DiffGEK: differential gene expression kinetics.

ABSTRACT:

Motivation

A defining characteristic of all metazoan organisms is the existence of different cell states or cell types, driven by changes in gene expression kinetics, principally transcription, splicing and degradation rates. The RNA velocity framework utilizes both spliced and unspliced reads in single cell mRNA preparations to predict future cellular states and estimate transcriptional kinetics. However, current models assume either constant kinetic rates, rates equal for all genes, or rates completely independent of progression through differentiation. Consequently, current models for rate estimation are either underparametrized or overparametrized.

Results

Here, we developed a new method (diffGEK) which overcomes this issue, and allows comparison of transcriptional rates

SUBMITTER: Barile M 

PROVIDER: S-EPMC12198498 | biostudies-literature | 2025 Jun

REPOSITORIES: biostudies-literature