I recently analyzed a scRNA-seq dataset with transcriptome and protein measurements and I would now like to enrich signatures from other datasets on the resulting clusters using the AUCell algorithm. For those not familiar with this tool, genes in each cell are ranked from highest to lowest value and then the signatures are tested for their enrichment in the top X genes for each cell.
However, I realized that since I used the top2000 genes to calculate the joint space for transcriptome and protein markers, my denoised matrix is smaller than normal and I end up with having signatures with less than 20% overlap in genes in my dataset to test the enrichment.
I was wondering whether someone has had any experience already and how they overcame this bottleneck.
Thanks in advance,