Are there any preferred trajectory/pseudotime analyses that do not require an arbitrary start point?
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5 weeks ago
nathansuek ▴ 10

Hello, many of the trajectory inference/pseudotime methods require prior knowledge of a starting point. I feel like this creates a lot of bias, especially when the biological basis for that starting point is not clear and can artificially bias conclusions. Two questions:

  1. Are there any community preferred methods for trajectory inference that don't rely/rely less heavily on strong biological priors?
  2. If not arbitrary, how do those methods identify starting points?

Thanks!

scRNA-seq pseudotime monocle scvelo trajectory-analysis • 739 views
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Maybe consider seriation/ordination as an alternative.

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Can you expand upon what you mean by this?

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4 weeks ago
ATpoint 85k

slingshot does not require an explicit start, it will estimate one if absent. Still, trajectory tools are not aware of biology, and integrating your biological expertise to find a meaningful start is in my experience a plus. After all, trajectories are fancy ways of fitting some sort of minimal spanning tree through a bunch of data points, I would really aide this analysis with known and citable biology as much as possible to ensure that the trajectories are meaningful.

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