{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,22]],"date-time":"2025-11-22T11:22:27Z","timestamp":1763810547589,"version":"3.37.3"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"22","license":[{"start":{"date-parts":[[2021,5,22]],"date-time":"2021-05-22T00:00:00Z","timestamp":1621641600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01GM129085","R01GM124531"],"award-info":[{"award-number":["R01GM129085","R01GM124531"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,11,18]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Gene alternative splicing plays an important role in development, tissue specialization and disease and differences in splicing patterns can reveal important factors for phenotypic differentiation. While multiple computational methods exist to determine splicing differences, there is a need for user-friendly visualizations that present an intuitive view of the data and work across methods.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We developed a toolkit, Jutils, for visualizing differential splicing events at the intron (splice junction) level. Jutils is method-agnostic, converting individual tools\u2019 output into a unified representation and using it to create visualizations. Jutils creates three types of visualizations, namely heatmaps of absolute and Z-score normalized splice ratios, sashimi plots and Venn diagrams of results from multiple comparisons. Jutils is lightweight, relying solely on the unified data file for visualizations.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Jutils is implemented in Python and is available from https:\/\/github.com\/Splicebox\/Jutils.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab401","type":"journal-article","created":{"date-parts":[[2021,5,21]],"date-time":"2021-05-21T19:13:55Z","timestamp":1621624435000},"page":"4272-4274","source":"Crossref","is-referenced-by-count":9,"title":["Jutils: a visualization toolkit for differential alternative splicing events"],"prefix":"10.1093","volume":"37","author":[{"given":"Guangyu","family":"Yang","sequence":"first","affiliation":[{"name":"Department of Computer Science, Johns Hopkins University , Baltimore, MD 21205, USA"}]},{"given":"Leslie","family":"Cope","sequence":"additional","affiliation":[{"name":"Department of Oncology, Johns Hopkins School of Medicine , Baltimore, MD 21205, USA"}]},{"given":"Zitong","family":"He","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Johns Hopkins University , Baltimore, MD 21205, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8124-2324","authenticated-orcid":false,"given":"Liliana","family":"Florea","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Johns Hopkins University , Baltimore, MD 21205, USA"},{"name":"Department of Genetic Medicine, Johns Hopkins School of Medicine , Baltimore, MD 21205, USA"}]}],"member":"286","published-online":{"date-parts":[[2021,5,22]]},"reference":[{"key":"2023051607093137100_btab401-B2","doi-asserted-by":"crossref","first-page":"e1006360","DOI":"10.1371\/journal.pcbi.1006360","article-title":"Ggsashimi: sashimi plot revised for browser and annotation-independent splicing visualization","volume":"14","author":"Garrido-Martin","year":"2018","journal-title":"PLoS Comput. Biol"},{"key":"2023051607093137100_btab401-B3","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":"2023051607093137100_btab401-B4","doi-asserted-by":"crossref","first-page":"1413","DOI":"10.1038\/ng.259","article-title":"Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing","volume":"40","author":"Pan","year":"2008","journal-title":"Nat. Genet"},{"key":"2023051607093137100_btab401-B5","doi-asserted-by":"crossref","first-page":"E5593","DOI":"10.1073\/pnas.1419161111","article-title":"rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-seq data","volume":"111","author":"Shen","year":"2014","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023051607093137100_btab401-B6","doi-asserted-by":"crossref","first-page":"e11752","DOI":"10.7554\/eLife.11752","article-title":"A new view of transcriptome complexity and regulation through the lens of local splicing variations","volume":"5","author":"Vaquero-Garcia","year":"2016","journal-title":"Elife"},{"year":"2020","author":"Yang","key":"2023051607093137100_btab401-B7"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btab401\/38608710\/btab401.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/22\/4272\/50335135\/btab401.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/22\/4272\/50335135\/btab401.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,16]],"date-time":"2023-05-16T07:12:44Z","timestamp":1684221164000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/37\/22\/4272\/6281071"}},"subtitle":[],"editor":[{"given":"Can","family":"Alkan","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2021,5,22]]},"references-count":6,"journal-issue":{"issue":"22","published-print":{"date-parts":[[2021,11,18]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btab401","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2021,11,15]]},"published":{"date-parts":[[2021,5,22]]}}}