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Published on: August 1, 2025
anndataR improves interoperability between R and Python in single-cell transcriptomics
Louise Deconinck1,2, Luke Zappia3, Robrecht Cannoodt1,2,3,4
1Data Mining and Modelling for Biomedicine, VIB Center for Inflammation Research, 9000 Ghent, Belgium.
Bioinformatics (Oxford, England)
|May 11, 2026
Summary
The anndataR package enables R users to seamlessly read and write AnnData (H5AD) files, facilitating cross-language data analysis. This ensures interoperability between R and Python for single-cell transcriptomics research.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Single-cell transcriptomics data is frequently stored in the AnnData (H5AD) format, popularized by the Python scverse ecosystem.
- Accessing H5AD files from R presents challenges, limiting cross-language data analysis.
- anndataR addresses this by enabling native H5AD file handling within R.
Purpose of the Study:
- To develop an R package, anndataR, for direct interaction with H5AD files.
- To facilitate the conversion of H5AD files to R-compatible formats like SingleCellExperiment and Seurat objects.
- To ensure robust interoperability between R and Python for single-cell data analysis.
Main Methods:
- Developing an R package (anndataR) for reading and writing H5AD files.
- Implementing conversion functions between H5AD, SingleCellExperiment, and Seurat objects.
- Conducting rigorous testing to validate H5AD file compatibility between R and Python.
Main Results:
- anndataR provides native read/write capabilities for H5AD files in R.
- The package allows seamless conversion between H5AD and common R single-cell data objects.
- Compatibility testing confirms reliable data exchange between R and Python-generated H5AD files.
Conclusions:
- anndataR enhances R's utility for single-cell transcriptomics by enabling direct H5AD file manipulation.
- The package promotes long-term interoperability and efficient cross-language workflows.
- anndataR is available under the MIT license with comprehensive documentation and Bioconductor integration.
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