Difficulty Annotating Brain Organoid Sample Using HNOCA Dataset

[nicola-palmieri]

Hello HNOCA Team,

I'm having trouble loading the HNOCA dataset into R for cell type annotation of my brain organoid samples. I've tried various packages (SingleR, BPCells), but the loading process doesn't complete, even after waiting 15 minutes. Is there a recommended method or package for efficiently loading the 40GB HNOCA dataset into R?

Thank you
Nicola

[zhisonghe]

Hi, Nicola,

Unfortunately the complete HNOCA dataset will be likely too large to be loaded as a whole in R, mostly because of the limitation on the sparse matrix non-zero item number there. If you think it is helpful we can generate an atlas subset for analysis on R.

All the best,
Zhisong

[nicola-palmieri]

That would be great! I also tried in many different ways in Python but did not manage. I am trying to characterize a dataset of brain organoids.