Hi, thank you so much for this wonderful resource. As someone who uses R mostly, is there any way to provide an rds file that includes both the raw counts and the normalized/integrated (with Harmony) object? Due to some issues with the conversion from an Anndata object to a Seurat object (e.g., https://github.com/mojaveazure/seurat-disk/issues/141), I'm struggling with adding the raw counts to the Anndata object and converting it to a workable Seurat object. If at all possible to provide the final object you worked with, it would be immensely appreciated for some exploratory work. I recognize this is extra work, so no worries if not possible! I'll continue to work on figuring this out. Thank you for considering.

Created by kamancherla
Sure, thank you for your kind words :) I really hope one of the methods will work for you. Kind regards, Marina
Hi @marina_terekhova, Thanks so much for that quick response! That's no worries at all! No inconvenience here - it's such a great dataset, I am grateful to you and your co-authors for sharing it in the first place. I will continue to see if I can figure out a way to convert it to a workable rds format. If so, I will update here with what I did in case it helps anyone else. Thank you.
Hi @kamancherla , As the study was performed before the Seurat v5 release, we did all the work for the subsets inside the Seurat v4, which do not support uploading the matrix with ~2mln of cells. That is why we have the rds files only for the subsets, but the final whole dataset was assembled in Python environment. I think the major issue why the seurat-disk is not working is the size of the dataset. Try to split the h5ad file into 2-3 parts and convert them separately. In case it doesn't work, the approaches that I can suggest to you are 1. using zellkonverter instead of seurat-disk (it is also suggested in the thread) or 2. splitting the data into smaller bins, saving it (even as a csv files), and later on assembling it inside the R environment. Sorry for any inconvenience. Kind regards, Marina

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