{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,24]],"date-time":"2026-01-24T03:38:49Z","timestamp":1769225929455,"version":"3.49.0"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2024,5,30]],"date-time":"2024-05-30T00:00:00Z","timestamp":1717027200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R35-GM128645"],"award-info":[{"award-number":["R35-GM128645"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,6,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>3D chromatin structure plays an important role in regulating gene expression and alterations to this structure can result in developmental abnormalities and disease. While genomic approaches like Hi-C and Micro-C can provide valuable insights in 3D chromatin architecture, the resulting datasets are extremely large and difficult to manipulate.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we present mariner, a rapid and memory efficient tool to extract, aggregate, and plot data from Hi-C matrices within the R\/Bioconductor environment. Mariner simplifies the process of querying and extracting contacts from multiple Hi-C files using a parallel and block-processing approach. Modular functions allow complete workflow customization for advanced users, yet all-in-one functions are available for running the most common types of analyses. Finally, tight integration with existing Bioconductor infrastructure enables complete analysis and visualization of Hi-C data in R.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Available on GitHub at https:\/\/github.com\/EricSDavis\/mariner and on Bioconductor at https:\/\/www.bioconductor.org\/packages\/release\/bioc\/html\/mariner.html.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae352","type":"journal-article","created":{"date-parts":[[2024,5,29]],"date-time":"2024-05-29T14:07:22Z","timestamp":1716991642000},"source":"Crossref","is-referenced-by-count":9,"title":["Mariner: explore the Hi-Cs"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4051-3217","authenticated-orcid":false,"given":"Eric S","family":"Davis","sequence":"first","affiliation":[{"name":"Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill , Chapel Hill, NC, 27599, United States"},{"name":"Thurston Arthritis Research Center, University of North Carolina at Chapel Hill , Chapel Hill, NC, 27599, United States"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2700-3979","authenticated-orcid":false,"given":"Sarah M","family":"Parker","sequence":"additional","affiliation":[{"name":"Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill , Chapel Hill, NC, 27599, United States"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9617-9671","authenticated-orcid":false,"given":"Nicole E","family":"Kramer","sequence":"additional","affiliation":[{"name":"Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill , Chapel Hill, NC, 27599, United States"}]},{"given":"J P","family":"Flores","sequence":"additional","affiliation":[{"name":"Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill , Chapel Hill, NC, 27599, United States"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0153-7072","authenticated-orcid":false,"given":"Manjari","family":"Kiran","sequence":"additional","affiliation":[{"name":"Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad , Hyderabad, Telangana 500046, India"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2123-0051","authenticated-orcid":false,"given":"Douglas H","family":"Phanstiel","sequence":"additional","affiliation":[{"name":"Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill , Chapel Hill, NC, 27599, United States"},{"name":"Thurston Arthritis Research Center, University of North Carolina at Chapel Hill , Chapel Hill, NC, 27599, United States"},{"name":"Department of Cell Biology & Physiology, University of North Carolina at Chapel Hill , Chapel Hill, NC, 27599, United States"},{"name":"Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill , Chapel Hill, NC, 27599, United States"},{"name":"Curriculum in Genetics & Molecular Biology, University of North Carolina at Chapel Hill , Chapel Hill, NC, 27599, United States"}]}],"member":"286","published-online":{"date-parts":[[2024,5,30]]},"reference":[{"key":"2024061500353586500_btae352-B1","author":"Abdennur"},{"key":"2024061500353586500_btae352-B2","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1186\/s12859-022-04589-y","article-title":"HiCmapTools: a tool to access HiC contact maps","volume":"23","author":"Chang","year":"2022","journal-title":"BMC Bioinformatics"},{"key":"2024061500353586500_btae352-B3","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1016\/j.cels.2016.07.002","article-title":"Juicer provides a One-Click system for analyzing Loop-Resolution Hi-C experiments","volume":"3","author":"Durand","year":"2016","journal-title":"Cell 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