How to use AUCell? Which of your cells are actively expressing a gene set? In R I use AUCell to label cells in a Seraut object which are enriched for user provided genes. This method is useful if you want to find which cells express a certain set of genes. These can be putative identity markers, response genes of some biological pathway, or any set of genes you are interested in. AUCell is a widely used and cited package.
I also show you how to use the PangloaDB, which is an extremely useful database for cell identity markers in human and mouse single-cell data.
Notebook:
github.com/mou...
0:00 Intro
0:28 Collecting genes and data
1:44 Preparing genes and data
5:15 Running AUCell
11:16 Caveats
Негізгі бет Single-cell gene set activity with AUCell
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