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

doi:10.1093/bioinformatics/btag288

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

2026-05-09

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Chananchida Sang-Aram

DOI：10.1093/bioinformatics/btag288

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Abstract

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Many 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.

Keywords:

single-cell transcriptomics

H5AD file format

R programming

Python programming

interoperability

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

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