In the data exploration section, I would like to know which dataset/tool is used to annotate the clusters with a particular cell type. For example, I can annotate the clusters with ScType-Immune system-human, but how is this annotation being done?
Hi Joshua, thanks for posting this question here.
The automatic annotation in Cellenics is using ScType, a marker gene-based tool developed by Aleksandr Ianevski et al.
It uses a marker genes database which was build using CellMarker, PanglaoDB, and 15 novel cell types with corresponding marker genes added by manual curation of more than 10 papers.
The current version of the ScType database contains a total of 3,980 cell markers for 194 cell types in 17 human tissues and 4,212 cell markers for 194 cell types in 17 mouse tissues.
You can find more details in their paper and in their github repo.
I hope this answered your question. Let me know if you have any other questions!