How do I see a list of marker genes for a specific cluster?
In the Data Exploration module, a marker heatmap for the Louvain clusters is shown by default. Hovering over the heatmap will show the gene names (screenshot 1). You can also zoom into particular areas (clusters) of interest by scrolling, in order to expand that area and view gene names (screenshot 2):
To see a full list of marker genes for a specific cluster you can perform Differential Expression, comparing your cluster of interest to all other cells (for all samples). You’ll find the Differential Expression tab on the right side of the ‘Genes’ tile in the Data Exploration module. The DE results show the full list of genes that are markers for the selected cluster. The list is ordered by descending logFC by default - the marker genes will be shown at the top. If you reverse the order of the list, to show by ascending logFC, then the genes that are absent in the selected cluster will be shown.
