Introduction | Neighbourhoods | Neighbourhoods as characterised by gene expression | Neighbourhoods as characterised by cell types | Calculation of neighbourhood celltype composition | Analysis of contact based interactions between cell types | Analysis of neighbourhoods based on cell type composition | Relating cell type clusters to neighbourhood clusters | Analysing cell types based on their neighbourhoods | Detection of genes with spatially variable expression. | Ligand receptor analysis | Visualising ligand-receptor interactions: Seurat objects of edges | Spatial autocorrelation of ligand-receptor interactions | Quality control of Delaunay neighbours | edgeLengthsAndCellTypePairs | Visualising the edge lengths | Estimating edge length cutoffs | edgeCutoffsByClustering | edgeCutoffsByPercentile | edgeCutoffsByZScore | edgeCutoffsByWatershed | cullEdges

Introduction | Exploring CatsCradle | Biologically relevant gene sets on UMAP | Determining statistical significance of clustering | Gene z-scores on gene UMAP | Nearby genes | Predicting gene function

Introduction | Clustering and annotation of genes | Gene clusters vs. cell clusters | Spatial co-location of genes on gene UMAP | Gene annotation | Analysis of spatial transcriptomic data | Neighbourhoods | Neighourhood Seurat objects. | Neighbourhoods and cell types | Aggregate gene expression | Ligand-receptor analysis | CatsCradle, Seurat objects, SingleCellExperiment objects and SpatialExperiment objects

Introduction | Clustering and annotation of genes | Gene clusters vs. cell clusters | Spatial co-location of genes on gene UMAP | Gene annotation | Analysis of spatial transcriptomic data | Neighbourhoods | Neighourhood objects. | Neighbourhoods and cell types | Aggregate gene expression | Ligand-receptor analysis | CatsCradle, Seurat objects, SingleCellExperiment objects and