RNA velocity unraveled

Creators: Gorin, Gennady; Fang, Meichen; Chari, Tara; Pachter, Lior

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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.

Additional Information

G.G. thanks Dr. John J. Vastola for fruitful discussions about landscape representations of biophysical systems. L.P. received the National Institutes of Health (nih.gov) award U19MH114830, administered by the National Institute of Mental Health (nimh.nih.gov). G.G., M.F., T.C., and L.P. were partially funded by this award. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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Resource type: Journal Article
Publisher: Public Library of Science
Published in: PLOS Computational Biology, 18(9), Art. No. e1010492, ISSN: 1553-7358.

Created:: August 22, 2023
Modified:: December 22, 2023