I need to analyze co-expression of 10 genes among populations of single cells. My approach is:
1. Download scRNA-seq data for selected genes only.from many studies and cells.
Is there any mechanism for downloading scRNA-seq read data for just selected genes of interest? As long as I have a unique identifier for each cell and study, I can do this independently for each gene, one at a time, but I'm unsure what resource to use. I would like to use data from as many studies as possible.
2. Analyze coexpression of reads across samples.
Is this even statistically reasonable? What is the best way to normalize reads between samples to permit unbiased and fair comparison?