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satijalab / sctransform

R package for modeling single cell UMI expression data using regularized negative binomial regression
GNU General Public License v3.0
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Disk-based data #63

Open willtownes opened 4 years ago

willtownes commented 4 years ago

It would be awesome to be able to run sctransform on data that are too big to fit in memory (eg, HDF5 files accessed through something like DelayedArray). Is this a feature that would be considered for the package in the future? We are hoping to wrap sctransform to facilitate interoperability with SingleCellExperiment objects via the scry package (kstreet13/scry#14 )

ChristophH commented 4 years ago

I agree that it would be awesome, but so far this feature has only been tested in a previous development version of sctransform (through loomR). I will look into the DelayedArray and HDF5Array packages to figure out what I need to do to make sctransform work with on-disk data.

PedroMilanezAlmeida commented 1 year ago

I believe glmGamPoi can handle DelayedArray out-of-the box, right?

Would it be of interest to have at least the "v2 flavor" workflow compatible with DelayedArray?

saketkc commented 1 year ago

Thanks for the suggestion! We will have some updates soon.

PedroMilanezAlmeida commented 1 year ago

Just checking if there were any updates on this that I may have missed. Any help would be appreciated.