16.1 Load settings and packages; 16.2 First look at the differentiation data from Deng et al. pseudotime Further Tutorials Conversion: AnnData, SingleCellExperiment, and Seurat objects See Seurat to AnnData for a tutorial on anndata2ri. Dissect cellular decisions with branch analysis. In addition to Slingshot’s core methodological components described above for lineage and pseudotime inference, we note the importance of upstream analysis choices. For the cell-level analysis, ... Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics. Monocle is an R package developed for analysing single cell gene expression data. 0. Trajectory inference Popular pseudotime inference methods—TSCAN , Slingshot , Monocle , and Monocle2 —include a built-in functionality for identifying DE genes after pseudotime inference. Slingshot: Cell lineage and pseudotime inference for single-cell transcriptomics Kelly Street1,8, Davide Risso2, Russell B. Fletcher 3, Diya Das , John Ngai3,6,7, Nir Yosef4,8, Elizabeth Purdom5,8, and Sandrine Dudoit 1,5,8 1Division of Biostatistics, School of Public Health, UC Berkeley. This may be useful if you have multiple time points, or a pseudotime trajectory. Now, RNA velocity is carried out using scvelo, and this package generates a metric known as latent time. Slingshot was designed to model developmental trajectories in single-cell RNA sequencing data and serve as a component in an analysis pipeline after dimensionality reduction and clustering. The new reconstruction algorithms introduced in Monocle 2 can robustly reveal branching trajectories, along with the genes that cells use to navigate these decisions. I am having a very had time seeing the difference between latent time and standard pseudotime analysis (usually carried out by slingshot, … A number of scRNA-seq protocols have been developed, and these methods possess their unique features with distinct advantages and disadvantages. Comparing pathways over pseudotime • Single Cell Pathway …

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