{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,16]],"date-time":"2026-04-16T20:39:11Z","timestamp":1776371951072,"version":"3.51.2"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"19","license":[{"start":{"date-parts":[[2017,5,29]],"date-time":"2017-05-29T00:00:00Z","timestamp":1496016000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,10,1]]},"abstract":"Abstract<\/jats:title>\n \n Motivation<\/jats:title>\n Data visualization is a crucial tool for data exploration, analysis and interpretation. For the visualization of genomic data there lacks a tool to create customizable non-circular plots of whole genomes from any species.<\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n We have developed karyoploteR, an R\/Bioconductor package to create linear chromosomal representations of any genome with genomic annotations and experimental data plotted along them. Plot creation process is inspired in R base graphics, with a main function creating karyoplots with no data and multiple additional functions, including custom functions written by the end-user, adding data and other graphical elements. This approach allows the creation of highly customizable plots from arbitrary data with complete freedom on data positioning and representation.<\/jats:p>\n <\/jats:sec>\n \n Availability and implementation<\/jats:title>\n karyoploteR is released under Artistic-2.0 License. Source code and documentation are freely available through Bioconductor (http:\/\/www.bioconductor.org\/packages\/karyoploteR) and at the examples and tutorial page at https:\/\/bernatgel.github.io\/karyoploter_tutorial.<\/jats:p>\n <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx346","type":"journal-article","created":{"date-parts":[[2017,5,26]],"date-time":"2017-05-26T07:09:09Z","timestamp":1495782549000},"page":"3088-3090","source":"Crossref","is-referenced-by-count":733,"title":["karyoploteR: an R\/Bioconductor package to plot customizable genomes displaying arbitrary data"],"prefix":"10.1093","volume":"33","author":[{"given":"Bernat","family":"Gel","sequence":"first","affiliation":[{"name":"Hereditary Cancer Group, Program for Predictive and Personalized Medicine of Cancer \u2013 Germans Trias i Pujol Research Institute (PMPPC-IGTP), Campus Can Ruti, Badalona, Spain"}]},{"given":"Eduard","family":"Serra","sequence":"additional","affiliation":[{"name":"Hereditary Cancer Group, Program for Predictive and Personalized Medicine of Cancer \u2013 Germans Trias i Pujol Research Institute (PMPPC-IGTP), Campus Can Ruti, Badalona, Spain"},{"name":"CIBERONC"}]}],"member":"286","published-online":{"date-parts":[[2017,5,29]]},"reference":[{"key":"2023020206440753700_btx346-B1","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1093\/bioinformatics\/btv562","article-title":"regioneR: an R\/Bioconductor package for the association analysis of genomic regions based on permutation tests","volume":"32","author":"Gel","year":"2016","journal-title":"Bioinformatics"},{"key":"2023020206440753700_btx346-B2","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1007\/978-1-4939-3578-9_16","article-title":"Visualizing genomic data using Gviz and bioconductor","volume":"1418","author":"Hahne","year":"2016","journal-title":"Methods Mol. Biol"},{"key":"2023020206440753700_btx346-B3","doi-asserted-by":"crossref","first-page":"1639","DOI":"10.1101\/gr.092759.109","article-title":"Circos: an information aesthetic for comparative genomics","volume":"19","author":"Krzywinski","year":"2009","journal-title":"Genome Res"},{"key":"2023020206440753700_btx346-B4","doi-asserted-by":"crossref","first-page":"2366","DOI":"10.1093\/bioinformatics\/btw137","article-title":"ChromPlot: Visualization of genomic data in chromosomal context","volume":"32","author":"Or\u00f3stica","year":"2016","journal-title":"Bioinformatics"},{"key":"2023020206440753700_btx346-B5","author":"Pai","year":"2014"},{"key":"2023020206440753700_btx346-B6","doi-asserted-by":"crossref","first-page":"R77.","DOI":"10.1186\/gb-2012-13-8-r77","article-title":"ggbio: an R package for extending the grammar of graphics for genomic data","volume":"13","author":"Yin","year":"2012","journal-title":"Genome Biol"},{"key":"2023020206440753700_btx346-B7","doi-asserted-by":"crossref","first-page":"244.","DOI":"10.1186\/1471-2105-14-244","article-title":"RCircos: an R package for Circos 2D track plots","volume":"14","author":"Zhang","year":"2013","journal-title":"BMC Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/19\/3088\/49041429\/bioinformatics_33_19_3088.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/19\/3088\/49041429\/bioinformatics_33_19_3088.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T01:44:23Z","timestamp":1675302263000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/19\/3088\/3857734"}},"subtitle":[],"editor":[{"given":"John","family":"Hancock","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2017,5,29]]},"references-count":7,"journal-issue":{"issue":"19","published-print":{"date-parts":[[2017,10,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx346","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/122838","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2017,10,1]]},"published":{"date-parts":[[2017,5,29]]}}}