Najafi, A and Jolly, MK and George, JT (2024) Protocol for inferring epithelial-to-mesenchymal transition trajectories from single-cell RNA sequencing data using R. In: STAR Protocols, 5 (1).
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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. © 2023 The Authors
| Item Type: | Journal Article |
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| Publication: | STAR Protocols |
| Publisher: | Cell Press |
| Additional Information: | The copyright for this article belongs to author. |
| Keywords: | algorithm; Article; cancer cell line; cytometry; dispersity; dynamic time warping; epithelial mesenchymal transition; epithelium cell; gene; human; hybrid; illness trajectory; limit of quantitation; mesenchyme cell; metastasis; single cell RNA seq; software; statistical analysis; stroma; tumor cell; tumor microenvironment |
| Department/Centre: | Division of Interdisciplinary Sciences > Centre for Biosystems Science and Engineering |
| Date Deposited: | 01 Mar 2024 06:22 |
| Last Modified: | 01 Mar 2024 06:22 |
| URI: | https://eprints.iisc.ac.in/id/eprint/83884 |
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