Package: MultiAssaySpatialExperiment 0.99.12

Installation | Citing MultiAssaySpatialExperiment | Why another spatial data structure? | When to use MASE | Prerequisites | A worked example | Building the object | Looking at what it holds | Subsetting keeps the links consistent | Annotating and aggregating | Handing the data to other tools | See also | Session info

Introduction | Building MASE objects | Optional: lazy Parquet I/O via BiocDuckDB | Minimal MASE | Adding spatial coordinates | Adding spatial shapes | Building from multiple SingleCellExperiment objects | prepMASE and buildSpatialMap | Validation checklist | Subsetting operations | Overview of subsetting operations | Basic subsetting | Subset by specimen | Subset by assay column | Bracket notation | Spatial subsetting | Subset by bounding box | Subset by polygon | Select data from multiple non-contiguous regions | Buffer-based subsets | Spatial annotation and aggregation | Example setup | Annotate with regions | Aggregate by region | Count points per region | Sum expression per region | Mean expression per region | Lower-level spatial joins | Aggregation strategies | Visualizing aggregated data | Labels ↔ shapes interoperability | Rasterization: shapes → labels | Vectorization: labels → shapes | Use cases | See also | Session info

Introduction | Part 1: Data import | Reading Xenium data | Basic usage | Options | When to load transcripts | Reading Visium data | Visium HD support | Reading CosMx data | FOV (Field of View) handling | Reading MERSCOPE data (MERFISH) | Choosing a reader | Converting from other Bioconductor classes | From SpatialExperiment | From SpatialFeatureExperiment | Reading multiple samples | Part 2: Real-world workflows | Workflow 1: Xenium + Visium integration | Background | Data preparation | Build MASE object | Exploratory analysis | Do the two assays overlap in space? | Which genes are shared between assays | Spatial annotation: Cell types in Visium spots | Reading the composition result | Spatial aggregation: Summarize Xenium by regions | Comparing expression between the two platforms | Integration insights | Workflow 2: Coordinate transformation and alignment | Converting Visium grid to microns | Applying affine transformations | Landmark-based alignment | Storing transformed coordinates | Checking the alignment visually | Workflow 3: Multi-sample analysis | Workflow 4: Iterative analysis pattern | Summary | See also | Session info

Scope | Anatomy of a MultiAssaySpatialExperiment | What it inherits from MultiAssayExperiment | The spatial layers it adds | The tables that tie observations to space | The relational schema | Session info

Summary of the MultiAssaySpatialExperiment API | Constructors | Platform readers | Spatial accessors | Inherited accessors used most often | Subsetting | Spatial operations | Coercion | Combining | Session info