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

broadinstitute / wot

A software package for analyzing snapshots of developmental processes

https://broadinstitute.github.io/wot/

BSD 3-Clause "New" or "Revised" License

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

Open Mingsenli opened 2 years ago

Mingsenli commented 2 years ago

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 commented 2 years ago

We use variable genes as input.