{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,20]],"date-time":"2026-06-20T03:50:51Z","timestamp":1781927451763,"version":"3.54.5"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2023,9,5]],"date-time":"2023-09-05T00:00:00Z","timestamp":1693872000000},"content-version":"vor","delay-in-days":4,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,9,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>We present PyDESeq2, a python implementation of the DESeq2 workflow for differential expression analysis on bulk RNA-seq data. This re-implementation yields similar, but not identical, results: it achieves higher model likelihood, allows speed improvements on large datasets, as shown in experiments on TCGA data, and can be more easily interfaced with modern python-based data science tools.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>PyDESeq2 is released as an open-source software under the MIT license. The source code is available on GitHub at https:\/\/github.com\/owkin\/PyDESeq2 and documented at https:\/\/pydeseq2.readthedocs.io. PyDESeq2 is part of the scverse ecosystem.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad547","type":"journal-article","created":{"date-parts":[[2023,9,4]],"date-time":"2023-09-04T13:53:19Z","timestamp":1693835599000},"source":"Crossref","is-referenced-by-count":365,"title":["PyDESeq2: a python package for bulk RNA-seq differential expression analysis"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1035-7017","authenticated-orcid":false,"given":"Boris","family":"Muzellec","sequence":"first","affiliation":[{"name":"Owkin France , Paris, 75009, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria","family":"Tele\u0144czuk","sequence":"additional","affiliation":[{"name":"Owkin France , Paris, 75009, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vincent","family":"Cabeli","sequence":"additional","affiliation":[{"name":"Owkin France , Paris, 75009, 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differences","volume":"35","author":"Zhu","year":"2019","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btad547\/51359184\/btad547.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/9\/btad547\/51556132\/btad547.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/9\/btad547\/51556132\/btad547.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,15]],"date-time":"2023-09-15T04:44:18Z","timestamp":1694753058000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btad547\/7260507"}},"subtitle":[],"editor":[{"given":"Yann","family":"Ponty","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2023,9,1]]},"references-count":10,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2023,9,2]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btad547","relation":{},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,9,1]]},"published":{"date-parts":[[2023,9,1]]},"article-number":"btad547"}}