convert MC to Seuratobject format

[jadewu77]

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]

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]

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

[orenbenkiki]

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.

[zoan128]

Hi, I used metacell on Rstudio to analysis my Seurat data.
I find I can use scm_export_mat_to_sce to turn the ‘mat’ to ‘sce’,
but how can I add the 'mc.Rda' and 'mc2d.Rda' into my mat?

[orenbenkiki]

Not sure what the question is. The metacells package uses the AnnData format - imports/exports to/from this format are handled by the AnnData package.