SCUBA

SCUBA implements a unified data access API for common R and Python single-cell object formats, facilitating interoperability and reducing the need for object conversion in single-cell data analysis workflows.

Key Features:

• Format-agnostic data access: SCUBA extends the data access approach from the Seurat package to SingleCellExperiment and anndata objects, with new data-specific access functions for all supported object types.
• Non-destructive data extraction: SCUBA extracts only data required for the operation at hand, leaving the original object unmodified.
• Consistent cross-format syntax: Code written with SCUBA uses any supported object class as input with simple and consistent syntax across object formats.
• Scalable performance: Performance scales well across all SCUBA-supported formats.

Scientific Applications:

• Cross-ecosystem single-cell analysis: A single analysis script or package can work seamlessly with multiple object types, reducing code complexity and improving readability and reproducibility.
• Visualization of pre-processed single-cell data: SCUBA enables visualization and further analysis of pre-processed single-cell data without requiring object conversion.
• Interactive single-cell browser support: SCUBA serves as a backend for tools such as scExploreR to function across multiple object types.

Methodology:

SCUBA extends the data access approach from the Seurat package and implements new data-specific access functions for all supported object types.