anndataR improves interoperability between R and Python in single-cell transcriptomics
SUMMARY:
Many single-cell transcriptomics datasets are stored in the HDF5-backed AnnData (H5AD) file format, as popularized 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.
AVAILABILITY AND IMPLEMENTATION:
anndataR’s 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 It is compatible with R version 4.5, has been archived at 10.5281/zenodo.18775712 and included within Bioconductor: 10.18129/B9.bioc.anndataR.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.
Citation
@article{deconinck2026,
author = {Deconinck, Louise and Zappia, Luke and Cannoodt, Robrecht
and Morgan, Martin and core, scverse and Virshup, Isaac and
Sang-aram, Chananchida and Bredikhin, Danila and Schilder, Brian and
Seurinck, Ruth and Saeys, Yvan and {scverse core}},
title = {anndataR Improves Interoperability Between {R} and {Python}
in Single-Cell Transcriptomics},
journal = {Bioinformatics},
volume = {42},
number = {6},
pages = {btag288},
date = {2026-06-01},
url = {https://doi.org/10.1093/bioinformatics/btag288},
doi = {10.1093/bioinformatics/btag288},
issn = {1367-4811},
langid = {en},
abstract = {**SUMMARY:** Many single-cell transcriptomics datasets are
stored in the HDF5-backed AnnData (H5AD) file format, as popularized
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. **AVAILABILITY AND IMPLEMENTATION:** anndataR’s
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.}
}