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.
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页数：18
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