Monocle3 Truly Complete

Monocle3-Truly-Complete Skill

Comprehensive assistance with Monocle 3 for single-cell trajectory analysis, including co-embedding, projection, and advanced visualization techniques.

When to Use This Skill

This skill should be triggered when:

Data Analysis & Processing

• Loading and preprocessing single-cell data - Working with CellDataSet objects, UMI filtering, size factor estimation
• Co-embedding multiple datasets - Combining reference and query datasets for comparative analysis
• Projecting query data onto reference - Using transform models to map new data into existing reference space
• Cell type label transfer - Transferring annotations from reference to query cells using nearest neighbor indexing

Installation & Setup

• Installing Monocle 3 - Setting up R environment, Bioconductor dependencies, GitHub installation