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Hi!
As I was trying to reproduce your results, I came to the point where you "calculated PCA projections with 100 components on the log2 centered normalized data". I'm a newbie and the term "log2 centered normalized data" makes me feel confused.
In your code you achieve this through "cent_norm" function, it cannot be found though. Couldn't you share it with me or describe its functionality? e.g. first, log-transorm the data, second, normalize and so on.

(function may be found in line 132 of early_neurogenesis_only_V2_KNN_v1.m)