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

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

cell rnaseq scrnaseq single
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updated by Kevin Blighe Kevin Blighe • written by michelle.tran • michelle.tran

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?

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written by ATpoint ATpoint

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

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written by michelle.tran • michelle.tran

1 answer

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.

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written by jared.andrews07 jared.andrews07

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

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written by michelle.tran • michelle.tran

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