Protocol for inferring epithelial-to-mesenchymal transition trajectories from single-cell RNA sequencing data using R
Summary: 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...
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| Format: | Article |
| Language: | English |
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Elsevier
2024-03-01
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| Series: | STAR Protocols |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166723007864 |
| _version_ | 1797363780456284160 |
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| author | Annice Najafi Mohit Kumar Jolly Jason T. George |
| author_facet | Annice Najafi Mohit Kumar Jolly Jason T. George |
| author_sort | Annice Najafi |
| collection | DOAJ |
| description | Summary: 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. : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. |
| first_indexed | 2024-03-08T16:25:53Z |
| format | Article |
| id | doaj.art-06508b4c96b84e8199bc0d7443f62c15 |
| institution | Directory Open Access Journal |
| issn | 2666-1667 |
| language | English |
| last_indexed | 2024-03-08T16:25:53Z |
| publishDate | 2024-03-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj.art-06508b4c96b84e8199bc0d7443f62c152024-01-07T04:32:30ZengElsevierSTAR Protocols2666-16672024-03-0151102819Protocol for inferring epithelial-to-mesenchymal transition trajectories from single-cell RNA sequencing data using RAnnice Najafi0Mohit Kumar Jolly1Jason T. George2Department of Biomedical Engineering, Texas A&M University, College Station, TX 77843, USACentre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India; Corresponding authorDepartment of Biomedical Engineering, Texas A&M University, College Station, TX 77843, USA; Intercollegiate School of Engineering Medicine, Texas A&M University, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA; Corresponding authorSummary: 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. : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.http://www.sciencedirect.com/science/article/pii/S2666166723007864BioinformaticsCancerRNA-seq |
| spellingShingle | Annice Najafi Mohit Kumar Jolly Jason T. George Protocol for inferring epithelial-to-mesenchymal transition trajectories from single-cell RNA sequencing data using R STAR Protocols Bioinformatics Cancer RNA-seq |
| title | Protocol for inferring epithelial-to-mesenchymal transition trajectories from single-cell RNA sequencing data using R |
| title_full | Protocol for inferring epithelial-to-mesenchymal transition trajectories from single-cell RNA sequencing data using R |
| title_fullStr | Protocol for inferring epithelial-to-mesenchymal transition trajectories from single-cell RNA sequencing data using R |
| title_full_unstemmed | Protocol for inferring epithelial-to-mesenchymal transition trajectories from single-cell RNA sequencing data using R |
| title_short | Protocol for inferring epithelial-to-mesenchymal transition trajectories from single-cell RNA sequencing data using R |
| title_sort | protocol for inferring epithelial to mesenchymal transition trajectories from single cell rna sequencing data using r |
| topic | Bioinformatics Cancer RNA-seq |
| url | http://www.sciencedirect.com/science/article/pii/S2666166723007864 |
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