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tanaylab / metacells

Metacells - Single-cell RNA Sequencing Analysis
MIT License
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question about divide_and_conquer_pipeline #78

Closed CCCBBG closed 2 hours ago

CCCBBG commented 3 hours ago

Excuse me. May I have a question about divide_and_conquer_pipeline？ This is my code and results.Is this code or result reasonable?

metacell_results = mc.pipeline.divide_and_conquer_pipeline( ... adata, ... # target_metacell_size=40, ... target_metacell_umis=160000, ... random_seed=123456 ... ) set unnamed.var[selected_gene]: * -> False set unnamed.var[rare_gene]: 0 true (0%) out of 36601 bools set unnamed.var[rare_gene_module]: 36601 int32 elements with all outliers (100%) set unnamed.obs[cells_rare_gene_module]: 45116 int32 elements with all outliers (100%) set unnamed.obs[rare_cell]: 0 true (0%) out of 45116 bools set unnamed.var[selected_gene]: 6159 true (16.83%) out of 36601 bools set unnamed.obs[metacell]: 45116 int32s set unnamed.obs[dissolved]: 0 true (0%) out of 45116 bools set unnamed.obs[metacell_level]: 45116 int32s

Why is it displaying "set unnamed.obs[metacell]: 45116 int32s"? Is there any manuscript or similar reference available? Thank you very much for your software. I am really looking forward to hearing back from you.

CCCBBG commented 3 hours ago

Vignettes I mean

orenbenkiki commented 2 hours ago

It means there is a per-cell property saying which metacell each cell belongs to. SInce you have 45K cells the length of this data is 45K entries, each is an int32s.

https://github.com/tanaylab/metacells-vignettes

CCCBBG commented 2 hours ago

Thanks a lot！ Have a good day！