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Dear URD Team,
I'm experiencing significant delays with calcDM when analyzing ~58,000 cells. My current command:
obj.urd <- calcDM(obj.urd, knn = 10, genes.use = obj.urd@var.genes)
I've already:
Reduced highly variable genes to 500
Lowered knn to 10
Tried basic parallel setup
Could you advise:
Optimal parameters for large datasets?
Proper way to enable multi-core processing?
Any progress tracking methods for calcDM?
Other optimization strategies?
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