Chuan Xu
Chuan Xu
@Xyihang, you can find relevant information at Table S2 of the paper [here](https://doi.org/10.1016/j.cell.2023.11.026)
@malonzm1, `predicted_labels` is only dependent on gene expression matrix, but `majority_voting` will be influenced by the neighborhood graph if it is constructed from scVI latent space.
@malonzm1, depends, but `majority_voting` is usually more readable.
@smallsmalltown, as I remember, Harmony will not change the expression values but produce only the corrected latent space. To predict your data using CellTypist, you need to provide a normalized...
@Flu09, celltypist does not use the latent space to predict cell types, namely, the `predicted_labels` is independent from the latent space. The `majority_voting` however may be impacted by the latent...
@Flu09, it's safer to do this for each dataset separately to ensure sufficient gene overlap between your data and the model used.
@cchd0001, if two classes A and B are not matched, it is likely that one of them (for example, A) aligns with another cell type C which has a greater...
@NPTL1201, for undetermined cell types, you can assign them as "UNASSIGNED" to make partial annotations. CellHint will incorporates these cells into every cell type group and thus expands the size...
@jhylwq123, yes, cell type names were already unified across organs.
@yxwucq, sounds interesting. Can you point me to a paper or document that uses LLM for such purpose? THX!