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

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.