{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,15]],"date-time":"2025-11-15T16:32:58Z","timestamp":1763224378314,"version":"3.45.0"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2025,10,23]],"date-time":"2025-10-23T00:00:00Z","timestamp":1761177600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Grant-in-Aid for Scientific Research","award":["23H02466"],"award-info":[{"award-number":["23H02466"]}]},{"DOI":"10.13039\/100009619","name":"Japan Agency for Medical Research and Development","doi-asserted-by":"publisher","award":["JP23gm6310012h0004"],"award-info":[{"award-number":["JP23gm6310012h0004"]}],"id":[{"id":"10.13039\/100009619","id-type":"DOI","asserted-by":"publisher"}]},{"name":"JST FOREST","award":["JPMJFR224Y"],"award-info":[{"award-number":["JPMJFR224Y"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Recent advances in single-cell analysis have introduced new computational challenges. Researchers often need to use multiple analysis tools written in different programming languages while managing version conflicts between related packages within a single workflow. For the research community, minimizing the time spent on environment setup and installation issues is essential. We present ShortCake, a containerized platform that integrates a suite of single-cell analysis tools written in R and Python. ShortCake isolates competing Python tools into separate virtual environments that can be easily accessed within a Jupyter notebook. This enables users to effortlessly transition between various environments, including R, even within a single notebook. Additionally, ShortCake offers multiple \u201cflavors,\u201d enabling users to select container images tailored to their specific needs. ShortCake provides a unified environment with fixed versions of various tools, thus streamlining workflows, reducing setup time, and improving reproducibility.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The ShortCake image is available on DockerHub (https:\/\/hub.docker.com\/r\/rnakato\/shortcake) and Zenodo (DOIs: 10.5281\/zenodo.17116765 and 10.5281\/zenodo.17118158). The source code is available on GitHub (https:\/\/github.com\/rnakato\/ShortCake).<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf559","type":"journal-article","created":{"date-parts":[[2025,10,2]],"date-time":"2025-10-02T12:02:34Z","timestamp":1759406554000},"source":"Crossref","is-referenced-by-count":0,"title":["ShortCake: an integrated platform for efficient and reproducible single-cell analysis"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3019-5817","authenticated-orcid":false,"given":"Ryuichiro","family":"Nakato","sequence":"first","affiliation":[{"name":"Laboratory of Computational Genomics, Institute for Quantitative Biosciences, The University of Tokyo , Tokyo 113-0032,","place":["Japan"]}]},{"given":"Luis Augusto Eijy","family":"Nagai","sequence":"additional","affiliation":[{"name":"Laboratory of Computational Genomics, Institute for Quantitative Biosciences, The University of Tokyo , Tokyo 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