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  • #52

Closed
Open
Created Sep 18, 2020 by Jeremy Mathews@s189701Developer

Generate QC Plot

In preparation for a Seurat analysis workflow, the addition of a Violin Plot to display QC for count results can be used to determine inputs for Seurat workflow.

@ghenry has an automated script to determine optimal cutoff values for filtering data. Use the violin plot code below and overlay it with markers of cutoff values.

If values are acceptable, then use "automatic" option in Seurat workflow, else use "manual" and select the cutoffs for filtering data by hand.

""" VlnPlot(object, features = c("nFeature_RNA", "nCount_RNA", "percent.mt"), ncol = 3) """

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