Seurat -Visualize biomarkers


With this tool user can visualize selected biomarkers with violin and feature plot. As input the user gives the Seurat R-object (.Robj) and the name of the biomarker of interest (for example MS4A1, LYZ, PF4...).



Violin plot shows the probability density at different expression levels of the gene for each cluster. The color coding of the clusters helps to see in which clusters the marker gene is expressed. Good marker genes will show strongly in a single cluster. The tSNE-plot is useful for viewing the expression of the selected marker gene in the context of all the cells and helps validate the specificity of the marker or the quality of the clustering.

For more details, please check the Seurat tutorials.