slingshot pseudotime analysis
16 Functional Pseudotime Analysis Slingshot cell lineage and pseudotime inference for Scanpy It looks like we can at least resolve the earliest time-point (0 hours) and there is some separation with the final time-point (72 hours). Pseudotime variables for each lineage inferred by Slingshot and Monocle 2 on the three-lineage OE dataset of [26]. In particular, we found that precursor clusters shared gene set enrichment patterns . Pseudotime less. Basic analysis of spatial data: → tutorial: spatial/basic-analysis. While the slingshot vignette uses SingleCellExperiment, slingshot can also take a matrix of cell embeddings in reduced dimension as input. Other cells in the dataset are grey. Now let’s calculate the Diffusion Pseudotime (DPT) by setting the first ranked cell as the root cell. The pseudotime analysis program Slingshot aligned cells along a 2D trajectory from the most transcriptionally similar LaTP population (LaTP-SynTII; LaTP2-SynTI; LaTP2-STGC) to each of the mature populations (Street et al., 2018; Figure 2C–E, Figure 2—source datas 2–4).
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slingshot pseudotime analysis