destiny
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Is density normalization applied to the kernel?
Hi,
I would like to know if the parameter density_norm represents a choice to wether normalize or not the Gaussian kernel. I'm particularly interested if this is the case because that's how Setty et al (https://www.nature.com/articles/s41587-019-0068-4) define their kernel prior to computing the diffusion operator, which seems an especially robust approach to single-cell data.
If that is not the case, is there any way to make it into destiny? In other words, how hard-coded is this into the implementation?
Edit: Sorry, I have one more question. Is it possible to set the alpha parameter to the diffusion operator?