TIPD: A Probability Distribution-Based Method for Trajectory … Figures ( 0) & Videos ( 0) Fig. Trajectory inference You can then use Monocle's differential analysis toolkit to find genes regulated over the course of the trajectory, as described in the section Finding genes that change as a function of pseudotime . The y axis is standard deviation (not variance), or the... Slingshot. The principle is the same as a two group comparison, but you just need to supply more populations. pseudotime Single-Cell Transcriptomic Comparison of Human Fetal Pseudotime Basic analysis of spatial data: → tutorial: spatial/basic-analysis. Pseudotime plot_cell_trajectory (cds, color_by = "Pseudotime", cell_size = 1) + scale_color_viridis_c () The pseudotime values are inverted. scvelo latent time vs pseudotime – Open Source Biology Monocle , TSCAN , Slingshot , DPT , Waterfall and scVelo ... We performed the pseudotime analysis on the entire dataset. For the cell-level analysis, ... Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics. TSCAN is an R package to support in silico reconstruction of cells’ pseudotime. We use the slingshot package (Street et al. Slingshot: cell lineage and pseudotime inference for single-cell ...