Find markers from multiple groups using bulk RNA-seq data
1 answer
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)
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