Is there a way of annotating the clusters with a custom gene list? Or somehow supplement the ScType approach?
thank you for posting your question on the Community forum.
No, there is no easy way to annotate clusters with a custom gene list. Currently, it is also not possible in the Cellenics platform to supplement ScType with a custom gene list.
I suggest two things you can try with your custom gene list that might help you annotate your cells, but neither is exactly a cluster annotation method.
Create a heatmap with your custom gene list:
From Plots and Tables, select the Heatmap. There, select Custom genes under Gene selection, and supply your list. If you are lucky, some clusters show up as clearly expressing those genes and you can use this to annotate those clusters. For cluster annotation, you have to return to Data Exploration.
This is a fast method, because you can insert your list in one go in the Gene selection. However, it is also likely you get no clear results from this method.
Create cell sets based on the expression levels of genes:
In Data Exploration, you can create Custom cell sets by filtering on the expression levels of genes (see this post in the forum).
This is definitely more work than the first option, but also more likely to give you insights from your data.