Luuk Harbers comments

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                                            Luuk Harbers

Node stack overflow error in dendro_data

Hi, I'm running into the same issue. Is there any update on this issue? Thanks a lot for your work! Luuk

Memory exceeded when running single cell data alignment

Hi @andrewprzh , Just commenting to let you know that I was running into the same issues. I have data from some custom spatial transcriptomics data with closer to a...

Memory exceeded when running single cell data alignment

@andrewprzh I realize it's a bit of an extreme scenario :') These are barcodes representing real spatial coordinates (so not really cell but for analysis purposes it doesn't matter). Each...

Memory exceeded when running single cell data alignment

> @ljwharbers > > Yes, the matrix is always stored in some way. Previously, IsoQuant was outputting the "long" format, but then we decided to use "wide" format for everything....

Memory exceeded when running single cell data alignment

@andrewprzh this is amazing, thanks! I'm testing it now and it runs smoothly so far, no memory issues (and this is with ~50 million barcodes!). Amazing work!

Memory exceeded when running single cell data alignment

Also follow-up from my side. I've ran the latest version with >50 million barcodes and there are no memory issues any more. The run time is (very) long due to...

Memory exceeded when running single cell data alignment

I think that ultimately the best option would be to, during processing, have the intermediate files in the 'linear' format and only in the final merging step transform it to...