{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,10]],"date-time":"2026-03-10T19:36:56Z","timestamp":1773171416887,"version":"3.50.1"},"reference-count":4,"publisher":"Oxford University Press (OUP)","issue":"22","license":[{"start":{"date-parts":[[2019,6,14]],"date-time":"2019-06-14T00:00:00Z","timestamp":1560470400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["U24 CA210989"],"award-info":[{"award-number":["U24 CA210989"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000879","name":"Alfred P. Sloan Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000879","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,11,1]]},"abstract":"Abstract<\/jats:title>\n \n Motivation<\/jats:title>\n The association of splicing signatures with disease is a leading area of study for prognosis, diagnosis and therapy. We present a novel fast-performing annotation-dependent tool called SCANVIS for scoring and annotating splice junctions (SJs), with an efficient visualization tool that highlights SJ details such as frame-shifts and annotation support for individual samples or a sample cohort.<\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n Using publicly available samples, we show that the tissue specificity inherent in splicing signatures is maintained with the Relative Read Support scoring method in SCANVIS, and we showcase some visualizations to demonstrate the usefulness of incorporating annotation details into sashimi plots.<\/jats:p>\n <\/jats:sec>\n \n Availability and implementation<\/jats:title>\n https:\/\/github.com\/nygenome\/SCANVIS and https:\/\/bioconductor.org\/packages\/SCANVIS.<\/jats:p>\n <\/jats:sec>\n \n Supplementary information<\/jats:title>\n Supplementary data are available at Bioinformatics online.<\/jats:p>\n <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz452","type":"journal-article","created":{"date-parts":[[2019,6,6]],"date-time":"2019-06-06T15:14:26Z","timestamp":1559834066000},"page":"4843-4845","source":"Crossref","is-referenced-by-count":3,"title":["SCANVIS: a tool for SCoring, ANnotating and VISualizing splice junctions"],"prefix":"10.1093","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1688-992X","authenticated-orcid":false,"given":"Phaedra","family":"Agius","sequence":"first","affiliation":[{"name":"Computational Biology, New York Genome Center , New York, NY, USA"}]},{"given":"Heather","family":"Geiger","sequence":"additional","affiliation":[{"name":"Computational Biology, New York Genome Center , New York, NY, USA"}]},{"given":"Nicolas","family":"Robine","sequence":"additional","affiliation":[{"name":"Computational Biology, New York Genome Center , New York, NY, USA"}]}],"member":"286","published-online":{"date-parts":[[2019,6,14]]},"reference":[{"key":"2023013108332043700_btz452-B1","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"2023013108332043700_btz452-B2","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1038\/s41588-017-0004-9","article-title":"Annotation-free quantification of RNA splicing using LeafCutter","volume":"50","author":"Li","year":"2018","journal-title":"Nat. Genet"},{"key":"2023013108332043700_btz452-B3","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1038\/nbt.1754","article-title":"Integrative genomic viewer","volume":"29","author":"Robinson","year":"2011","journal-title":"Nat. Biotechnol"},{"key":"2023013108332043700_btz452-B4","first-page":"E8181","article-title":"JUM is a computational method for comprehensive annotation-free analysis of alternative pre-mRNA splicing","volume":"115","author":"Wang","year":"2018","journal-title":"Proc. Natl. Acad. Sci. USA"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btz452\/28822263\/btz452.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/22\/4843\/48977697\/bioinformatics_35_22_4843.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/22\/4843\/48977697\/bioinformatics_35_22_4843.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T12:37:44Z","timestamp":1675168664000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/35\/22\/4843\/5514043"}},"subtitle":[],"editor":[{"given":"Jonathan","family":"Wren","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2019,6,14]]},"references-count":4,"journal-issue":{"issue":"22","published-print":{"date-parts":[[2019,11,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btz452","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/549261","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":[[2019,11,15]]},"published":{"date-parts":[[2019,6,14]]}}}