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Closes #867

Here I'm adding a new chunk to remove the non-detected genes from the SCE object before building the rankings for AUCell. This is mostly important because we calculate the max rank using all possible genes rather than just the genes found in this object. I ran the whole notebook and the results or message do not change, but I think this more properly represents how we run AUcell in the wild.

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LGTM

@allyhawkins allyhawkins merged commit 1f4ec21 into master Nov 18, 2025
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@allyhawkins allyhawkins deleted the allyhawkins/aucell-remove-detected branch November 18, 2025 19:17
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Remove genes that are not found in any cells before determining the max rank for AUCell

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