{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,11]],"date-time":"2026-08-11T15:06:30Z","timestamp":1786460790570,"version":"build-2736575974"},"reference-count":24,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,8,10]],"date-time":"2026-08-10T00:00:00Z","timestamp":1786320000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2026,8,11]],"date-time":"2026-08-11T00:00:00Z","timestamp":1786406400000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"name":"Albert-Ludwigs-Universit\u00e4t Freiburg im Breisgau"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Standardisation, accessibility, and reproducibility remain persistent challenges in data\u2011intensive scientific research. The Galaxy platform addresses these issues by providing a web-based environment for executing, sharing, and publishing computational workflows, yet programmatic access has been largely centred on the Python ecosystem through BioBlend.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>Here, we introduce GalaxyR, a native R package that provides a comprehensive and structured interface to the Galaxy application programming interface. GalaxyR enables users to manage histories, upload and retrieve data, execute tools and workflows, monitor jobs, and inspect results directly from within the R environment. By integrating Galaxy\u2019s scalable computational infrastructure with R\u2019s widely adopted data analysis ecosystem, GalaxyR facilitates automated, reproducible, and resource\u2011efficient workflows without requiring local high\u2011performance computing resources. The package supports both HTTPS\u2011 and FTP\u2011based data transfer, robust history and dataset management, and programmatic workflow orchestration across Galaxy instances.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>An application example demonstrates the use of GalaxyR for large-scale processing of drone-based laser scanning data, where computationally intensive tree\u2011level segmentation was delegated to the Galaxy infrastructure, while workflow control and preprocessing were handled in R within a few lines of code.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>GalaxyR thus bridges a critical gap for R users, significantly expanding access to Galaxy\u2011based analyses and enabling scalable, reproducible research across bioinformatics, ecology, remote sensing, and related data-driven disciplines.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12859-026-06591-0","type":"journal-article","created":{"date-parts":[[2026,8,10]],"date-time":"2026-08-10T03:24:30Z","timestamp":1786332270000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Introducing GalaxyR: an easy-to-use R implementation of the Galaxy API"],"prefix":"10.1186","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7895-702X","authenticated-orcid":false,"given":"Julian","family":"Frey","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2972-1920","authenticated-orcid":false,"given":"Zoe","family":"Schindler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1517-8851","authenticated-orcid":false,"given":"Muhammad","family":"Ali","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-9649-5920","authenticated-orcid":false,"given":"Joshua","family":"Braun-Wimmer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-5001-2571","authenticated-orcid":false,"given":"Kilian","family":"Gerberding","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-9896-8057","authenticated-orcid":false,"given":"Katja","family":"Kr\u00f6ner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1191-5770","authenticated-orcid":false,"given":"Elena","family":"Larysch","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-9745-5011","authenticated-orcid":false,"given":"Daniel","family":"Lusk","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-9195-5633","authenticated-orcid":false,"given":"Janusch","family":"Vanja-Jehle","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-1361-664X","authenticated-orcid":false,"given":"Yannik","family":"Wardius","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-8914-1543","authenticated-orcid":false,"given":"Maximilian","family":"Weidenfeller","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7381-3828","authenticated-orcid":false,"given":"Teja","family":"Kattenborn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9611-6272","authenticated-orcid":false,"given":"Thomas","family":"Seifert","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,8,10]]},"reference":[{"key":"6591_CR1","doi-asserted-by":"publisher","first-page":"622","DOI":"10.1038\/s41597-022-01710-x","volume":"9","author":"M Barker","year":"2022","unstructured":"Barker M, Chue Hong NP, Katz DS, Lamprecht A-L, Martinez-Ortiz C, Psomopoulos F, et al. 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