Monocle 3 Clustering and Trajectory Analysis

Single-cell RNA-seq trajectory analysis using Monocle 3 with C. elegans embryo and L2 larval data from the Trapnell lab. This project follows the Monocle 3 tutorials, with supplementary code for steps not fully covered in the documentation.

Scripts

• monocle_3_installation.R - Package installation
• monocle_3_clustering.R - Cell clustering workflow
• monocle_3_single_cell_trajectories.R - Trajectory inference and pseudotime analysis

Analysis Overview

• Preprocessing and batch correction
• UMAP dimensionality reduction
• Trajectory learning and pseudotime ordering
• Differential expression with fit_models() and graph_test()
• Example of cross-dataset label transfer

Data Sources

• Packer et al. C. elegans embryo data
• Cao et al. C. elegans L2 larval data

Requirements

• R 4.x
• Monocle 3
• Seurat
• SeuratWrappers