{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,14]],"date-time":"2026-10-14T16:56:58Z","timestamp":1791997018010,"version":"4.4.0"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2025,1,16]],"date-time":"2025-01-16T00:00:00Z","timestamp":1736985600000},"content-version":"vor","delay-in-days":21,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000272","name":"National Institute for Health Research","doi-asserted-by":"publisher","award":["131575"],"award-info":[{"award-number":["131575"]}],"id":[{"id":"10.13039\/501100000272","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,12,26]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Locuszoomr is an R package for visualizing and creating publication-ready regional gene locus plots similar to those produced by the original web interface \u2018LocusZoom\u2019, but running locally in R. Genetic or genomic data with gene annotation tracks are plotted via R base graphics or \u2018ggplot2\u2019, allowing flexibility and easy customization. Modular plotting functions enable layering of multiple GWAS plots such as for PheWAS, comparing GWAS with eQTL signals, and aligning multiple locus plots on the same page. Interactive plots can be visualized using \u2018plotly\u2019 enabling quick identification of data points for labelling. The \u2018LDlink\u2019 API (https:\/\/ldlink.nih.gov\/) can be programmatically queried to obtain linkage disequilibrium (LD) data from the 1000 Genomes Project which is overlaid on plots. The package allows users to query Ensembl databases from Bioconductor or AnnotationHub for genomic information, so it can be used to show gene track information for any species available in Ensembl. Helper functions enable recombination rate data from UCSC to be overlaid on plots. The package has a detailed vignette and includes embedded example GWAS data to allow users to try out different features. Locuszoomr is also fast: identifying 50 peaks in a GWAS of around 8 million SNPs takes around 0.6\u2009s. Exporting 50 locus plots with 1 Mb window with recombination rate takes around 30\u2009son Intel ninth gen CPU or 14\u2009son Apple ARM M3.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The R package locuszoomr is open-source and available from CRAN: https:\/\/cran.r-project.org\/package=locuszoomr and GitHub: https:\/\/github.com\/myles-lewis\/locuszoomr<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioadv\/vbaf006","type":"journal-article","created":{"date-parts":[[2025,1,14]],"date-time":"2025-01-14T07:16:10Z","timestamp":1736838970000},"source":"Crossref","is-referenced-by-count":42,"title":["locuszoomr: an R package for visualizing publication-ready regional gene locus plots"],"prefix":"10.1093","volume":"5","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9365-5345","authenticated-orcid":false,"given":"Myles J","family":"Lewis","sequence":"first","affiliation":[{"name":"Centre for Experimental Medicine & Rheumatology, William Harvey Research Institute, Queen Mary University of London , London EC1M 6BQ,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Susan","family":"Wang","sequence":"additional","affiliation":[{"name":"Centre for Experimental Medicine & Rheumatology, William Harvey Research Institute, Queen Mary University of London , London EC1M 6BQ,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,1,16]]},"reference":[{"key":"2025061901524057200_vbaf006-B1","doi-asserted-by":"crossref","first-page":"1457","DOI":"10.1038\/ng.3434","article-title":"Genetic association analyses implicate aberrant regulation of innate and adaptive immunity genes in the pathogenesis of systemic lupus 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