{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,30]],"date-time":"2025-12-30T04:40:35Z","timestamp":1767069635924,"version":"3.37.3"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"21","license":[{"start":{"date-parts":[[2021,7,1]],"date-time":"2021-07-01T00:00:00Z","timestamp":1625097600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["HG004483","GM080203"],"award-info":[{"award-number":["HG004483","GM080203"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,11,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Genome browsers are an essential tool in genome analysis. Modern genome browsers enable complex and interactive visualization of a wide variety of genomic data modalities. While such browsers are very powerful, they can be challenging to configure and program for bioinformaticians lacking expertise in web development.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We have developed an R package that provides an interface to the JBrowse 2 genome browser. The package can be used to configure and customize the browser entirely with R code. The browser can be deployed from the R console, or embedded in Shiny applications or R Markdown documents.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>JBrowseR is available for download from CRAN, and the source code is openly available from the Github repository at https:\/\/github.com\/GMOD\/JBrowseR\/.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab459","type":"journal-article","created":{"date-parts":[[2021,6,29]],"date-time":"2021-06-29T19:09:03Z","timestamp":1624993743000},"page":"3914-3915","source":"Crossref","is-referenced-by-count":19,"title":["JBrowseR: an R interface to the JBrowse 2 genome browser"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2068-3366","authenticated-orcid":false,"given":"Elliot A","family":"Hershberg","sequence":"first","affiliation":[{"name":"Department of Bioengineering, University of California , Berkeley, Berkeley, CA 94720, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9781-5323","authenticated-orcid":false,"given":"Garrett","family":"Stevens","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, University of California , Berkeley, Berkeley, CA 94720, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Colin","family":"Diesh","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, University of California , Berkeley, Berkeley, CA 94720, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peter","family":"Xie","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, University of California , Berkeley, Berkeley, CA 94720, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Teresa","family":"De Jesus Martinez","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, University of California , Berkeley, Berkeley, CA 94720, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Robert","family":"Buels","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, University of California , Berkeley, Berkeley, CA 94720, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lincoln","family":"Stein","sequence":"additional","affiliation":[{"name":"Adaptive Oncology, Ontario Institute for Cancer Research , Toronto, ON M5G 0A3, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ian","family":"Holmes","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, University of California , Berkeley, Berkeley, CA 94720, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,7,1]]},"reference":[{"key":"2023051608255153200_btab459-B1","doi-asserted-by":"crossref","first-page":"925","DOI":"10.1101\/gr.1860604","article-title":"An overview of Ensembl","volume":"14","author":"Birney","year":"2004","journal-title":"Genome Res"},{"key":"2023051608255153200_btab459-B2","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1186\/s13059-016-0924-1","article-title":"Jbrowse: a dynamic web platform for genome visualization and analysis","volume":"17","author":"Buels","year":"2016","journal-title":"Genome Biol"},{"key":"2023051608255153200_btab459-B3","doi-asserted-by":"crossref","first-page":"938","DOI":"10.1038\/nmeth.3038","article-title":"Epiviz: interactive visual analytics for functional genomics data","volume":"11","author":"Chelaru","year":"2014","journal-title":"Nat. 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