MultistageOT: Multistage optimal transport infers trajectories from a snapshot of single-cell data.

ABSTRACT: Single-cell RNA-sequencing captures a temporal slice, or a snapshot, of a cell differentiation process. A major bioinformatical challenge is the inference of differentiation trajectories from a single snapshot, and methods that account for outlier cells that are unrelated to the differentiation process have yet to be established. We present MultistageOT (https://github.com/dahlinlab/MultistageOT), a generalized optimal transport-based framework that models cell differentiation in a single snapshot as a series of intermediate cell transitions. MultistageOT employs multiple transport stages to establish temporal progression within the snapshot-overcoming limitations with the classic bimarginal formulation of optimal transport. Moreover, our multistage framework uses global information across

SUBMITTER: Tronstad M 

PROVIDER: S-EPMC12718350 | biostudies-literature | 2025 Dec

REPOSITORIES: biostudies-literature