Celltype granularity

[Thapeachydude]

Hello,

another quick question: How granular should the cell type annotation be?
i.e. should we favour broad cell types (i.e. T-cell, epithelial, stromal) or should the cell type annotation be more granuar (i.e. provide subtypes like CD4 memory T-cells, CD8 naive T-cells) etc.

Many thanks!

[ForwardYang98]

In general, scNiche is robust to the granularity of cell population annotation, as shown in the Supplementary Fig.S9 of our article:

You could run scNiche with either broad cell type labels or more fine-grained labels. However, it is important to ensure that the dimensionality of this view remains balanced with that of other views.