Pumping the brakes on RNA velocity by understanding and interpreting RNA velocity estimates.

ABSTRACT:

Background

RNA velocity analysis of single cells offers the potential to predict temporal dynamics from gene expression. In many systems, RNA velocity has been observed to produce a vector field that qualitatively reflects known features of the system. However, the limitations of RNA velocity estimates are still not well understood.

Results

We analyze the impact of different steps in the RNA velocity workflow on direction and speed. We consider both high-dimensional velocity estimates and low-dimensional velocity vector fields mapped onto an embedding. We conclude the transition probability method for mapping velocity estimates onto an embedding is effectively interpolating in the embedding space. Our findings reveal a significant dependence of the RNA velocity workflow on s

SUBMITTER: Zheng SC 

PROVIDER: S-EPMC10601342 | biostudies-literature | 2023 Oct

REPOSITORIES: biostudies-literature