Generating volcano plots of high and low expressed gene in scRNAseq data?

Question

[michelle.tran]

Hi!

I have scRNAseq data and I want to create DEG lists between cells with high expression of a gene vs. low. Ultimately, I would like to generate a volcano plot to visualize this and see co-expression of markers between cells that express this gene and cells that don't express this gene as much.

What package is the best to use for this?

Thanks in advance

[ATpoint]

Do you need a package for the plot or for the DE analysis itself? Do you have experimental replicates per group or do you plan to treat every single cell as a replicate?

[michelle.tran]

For both ! No experimental replicates per group. Just want divide all cells by high expression of one gene vs low expression. Basically to help see co-expressed markers and markers inversely correlated

Answer 1

[jared.andrews07]

I'd just pull the cell names with low or high expression of your gene and feed them into Seurat's FindMarkers function, then feed the output into EnhancedVolcano.

[michelle.tran]

Thank you so much. This worked. I appreciate your help!