LineageOT is a unified framework for lineage tracing and trajectory inference.

ABSTRACT: Understanding the genetic and epigenetic programs that control differentiation during development is a fundamental challenge, with broad impacts across biology and medicine. Measurement technologies like single-cell RNA-sequencing and CRISPR-based lineage tracing have opened new windows on these processes, through computational trajectory inference and lineage reconstruction. While these two mathematical problems are deeply related, methods for trajectory inference are not typically designed to leverage information from lineage tracing and vice versa. Here, we present LineageOT, a unified framework for lineage tracing and trajectory inference. Specifically, we leverage mathematical tools from graphical models and optimal transport to reconstruct developmental trajectories from time courses

SUBMITTER: Forrow A 

PROVIDER: S-EPMC8367995 | biostudies-literature | 2021 Aug

REPOSITORIES: biostudies-literature