{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,16]],"date-time":"2026-04-16T06:52:21Z","timestamp":1776322341270,"version":"3.50.1"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2017,5,19]],"date-time":"2017-05-19T00:00:00Z","timestamp":1495152000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100008730","name":"Norwegian Cancer Society","doi-asserted-by":"publisher","award":["PR-2007-0166"],"award-info":[{"award-number":["PR-2007-0166"]}],"id":[{"id":"10.13039\/100008730","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100008730","name":"Norwegian Cancer Society","doi-asserted-by":"publisher","award":["NN9313K"],"award-info":[{"award-number":["NN9313K"]}],"id":[{"id":"10.13039\/100008730","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005416","name":"Research Council of Norway","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100005416","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Advances in high-throughput RNA sequencing have enabled more efficient detection of fusion transcripts, but the technology and associated software used for fusion detection from sequencing data often yield a high false discovery rate. Good prioritization of the results is important, and this can be helped by a visualization framework that automatically integrates RNA data with known genomic features. Here we present chimeraviz, a Bioconductor package that automates the creation of chimeric RNA visualizations. The package supports input from nine different fusion-finder tools: deFuse, EricScript, InFusion, JAFFA, FusionCatcher, FusionMap, PRADA, SOAPfuse and STAR-FUSION.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>chimeraviz is an R package available via Bioconductor (https:\/\/bioconductor.org\/packages\/release\/bioc\/html\/chimeraviz.html) under Artistic-2.0. Source code and support is available at GitHub (https:\/\/github.com\/stianlagstad\/chimeraviz).<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx329","type":"journal-article","created":{"date-parts":[[2017,5,18]],"date-time":"2017-05-18T11:12:31Z","timestamp":1495105951000},"page":"2954-2956","source":"Crossref","is-referenced-by-count":36,"title":["<i>chimeraviz<\/i>: a tool for visualizing chimeric RNA"],"prefix":"10.1093","volume":"33","author":[{"given":"Stian","family":"L\u00e5gstad","sequence":"first","affiliation":[{"name":"Department of Molecular Oncology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway"},{"name":"Department of Informatics, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway"},{"name":"Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway"}]},{"given":"Sen","family":"Zhao","sequence":"additional","affiliation":[{"name":"Department of Molecular Oncology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway"},{"name":"Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway"}]},{"given":"Andreas M","family":"Hoff","sequence":"additional","affiliation":[{"name":"Department of Molecular Oncology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway"},{"name":"Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway"}]},{"given":"Bjarne","family":"Johannessen","sequence":"additional","affiliation":[{"name":"Department of Molecular Oncology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway"},{"name":"Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway"}]},{"given":"Ole Christian","family":"Lingj\u00e6rde","sequence":"additional","affiliation":[{"name":"Department of Informatics, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway"},{"name":"Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway"}]},{"given":"Rolf I","family":"Skotheim","sequence":"additional","affiliation":[{"name":"Department of Molecular Oncology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway"},{"name":"Department of Informatics, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway"},{"name":"Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway"}]}],"member":"286","published-online":{"date-parts":[[2017,5,19]]},"reference":[{"key":"2023020206433938100_btx329-B1","doi-asserted-by":"crossref","first-page":"3232","DOI":"10.1093\/bioinformatics\/bts617","article-title":"Discovering chimeric transcripts in paired-end RNA-seq data by using EricScript","volume":"28","author":"Benelli","year":"2012","journal-title":"Bioinformatics"},{"key":"2023020206433938100_btx329-B2","doi-asserted-by":"crossref","first-page":"43.","DOI":"10.1186\/s13073-015-0167-x","article-title":"JAFFA: high sensitivity transcriptome-focused fusion gene detection","volume":"7","author":"Davidson","year":"2015","journal-title":"Genome Med"},{"key":"2023020206433938100_btx329-B3","doi-asserted-by":"crossref","first-page":"1231","DOI":"10.1101\/gr.130062.111","article-title":"Chimeras taking shape: potential functions of proteins encoded by chimeric RNA transcripts","volume":"22","author":"Frenkel-Morgenstern","year":"2012","journal-title":"Genome 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Res"},{"key":"2023020206433938100_btx329-B8","doi-asserted-by":"crossref","first-page":"R12.","DOI":"10.1186\/gb-2013-14-2-r12","article-title":"SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data","volume":"14","author":"Jia","year":"2013","journal-title":"Genome Biol"},{"key":"2023020206433938100_btx329-B9","doi-asserted-by":"crossref","first-page":"21597.","DOI":"10.1038\/srep21597","article-title":"Comparative assessment of methods for the fusion transcripts detection from RNA-Seq data","volume":"6","author":"Kumar","year":"2016","journal-title":"Sci. Rep"},{"key":"2023020206433938100_btx329-B10","doi-asserted-by":"crossref","first-page":"e1001138.","DOI":"10.1371\/journal.pcbi.1001138","article-title":"deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data","volume":"7","author":"McPherson","year":"2011","journal-title":"PLoS Comput. Biol"},{"key":"2023020206433938100_btx329-B11","author":"Nicorici","year":"2014"},{"key":"2023020206433938100_btx329-B12","author":"Okonechnikov","year":"2016"},{"key":"2023020206433938100_btx329-B13","doi-asserted-by":"crossref","first-page":"2224","DOI":"10.1093\/bioinformatics\/btu169","article-title":"PRADA: pipeline for RNA sequencing data analysis","volume":"30","author":"Torres-Garcia","year":"2014","journal-title":"Bioinformatics"},{"key":"2023020206433938100_btx329-B14","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\/18\/2954\/49041255\/bioinformatics_33_18_2954.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/18\/2954\/49041255\/bioinformatics_33_18_2954.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T06:44:15Z","timestamp":1675320255000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/18\/2954\/3835381"}},"subtitle":[],"editor":[{"given":"Bonnie","family":"Berger","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2017,5,19]]},"references-count":14,"journal-issue":{"issue":"18","published-print":{"date-parts":[[2017,9,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx329","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2017,9,15]]},"published":{"date-parts":[[2017,5,19]]}}}