How to annotate clusters scleroderma skin cell types? Is there a possibility that skin will be added to the list? Thank you
Unfortunately, it is currently not possible to add custom tissue types directly in the Cellenics implementation of ScType. We understand that this feature would be valuable, and we are always working to improve our platform’s capabilities.
In the meantime, I can suggest some possible workarounds:
The authors of ScType suggest in their paper (https://www.nature.com/articles/s41467-022-28803-w ) that the community can propose new marker genes for cell type annotation. These can potentially be included in future versions of the ScType database. They recommend using GitHub’s “Pull Request” feature or directly emailing the authors. As we utilize the same marker gene database as ScType, any updates to the database would also become available within Cellenics.
Another option would be to download the rds object and perform the annotation outside of Cellenics. While this requires a bit more work, it provides a good deal of flexibility.
Alternatively, the only other way would be to manually annotate clusters using marker genes in Cellenics.
I hope this helps.