Organoid modeling of functional tumor-associated macrophages reveals phagocytosis-induced immune cell dynamics
- Sample QC
- Integration and preprocessing 2-1. Pre-processing: SCTransform v2, and Principal component analysis 2-2. Integration of dataset using Harmony v2 2-3. Dimensionality reduction: Uniform manifold approximation and projection (UMAP) 2-4. Clustering using Louvain algorithm 2-5. Manual cell type annotation based on well-know marker genes
- Identification of minor types of macrophages (TAMs, and Monocyte)
- Trajectory inference analysis using Monocle 3
- Cell-cell interaction based on ligand-receptor database using CellChat v2