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Single-cell Trajectory analysis using Monocle3 and Seurat | Step-by-step tutorial

A detailed walk-though of steps to perform trajectory analysis using Monocle3 + Seurat for single-cell RNA-Seq data. In this video I cover various aspects of trajectory analysis including what is trajectory analysis, when to perform this analysis, which trajectory inference method to choose and how to perform trajectory analysis. In addition, I go over workflow steps and talk about cell data set object which monocle3 requires and finally demonstrate this workflow step-by-step in R. I hope you find the video informative. I look forward to your comments in the comments section! Link to code: https://github.com/kpatel427/YouTubeT... Data: http://scrna.sklehabc.com/ Alternate Data Link: https://drive.google.com/file/d/1CJ9V... Publication associated with the data: https://academic.oup.com/nsr/article/... Monocle3 tutorial: https://cole-trapnell-lab.github.io/m... R package collection for Trajectory Inference: https://dynverse.org/ Publication comparing various Trajectory Inference methods: https://www.biorxiv.org/content/10.11... Chapters: 0:00 Intro 0:52 WHAT is Trajectory analysis? 2:11 What is pseudotime? 2:43 WHEN to perform trajectory analysis? 3:57 WHICH trajectory inference method to choose? 5:52 HOW to perform trajectory analysis? - Workflow steps 7:04 cell_data_set class 8:29 Data for demo 9:20 Fetching the data 9:47 Load libraries and read data in R 12:39 Create Seurat object 16:39 Subset Seurat object to only retain B cells 19:53 Processing steps in Seurat (NormalizeData, ScaleData, RunPCA, RunUMAP and FindClusters) 25:25 Convert Seurat object to object of cell_data_set class 26:06 Retrieving data from cds object 28:11 Transfer clustering information from Seurat object to cds object 33:37 Visualize clustering using monocle3: plot_cells() 36:44 Learn trajectory graph: learn_graph() 39:06 Order cells in pseudotime: order_cells() 41:00 Plotting pseudotime for cell types in ggplot2 43:43 Find genes that change expression along a trajectory: graph_test() 47:03 Visualizing pseudotime in Seurat's FeaturePlot() Show your support and encouragement by buying me a coffee: https://www.buymeacoffee.com/bioinfor... To get in touch: Website: https://bioinformagician.org/ Github: https://github.com/kpatel427 Email: [email protected] #bioinformagician #bioinformatics #monocle3 #monocle #trajectoryinference #trajectory #singlecell #deg #seurat #integration#R #genomics #beginners #tutorial #howto ##research #omics #biology #ncbi #rnaseq #ngs