SCUBA implements a storage format-agnostic API for single-cell data access in R

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Abstract
While robust tools exist for the analysis of single-cell datasets in both Python and R, interoperability is limited, and analysis tools generally only accept one object class. Considerable programming expertise is required to integrate tools across package ecosystems into a comprehensive analysis, due to their differing languages and internal data structures. This complicates validation of results and leads to inconsistent visualizations between analysis suites. Conversion between object formats is the most common solution, but this is difficult and error-prone due to the rapid pace of development of the analysis suites and their underlying data structures. To address this, we created SCUBA (Single-Cell Unified Backend API), an R package that implements a unified data access API for all common R and Python single-cell object formats. SCUBA extends the data access approach from the widely used Seurat package to SingleCellExperiment and anndata objects. SCUBA also implements new data-specific access functions for all supported object types. Performance scales well across all SCUBA-supported formats. In addition to performance, SCUBA offers several advantages over object conversion for the visualization and further analysis of pre-processed single-cell data. First, SCUBA extracts only data required for the operation at hand, leaving the original object unmodified. This process is simpler, less error prone, and less memory intensive than object conversion, which operates on the entire dataset. Second, code written with SCUBA can use any supported object class as input, with simple and consistent syntax across object formats. This allows a single analysis script or package (like our interactive single-cell browser, scExploreR) to work seamlessly with multiple object types, reducing the complexity of the code and improving both readability and reproducibility. Adoption of SCUBA will ultimately improve collaboration and reproducible research in single-cell analysis by lowering the barriers between package ecosystems.
Funding Information
  • National Institutes of Health (R35CA242376)
  • U.S. Department of Veterans Affairs (IK2BX004952-01A1)

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