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.
02 /Specification & Classification
Click any tag to browse matching papersReproducibility ledger
Nobody has reported trying to reproduce this paper yet. Did you replicate an experiment or run the code? Your report saves the next lab a week.
Sign in to file a reproducibility report.
Related papers
- Benchmarking RNA velocity methods across 17 independent studies
Ya Hong Luo, Jun Ren, … Qiyuan Li·Cell Reports MethodsPeer-reviewed·Mar 30, 2026
- On the Mathematics of RNA Velocity I: Theoretical Analysis
Tiejun Li, Jifan Shi, … Peijie Zhou·CSIAM Transactions on Applied MathematicsPeer-reviewed·Feb 25, 2021
- Pumping the brakes on RNA velocity - understanding and interpreting RNA velocity estimates
Shijie Zheng, Genevieve Stein-O’Brien, … Kasper D. Hansen·Genome biologyPeer-reviewed·Oct 26, 2023
- Quantifying stability via count splitting to guide model selection in RNA velocity analyses
Yuhong Li, Zeyu Wei, … Kevin Lin·Bioinformatics AdvancesPeer-reviewed·Jan 1, 2026
- Benchmarking algorithms for RNA velocity inference
Kexin Huang, Yu Zhou, … J Liu·bioRxiv·Jan 3, 2026
- Quantifying uncertainty in RNA velocity
Huizi Zhang, Natalia Bochkina, Sara Wade·BiometricsPeer-reviewed·Jan 6, 2026