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tanaylab / metacells

Metacells - Single-cell RNA Sequencing Analysis
MIT License
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Number of metacells generated #18

Closed yuhanH closed 2 years ago

yuhanH commented 2 years ago

Hi, Is there a way to determine the number of metacells generated by divide_and_conquer_pipeline?

orenbenkiki commented 2 years ago

Intentionally no.

You should not expect the number of metacells to be the number of cell types or anything like that. The metacells concept is to have as many as possible metacells, as long as we get a reliable estimate of gene expression levels in each one, and then annotate these metacells with cell types (using various techniques, clustering being one).

That said, playing with the target_metacell_size will increase/decrease the size (and therefore the amount) of metacells. The default aims at ~160K UMIs per metacell (there's also a minimum of 12 cells per metacell); playing with this might make sense for specific data sets, but should be done with care.

yuhanH commented 2 years ago

Thanks for your rapid reply. Very helpful!