Introduction | Load data | Pre-processing | Create a Milo object | From SingleCellExperiment object | From AnnData object (.h5ad) | From Seurat object | Construct KNN graph | 1. Defining representative neighbourhoods | Counting cells in neighbourhoods | Differential abundance testing | Visualize neighbourhoods displaying DA

Introduction | Load data | Data processing and normalisation | Define cell neighbourhoods | Demonstrating the GLMM syntax | A note on when to use GLMM vs. GLM

Introduction | Load data | Define cell neighbourhoods | Differential abundance testing with contrasts

Load data | Visualize the data | Differential abundance testing | Create a Milo object | Construct KNN graph | Defining representative neighbourhoods on the KNN graph | Counting cells in neighbourhoods | Defining experimental design | Computing neighbourhood connectivity | Testing | Inspecting DA testing results | Finding markers of DA populations | Custom grouping | Automatic grouping of neighbourhoods | Finding gene signatures for neighbourhoods | Visualize detected markers | DGE testing within a group

Introduction | Installation | Processsing Overview | Package data format | Data access | Session Information | References