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It enables the integrative analysis of chromosome conformation by providing tools and computational resources to pre-process, analyse and visualize Hi-C, Capture Hi-C (cHi-C) and single-cell Hi-C (scHi-C) data. Since the last publication, Galaxy HiCExplorer has been expanded considerably with new tools to facilitate the analysis of cHi-C and to provide an in-depth analysis of Hi-C data. Moreover, it supports the analysis of scHi-C data by offering a broad range of tools. With the help of the standard graphical user interface of Galaxy, presented workflows, extensive documentation and tutorials, novices as well as Hi-C experts are supported in their Hi-C data analysis with Galaxy HiCExplorer.<\/jats:p>","DOI":"10.1093\/nar\/gkaa220","type":"journal-article","created":{"date-parts":[[2020,3,24]],"date-time":"2020-03-24T20:11:47Z","timestamp":1585080707000},"page":"W177-W184","source":"Crossref","is-referenced-by-count":419,"title":["Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization"],"prefix":"10.1093","volume":"48","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9985-955X","authenticated-orcid":false,"given":"Joachim","family":"Wolff","sequence":"first","affiliation":[{"name":"Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-K\u00f6hler-Allee 106, 79110 Freiburg, Germany"}]},{"given":"Leily","family":"Rabbani","sequence":"first","affiliation":[{"name":"Max Planck Institute of Immunobiology and Epigenetics, St\u00fcbeweg 51, 79108 Freiburg im Breisgau, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0895-1535","authenticated-orcid":false,"given":"Ralf","family":"Gilsbach","sequence":"first","affiliation":[{"name":"Institute for Cardiovascular Physiology, Goethe University, Frankfurt am Main, Germany"},{"name":"German Center of Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt am Main, Germany"},{"name":"Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3663-4569","authenticated-orcid":false,"given":"Gautier","family":"Richard","sequence":"first","affiliation":[{"name":"INRAE, Agrocampus Ouest, Universit\u00e9 de Rennes, IGEPP, F-35650 Le Rheu, France"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3702-0868","authenticated-orcid":false,"given":"Thomas","family":"Manke","sequence":"first","affiliation":[{"name":"Max Planck Institute of Immunobiology and Epigenetics, St\u00fcbeweg 51, 79108 Freiburg im Breisgau, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8231-3323","authenticated-orcid":false,"given":"Rolf","family":"Backofen","sequence":"first","affiliation":[{"name":"Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-K\u00f6hler-Allee 106, 79110 Freiburg, Germany"},{"name":"Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Sch\u00e4nzlestr. 18, 79104 Freiburg, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3079-6586","authenticated-orcid":false,"given":"Bj\u00f6rn A","family":"Gr\u00fcning","sequence":"first","affiliation":[{"name":"Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-K\u00f6hler-Allee 106, 79110 Freiburg, Germany"}]}],"member":"286","published-online":{"date-parts":[[2020,4,17]]},"reference":[{"key":"2020062614040059400_B1","doi-asserted-by":"crossref","first-page":"1306","DOI":"10.1126\/science.1067799","article-title":"Capturing chromosome conformation","volume":"295","author":"Dekker","year":"2002","journal-title":"Science"},{"key":"2020062614040059400_B2","doi-asserted-by":"crossref","first-page":"1348","DOI":"10.1038\/ng1896","article-title":"Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture\u2013on-chip (4C)","volume":"38","author":"Simonis","year":"2006","journal-title":"Nat. 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