Protocol for inferring epithelial-to-mesenchymal transition trajectories from single-cell RNA sequencing data using R. Academic Article

abstract

• The epithelial-to-mesenchymal transition (EMT) provides crucial insights into the metastatic process and possesses prognostic value within the cancer context. Here, we present COMET, an R package for inferring EMT trajectories and inter-state transition rates from single-cell RNA sequencing data. We describe steps for finding the optimal number of EMT genes for a specific context, estimating EMT-related trajectories, optimal fitting of continuous-time Markov chain to inferred trajectories, and estimating inter-state transition rates.

authors

• George, Jason

published proceedings

• STAR Protoc

altmetric score

• 4.45

author list (cited authors)

• Najafi, A., Jolly, M. K., & George, J. T.

citation count

• 0

complete list of authors

• Najafi, Annice||Jolly, Mohit Kumar||George, Jason T

publication date

• January 2024

publisher

• Elsevier  Publisher

published in

• STAR Protocols  Journal

keywords

• Bioinformatics
• Cancer
• RNA-seq

PubMed Central ID

• 38183653

Digital Object Identifier (DOI)

• 10.1016/j.xpro.2023.102819

start page

• 102819

volume

• 5

issue

• 1