How to enable multicore processing and verbosity

Nanostring-Biostats / SpatialDecon

The SpatialDecon library implements the SpatialDecon algorithm for mixed cell deconvolution in spatial gene expression datasets. (This algorithm also works in bulk expression profiling data.)

MIT License

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How to enable multicore processing and verbosity #52

Open borexino opened 1 year ago

borexino commented 1 year ago

I went through the documentation of spatialdecon and reverseDecon functions, however it seems that no arguments are implemented for multicore processing and verbosity.
Does anyone have any suggestions to enhance spatialdecon and reverseDecon performances?

maddygriz commented 1 year ago

Hi @borexino,

We have not seen an issue with the performance of SpatialDecon before so parallelization was not on our roadmap. Our customer support team will be able to help you with this. Please email support@nanostring.com with your issue.

Please include answers to the following questions in that email:

what platform are you running on (windows, mac)?
how many samples and genes are in your study?
how big is your reference profile?

Thanks, Maddy