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@zrlewis zrlewis commented May 22, 2025

I needed to extract all cells from a certain subclass. This function allows one to specify the taxonomic level and name of the branch within that level and subset down to all cells/nuclei within that group. It creates an .h5ad output so that users can do downstream analyses on this subset.

I am not certain whether you want to have this as its own page or just fold it into tutorial 2b or another one. It might be good to have a list of the purpose of each notebook (2a, 2b, 2c) to refer to in the parent document because the purpose of each notebook is not evident from their titles alone.

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