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bioRxiv · 10.1101/2025.08.18.669052

anndataR improves interoperability between R and Python in single-cell transcriptomics

Deconinck, L.·Zappia, L.·Cannoodt, R.·Morgan, M.·scverse core,·Virshup, I.·Sang-aram, C.·Bredikhin, D.·Seurinck, R.·Saeys, Y.
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Abstract

SummaryMany single-cell transcriptomics datasets are stored in the HDF5-backed AnnData (H5AD) file format, as popularised by the Python scverse ecosystem. However, accessing these datasets from R, allowing users to take advantage of the strengths of each language, can be difficult. anndataR facilitates this access by allowing users to natively read and write H5AD files in R, convert them to and from SingleCellExperiment or Seurat objects, or even work with the resulting R AnnData object directly. We perform rigorous testing to ensure compatibility between Python-written and R-written H5AD files, guaranteeing long-term interoperability between languages. AvailabilityanndataRs source code is available on GitHub at scverse/anndataR under the MIT license. It is compatible with R version 4.5, has been archived at 10.5281/zenodo.18775712 and included within Bioconductor: 10.18129/B9.bioc.anndataR. Installation instructions and tutorials can be found in the online documentation at anndatar.scverse.org. Issues can be reported at the GitHub repository. Code to reproduce the analyses performed can be found on GitHub at LouiseDck/anndataR-paper, archived at 10.5281/zenodo.18792241. Contactrobrecht.cannoodt@gmail.com

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Deconinck, L., Zappia, L., Cannoodt, R., Morgan, M., scverse core,, Virshup, I., Sang-aram, C., Bredikhin, D., Seurinck, R., Saeys, Y.. 2025-08-22. anndataR improves interoperability between R and Python in single-cell transcriptomics. https://doi.org/10.1101/2025.08.18.669052

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