{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,19]],"date-time":"2026-10-19T22:08:57Z","timestamp":1792447737392,"version":"4.5.0"},"reference-count":0,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2026,5,11]],"date-time":"2026-05-11T00:00:00Z","timestamp":1778457600000},"content-version":"am","delay-in-days":2,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability<\/jats:title>\n                    <jats:p>anndataR\u2019s 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 It is compatible with R version 4.5, has been archived at 10.5281\/zenodo.18775712 and included within Bioconductor: 10.18129\/B9.bioc.anndataR.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.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag288","type":"journal-article","created":{"date-parts":[[2026,5,5]],"date-time":"2026-05-05T11:29:10Z","timestamp":1777980550000},"source":"Crossref","is-referenced-by-count":3,"title":["anndataR improves interoperability between R and Python in single-cell transcriptomics"],"prefix":"10.1093","author":[{"given":"Louise","family":"Deconinck","sequence":"first","affiliation":[{"name":"VIB Center for Inflammation Research Data Mining and Modelling for Biomedicine,"},{"name":"Ghent University Department of Mathematics, Computer Science and Statistics, ,","place":["Belgium"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luke","family":"Zappia","sequence":"additional","affiliation":[{"name":"Data Intuitive , Lebbeke,","place":["Belgium"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robrecht","family":"Cannoodt","sequence":"additional","affiliation":[{"name":"VIB Center for Inflammation Research Data Mining and Modelling for Biomedicine,"},{"name":"Ghent University Department of Mathematics, Computer Science and Statistics, ,","place":["Belgium"]},{"name":"Data Intuitive , Lebbeke,","place":["Belgium"]},{"name":"Edaro , Destelbergen,","place":["Belgium"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martin","family":"Morgan","sequence":"additional","affiliation":[{"name":"Roswell Park Comprehensive Cancer Center Department of Biostatistics and Bioinformatics,"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"scverse","family":"core","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Isaac","family":"Virshup","sequence":"additional","affiliation":[{"name":"Institute of Computational Biology , Center Munich Germany Helmholtz, Munich"},{"name":"Chan Zuckerberg Initiative , Redwood City, CA","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chananchida","family":"Sang-Aram","sequence":"additional","affiliation":[{"name":"VIB Center for Inflammation Research Data Mining and Modelling for Biomedicine,"},{"name":"Ghent University Department of Mathematics, Computer Science and Statistics, ,","place":["Belgium"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Danila","family":"Bredikhin","sequence":"additional","affiliation":[{"name":"Stanford University Department of Genetics, , Stanford, CA","place":["United States"]},{"name":"scverse"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brian","family":"Schilder","sequence":"additional","affiliation":[{"name":"Imperial College London Department of Brain Sciences, Faculty of Medicine, , London,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruth","family":"Seurinck","sequence":"additional","affiliation":[{"name":"VIB Center for Inflammation Research Data Mining and Modelling for Biomedicine,"},{"name":"Ghent University Department of Mathematics, Computer Science and Statistics, ,","place":["Belgium"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yvan","family":"Saeys","sequence":"additional","affiliation":[{"name":"VIB Center for Inflammation Research Data Mining and Modelling for Biomedicine,"},{"name":"Ghent University Department of Mathematics, Computer Science and Statistics, ,","place":["Belgium"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,5,9]]},"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btag288\/68263312\/btag288.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btag288\/68263312\/btag288.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,5,11]],"date-time":"2026-05-11T04:31:54Z","timestamp":1778473914000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article\/doi\/10.1093\/bioinformatics\/btag288\/8675377"}},"subtitle":[],"editor":[{"given":"Laura","family":"Cantini","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,5,9]]},"references-count":0,"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btag288","relation":{},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,5,9]]},"article-number":"btag288"}}