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tanaylab / metacells

Metacells - Single-cell RNA Sequencing Analysis
MIT License
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convert MC to Seuratobject format #72

Open jadewu77 opened 2 months ago

jadewu77 commented 2 months ago

Hi metacell team,

When I used the metacell package, I generated metacells, but I am not used to the storage format of MC. Is there a way to convert MC to Seurat object format? Thank you.

aviezerl commented 2 months ago

Hi,

We currently recommend using metacell2 - the metacells python package, that supports export from anndata objects. Unfortunately, we do not yet support conversion to Seurat.

Aviezer

jadewu77 commented 2 months ago

I initially tried using Metacell2 for my analysis, but I encountered an issue where the task keeps getting suspended when using the mc.pl.collect_metacells function. The traceback suggests that the problem is related to thread and core management. I attempted to set the maximum number of threads, but this did not resolve the issue. Could you provide some guidance or suggest a solution for this problem? Thank you. @aviezerl

Untitled

orenbenkiki commented 2 months ago

Parallelism in Python seems fragile; whetever the problem is, it seems somewhere in the internals?

One thing you can do is to disable parallelism during collect_metacells using mc.ut.set_processors_count- that however would make it take much longer time. Alternatively, you might use a lower number of threads than the maximal and still get away with it.