monocle3-truly-complete

What problem does it solve?

This skill enables researchers to analyze single-cell trajectory data to reconstruct developmental paths and dynamic cellular processes using Monocle 3.

Core Features & Use Cases

• Co-embedding and projecting multiple datasets into a common space for comparative analysis.
• Trajectory inference, pseudotime ordering, and visualization of lineage relationships.
• Label transfer and annotation across references, batch correction, and integration workflows for scRNA-seq data.
• Real-world scenarios include comparing reference trajectories with new samples, visualizing branchpoints, and diagnosing cellular state transitions in development or disease.

Quick Start

Install Monocle 3 in R, load the package, and run a basic trajectory workflow to preprocess, reduce dimension, cluster, learn_graph, and order_cells.