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RNA velocity unraveled.

ABSTRACT: We perform a thorough analysis of RNA velocity methods, with a view towards understanding the suitability of the various assumptions underlying popular implementations. In addition to providing a self-contained exposition of the underlying mathematics, we undertake simulations and perform controlled experiments on biological datasets to assess workflow sensitivity to parameter choices and underlying biology. Finally, we argue for a more rigorous approach to RNA velocity, and present a framework for Markovian analysis that points to directions for improvement and mitigation of current problems.

SUBMITTER: Gorin G 

PROVIDER: S-EPMC9499228 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature

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RNA velocity unraveled.

Gorin Gennady G   Fang Meichen M   Chari Tara T   Pachter Lior L  

PLoS computational biology 20220912 9

We perform a thorough analysis of RNA velocity methods, with a view towards understanding the suitability of the various assumptions underlying popular implementations. In addition to providing a self-contained exposition of the underlying mathematics, we undertake simulations and perform controlled experiments on biological datasets to assess workflow sensitivity to parameter choices and underlying biology. Finally, we argue for a more rigorous approach to RNA velocity, and present a framework  ...[more]

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