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Are all genes or highly variable genes used as input expression matrix in Waddington-OT? #100

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Mingsenli opened this issue Jun 15, 2022 · 1 comment
Open

Are all genes or highly variable genes used as input expression matrix in Waddington-OT? #100

Mingsenli opened this issue Jun 15, 2022 · 1 comment

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@Mingsenli
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The Waddington-OT is really a helpful tool for sc-RNA data.
In seurat，top 2000 variable genes were used to generate umap graph. Similarily, the monocle2 also uses highly variable genes to perform trajectory analysis.

I do not know if all genes or highly variable genes are used as input expression matrix in Waddington-OT?

If all genes are used, could you please explain why?

Thank you
Mingsen Li
@joshua-gould
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We use variable genes as input.

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@joshua-gould @Mingsenli