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data2intelligence / SpaCET

Spatial Cellular Estimator for Tumors
GNU General Public License v3.0
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Suggestion : use BiocParallel instead of Parallel #12

Open BenjaminDEMAILLE opened 1 year ago

BenjaminDEMAILLE commented 1 year ago

Hi !

is it possible to change the parallel package from Parallel to BiocParallel ? Parallel RAM consumption is very high and BiocParallel don't copy data for each core

Thanks

beibeiru commented 1 year ago

Hi, Benjamin,

Thanks a lot for your suggestion. We will consider different parallel packages in the future. Based on our previous test, it costs ~8min to deconvolve a visium sample by using 8 cores. Currently, if the parallel RAM consumption is very high, you might reduce the number of cores in SpaCET.deconvolution.

Best, Beibei