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kstreet13 / slingshot

Functions for identifying and characterizing continuous developmental trajectories in single-cell data.
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is slingshot using only the variable genes? #240

Closed TdzBAS closed 8 months ago

TdzBAS commented 9 months ago

Hi @kstreet13,

thanks for this awesome algorithm!

I am using a seurat object, which i later on convert to a scve in order to run the slingshot function. I am just wondering if slingshot uses the only the highly variable genes fromt the seurat object to calculate pseudotime or does it use alle genes from a cell? Thanks!

Best, Tolga

kstreet13 commented 9 months ago

Hi Tolga,

Slingshot doesn't actually use the gene-level data, but instead a dimensionality reduction. So, for example, if you ran PCA on the most variable genes and then ran Slingshot on that dimensionality reduction, you could say that Slingshot only used the most variable genes, but there's actually an additional step in there.

Hope this helps! Kelly

TdzBAS commented 8 months ago

Hi @kstreet13,

big thanks!

Tolga