Single-Cell Trajectory Analysis Using Monocle3 and Seurat - Step-by-Step Tutorial

Intro
WHAT is Trajectory analysis?
What is pseudotime?
WHEN to perform trajectory analysis?
WHICH trajectory inference method to choose?
HOW to perform trajectory analysis? - Workflow steps
cell_data_set class
Data for demo
Fetching the data
Load libraries and read data in R
Create Seurat object
Subset Seurat object to only retain B cells
Processing steps in Seurat NormalizeData, ScaleData, RunPCA, RunUMAP and FindClusters
Convert Seurat object to object of cell_data_set class
Retrieving data from cds object
Transfer clustering information from Seurat object to cds object
Visualize clustering using monocle3: plot_cells
Learn trajectory graph: learn_graph
Order cells in pseudotime: order_cells
Plotting pseudotime for cell types in ggplot2
Find genes that change expression along a trajectory: graph_test
Visualizing pseudotime in Seurat's FeaturePlot