Closed RolantusdataExp closed 3 years ago
I'm also interested on this topic. Also is it possible to include the Raw counts when converting Seurat --> AnnData?
You could try passing assay=<assay_name>
to the function. By default, <assay_name>
is set to "RNA"
.
Thanks for the reply, @nh3.
@nh3 How about slot? Like what if I wanted to export the raw RNA counts in the anndata object?
@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"
.
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