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This time, approximately 500 cells show positive expression for the CD4 marker gene. This means that the protein data is also less sparse than the gene expression data, which further helps to reliably detect sub-populations.

T cells

Based on the exploratory analysis above, most of the CD3 positive cells are in the group of cells in the bottom right corner of the UMAP plot. This is likely to be a group of T cells. We will now examine this group in more detail to identify T cell sub-populations.

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