scvelo latent time vs pseudotime
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24 days ago
Badran ▴ 50

ScVelo Latent Time vs Pseudotime

Hi, I am doing RNA velocity and pseudotime analyses on my single-cell RNA-Seq datasets. For RNA velocity, I am using python's scvelo package, which computes velocity as well as latent time.

How is scvelo's latent time different from pseudotime generated by packages like slingshot and monocle 3?

pseudotime scvelo ScRNA-Seq • 136 views
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To my knowledge both are the inferred developmental trajectories, with early time being more undifferentiated- and late time being more differentiated cells. Slingshot and company use reduced dimensions such as PCA or UMAP to construct that time by finding some sort of minimal spanning tree to connect the cells (so basically fitting a line through the cells in multidimensional space). Velocity constructs that by using the ratios of spliced- and unspliced transcripts. I think the message is the same, which is then called latent or pseudotime, just the inference method is different.


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