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SingleR-inc / SingleR

Clone of the Bioconductor repository for the SingleR package.
https://bioconductor.org/packages/devel/bioc/html/SingleR.html
GNU General Public License v3.0
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can i annotate cells in specific cell types? #172

Closed hansonglee closed 3 years ago

hansonglee commented 3 years ago

Hi, I'm using SingleR for annotating my pbmc data.

I have annotated cells (CD4T cell, CD8T cell, B cell, monocyte and so on) and now, i want to assign annotated CD4T cells into more detailed subtypes like Th1, Th2, T reg..

Is there any way to specify main cell types (CD4T) to assign related fine clusters (Th1, Th2, T reg..)?

j-andrews7 commented 3 years ago

Sure, just split your input matrix (or SCE) by your initial annotations and run SingleR on each main cell type individually. You might consider splitting the reference dataset to use only the subtypes of interest as well (e.g. only use the T cell subtypes).