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RNA velocity unraveled

Gorin, Gennady and Fang, Meichen and Chari, Tara and Pachter, Lior (2022) RNA velocity unraveled. PLOS Computational Biology, 18 (9). Art. No. e1010492. ISSN 1553-7358. PMCID PMC9499228. doi:10.1371/journal.pcbi.1010492.

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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.

Item Type:Article
Related URLs:
URLURL TypeDescription CentralArticle ItemDiscussion Paper
Gorin, Gennady0000-0001-6097-2029
Fang, Meichen0000-0002-8217-0710
Chari, Tara0000-0002-6953-4313
Pachter, Lior0000-0002-9164-6231
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 ( award U19MH114830, administered by the National Institute of Mental Health ( 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.
Funding AgencyGrant Number
Issue or Number:9
PubMed Central ID:PMC9499228
Record Number:CaltechAUTHORS:20220916-665804000.785
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Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:116968
Deposited By: Donna Wrublewski
Deposited On:08 Dec 2022 04:59
Last Modified:08 Dec 2022 04:59

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