Find markers from multiple groups using bulk RNA-seq data

Question

[ccfpwll]

In the case of bulk RNA-seq data from multiple groups, is there any way to find markers for each group? I think DEGs and PCA analysis will give some clues. But is there any way to do it like FindAllMarkers in Seurat for scRNA-seq?

Answer 1

[Chris S.]

You can create a Seurat object using the normalized counts and then select one of the sample table columns as the identify class and run FindAllMarkers. The row names in the samples data.frame should match the count columns.

bulk <- CreateSeuratObject(counts=rlog_matrix, meta.data=samples_df, assay = "RNA")
Idents(bulk) <- 'patient'
x <- FindAllMarkers(object = bulk, only.pos = TRUE, logfc.threshold = 0.5)