SpatialExperiment

SpatialExperiment provides an R/Bioconductor data infrastructure to store, access, and analyze spatially resolved transcriptomics data (e.g., 10x Genomics Visium and seqFISH) for representing spatial coordinates and platform-specific parameters to support spatial gene expression analyses.

Key Features:

• Modular data infrastructure: Provides a structured environment for storing and manipulating spatial transcriptomics datasets within R/Bioconductor.
• Interoperability and standardization: Integrates with Bioconductor packages to enable standardized data exchange and compatibility with downstream analytical methods.
• S4 specialized data classes: Uses S4 classes for spatial experiments to store spatial coordinates and platform-specific metadata and parameters.
• Visualization integration: Offers integration with visualization packages such as ggspavis for plotting spatial transcriptomics data.
• Example dataset access: Provides access to example datasets via packages including STexampleData and TENxVisiumData.
• Technology support: Handles data and parameters specific to technologies such as 10x Genomics Visium and seqFISH.

Scientific Applications:

• Tissue mapping: Analyzing spatial patterns of gene expression to map tissue architecture and delineate regions of interest.
• Cellular interaction studies: Investigating cell–cell and cell–microenvironment interactions through spatially resolved expression profiles.
• Disease research: Exploring spatial heterogeneity in disease contexts, including cancer, to characterize tumor biology and progression.

Methodology:

Utilizes S4 classes to store and retrieve complex spatial transcriptomics datasets, including spatial coordinates and platform-specific parameters, and provides access to example datasets via STexampleData and TENxVisiumData.