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cellgeni / sceasy

A package to help convert different single-cell data formats to each other
GNU General Public License v3.0
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Selecting assay type to convert in SCeasy #23

Closed RolantusdataExp closed 3 years ago

RolantusdataExp commented 3 years ago

Hi, Really enjoy this package! Way easier than other solutions. I have run into the issue that when I convert from seurat -> anndata it only takes my RNA assay (assay = RNA), but I would prefer to convert my SCTransformed assay instead. I can't find a way to do this in your vignette.

Best regards, Peter University of Southern Denmark

ShanSabri commented 3 years ago

I'm also interested on this topic. Also is it possible to include the Raw counts when converting Seurat --> AnnData?

nh3 commented 3 years ago

You could try passing assay=<assay_name> to the function. By default, <assay_name> is set to "RNA".

RolantusdataExp commented 3 years ago

Thanks for the reply, @nh3.

ShanSabri commented 3 years ago

@nh3 How about slot? Like what if I wanted to export the raw RNA counts in the anndata object?

nh3 commented 3 years ago

@nh3 How about slot? Like what if I wanted to export the raw RNA counts in the anndata object?

You could pass main_layer="counts".