scDIOR

scDIOR facilitates transformation of single-cell omics data between R and Python using Hierarchical Data Format Version 5 (HDF5) to enable interoperability among Seurat, SingleCellExperiment, Monocle, and Scanpy.

Key Features:

• Cross-Platform Compatibility: Bridges R and Python ecosystems and targets Seurat, SingleCellExperiment, Monocle, and Scanpy for interoperable single-cell analyses.
• Data Transformation Efficiency: Leverages HDF5 to reduce I/O overhead and streamline transformations between platform-specific object formats.
• Versatile Data Handling: Supports single-cell RNA sequencing and spatial resolved transcriptomics and allows selective loading of components such as cell annotations without loading full gene expression matrices.
• Modular Design: Implements two modules—dior for R and diopy for Python—to enable bidirectional data transformation and comparison of algorithmic performance across platforms.

Scientific Applications:

• Cell state identification: Enables transfer of annotated cell metadata and expression data to support identification of cell states across toolsets.
• Developmental trajectory reconstruction: Facilitates use of trajectory analysis outputs across R and Python workflows.
• Spatial expression deconvolution: Supports integration and transfer of spatial resolved transcriptomics data components for spatial pattern analysis.
• Cross-platform algorithm comparison: Allows benchmarking and comparison of algorithmic results between Seurat/SingleCellExperiment/Monocle and Scanpy.

Methodology:

Uses Hierarchical Data Format Version 5 (HDF5) for data storage and transfer, provides dior (R) and diopy (Python) modules for bidirectional conversion, and implements selective component loading to minimize I/O.