<p>Is there a good definition of pseudotime? Some tools are clearly labeled as pseudotime and produce values along a trajectory, but there are more complex approaches that involve branching and disconnected populations. There are 70 of them in the <a href="https://dynverse.org/" rel="nofollow noreferrer">dynverse</a>, so there are many options.</p>
<p>UMAP will also order cells, but that is generally not considered pseudotime. You can even overlay Monocle or PAGA results onto a UMAP so the cells are still ordered the same way. SPRING is specifically designed to capture continuous trajectories, but is also not considered pseudotime. Why not?</p>

<scrnaseq><visualization><umap><monocle>
Is there a difference between any scRNA-seq visualization and pseudotime?
# Is there a difference between any scRNA-seq visualization and pseudotime?

(Asked by: username_0 on 2021-02-08)

Is there a good definition of pseudotime? Some tools are clearly labeled as pseudotime and produce values along a trajectory, but there are more complex approaches that involve branching and disconnected populations. There are 70 of them in the [dynverse](https://dynverse.org/), so there are many options.

UMAP will also order cells, but that is generally not considered pseudotime. You can even overlay Monocle or PAGA results onto a UMAP so the cells are still ordered the same way. SPRING is specifically designed to capture continuous trajectories, but is also not considered pseudotime. Why not?

**Tags:** scrnaseq, visualization, umap, monocle

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## 0 answers

