi all,
Is there a method or package (R or python) which can compute a conservation score which includes enhancers (proximal and or distal) between mouse and human genes? I am training a model on single cell rnaseq data using mouse gene expression data to run it on human gene expression to detect a rare cell type. I am considering filtering genes out by their conservations score. What would be a good exclusion criteria using conservation?
Rather than doing this why not deriving a gene signature from these rare cells and scoring your human samples with it, for example using UCell. Then see whether it credibly exists, and validate using FACS.
Our lab only uses publicly available data we don't do experiments ourselves so FACS is out of the question. Also the training data was collected with FACS. Calling it a cell type is not entirely accurate its a transient cell state that we know is in human cells as well, but its a question of if the genes involved are the same.
Thanks for the suggestion about UCell I will try this out.