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

被引：0

作者：

Najafi, Annice ^{[1
]}

Jolly, Mohit Kumar ^{[2
]}

George, Jason T. ^{[1
,3
,4
]}

机构：

[1] Texas A&M Univ, Dept Biomed Engn, College Stn, TX 77843 USA

[2] Indian Inst Sci, Ctr Biosyst Sci & Engn, Bangalore 560012, India

[3] Texas A&M Univ, Intercollegiate Sch Engn Med, Houston, TX 77030 USA

[4] Rice Univ, Ctr Theoret Biol Phys, Houston, TX 77030 USA

来源：

STAR PROTOCOLS | 2024年 / 5卷 / 01期

关键词：

EMT;

D O I：

10.1016/j.xpro.2023.102819

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页数：18

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