SODB

SODB provides a unified repository and analysis environment for spatial omics datasets, hosting over 2,400 experiments from more than 25 spatial omics technologies to enable exploration, visualization (including SOView), and comparative analysis such as delineation of functional tissue domains and marker gene identification.

Key Features:

• Extensive Data Repository: Hosts over 2,400 experiments from more than 25 spatial omics technologies in a unified data format compatible with various computational packages.
• Spatial Omics View (SOView): Visualizes spatial omics data and can recover known anatomical structures from brain spatial transcriptomics datasets.
• Analytical Capabilities: Supports basic and advanced statistical analyses across multiple spatial omics datasets to delineate functional tissue domains and identify associated marker genes.
• Command-line package (pysodb): Provides a pysodb command-line package for programmatic access and integration into computational workflows.
• Support for Method Development: Serves as a resource for development and evaluation of new computational methodologies for spatial omics.

Scientific Applications:

• Neuroscience: Recovery of anatomical structures and study of spatial molecular organization in brain spatial transcriptomics datasets.
• Functional tissue domain analysis: Delineation of tissue domains and identification of marker genes across spatial omics experiments.
• Comparative and cross-dataset analysis: Comparative statistical analysis across multiple spatial omics datasets and technologies.
• Computational method benchmarking: Development and evaluation of new computational methods for spatial omics data analysis.

Methodology:

Integration of the pysodb command-line package for programmatic access to the unified spatial omics data format.