Find markers from multiple groups using bulk RNA-seq data
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3 months ago
ccfpwll • 0

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?

RNA-seq findMarkers bulk DEG • 222 views
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Entering edit mode
4 weeks ago
Chris S. ▴ 320

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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