Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. It only takes a minute to sign up.
Sign up to join this community
I'm currently working with a seurat object and I'd like to calculate the expression values per gene for all cells within a particular cluster.
I've gone ahead and subsetted the cluster of interest.
tumor <- subset(x = data, idents = c("Tumor"), invert = FALSE)
How would I calculate the expression values per gene per cell?
FindAllMarkers
Finds markers (differentially expressed genes) for each of the identity classes in a dataset per ident.
No Seurat function is needed. In the seurat object "cells", you can access the raw counts or normalized counts using cells@assays$RNA@counts (raw counts) or cells@assays$SCT@data (SCT normalized data)
