Hello,
How can I add fibroblast and breast cancer cell types to the scType in the Annotate cluster, not the custom cell set? Thanks in advance.
Hi Juhee,
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 two 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. If this is an avenue you’re interested in exploring, we can assist you through a small consulting project.
Please let me know if you would like to discuss these options in more detail or if you have any other questions.