{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,30]],"date-time":"2026-03-30T21:20:09Z","timestamp":1774905609636,"version":"3.50.1"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2020,9,29]],"date-time":"2020-09-29T00:00:00Z","timestamp":1601337600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["UM1 HG009443"],"award-info":[{"award-number":["UM1 HG009443"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,6,9]]},"abstract":"Abstract<\/jats:title>\n \n Motivation<\/jats:title>\n Long-read RNA-sequencing technologies such as PacBio and Oxford Nanopore have discovered an explosion of new transcript isoforms that are difficult to visually analyze using currently available tools. We introduce the Swan Python library, which is designed to analyze and visualize transcript models.<\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n Swan finds 4909 differentially expressed transcripts between cell lines HepG2 and HFFc6, including 279 that are differentially expressed even though the parent gene is not. Additionally, Swan discovers 285 reproducible exon skipping and 47 intron retention events not recorded in the GENCODE v29 annotation.<\/jats:p>\n <\/jats:sec>\n \n Availability and implementation<\/jats:title>\n The Swan library for Python 3 is available on PyPi at https:\/\/pypi.org\/project\/swan-vis\/ and on GitHub at https:\/\/github.com\/mortazavilab\/swan_vis.<\/jats:p>\n <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa836","type":"journal-article","created":{"date-parts":[[2020,9,15]],"date-time":"2020-09-15T23:25:55Z","timestamp":1600212355000},"page":"1322-1323","source":"Crossref","is-referenced-by-count":30,"title":["Swan: a library for the analysis and visualization of long-read transcriptomes"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9240-0102","authenticated-orcid":false,"given":"Fairlie","family":"Reese","sequence":"first","affiliation":[{"name":"Department of Developmental and Cell Biology"},{"name":"Center for Complex Biological Systems , UC Irvine, Irvine, CA 92697, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4259-6362","authenticated-orcid":false,"given":"Ali","family":"Mortazavi","sequence":"additional","affiliation":[{"name":"Department of Developmental and Cell Biology"},{"name":"Center for Complex Biological Systems , UC Irvine, Irvine, CA 92697, USA"}]}],"member":"286","published-online":{"date-parts":[[2020,11,23]]},"reference":[{"key":"2023051706062656200_btaa836-B1","first-page":"1","article-title":"A survey of best practices for RNA-seq data analysis","volume":"17","author":"Conesa","year":"2016","journal-title":"Genome Biol"},{"key":"2023051706062656200_btaa836-B2","doi-asserted-by":"crossref","first-page":"1760","DOI":"10.1101\/gr.135350.111","article-title":"GENCODE: the reference human genome annotation for the ENCODE project","volume":"22","author":"Harrow","year":"2012","journal-title":"Genome Res"},{"key":"2023051706062656200_btaa836-B3","doi-asserted-by":"crossref","first-page":"2400","DOI":"10.1093\/bioinformatics\/btv034","article-title":"Quantitative visualization of alternative exon expression from RNA-seq data","volume":"31","author":"Katz","year":"2015","journal-title":"Bioinformatics"},{"key":"2023051706062656200_btaa836-B4","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":"2023051706062656200_btaa836-B5","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1186\/s13059-017-1382-0","article-title":"SCANPY: large-scale single-cell gene expression data analysis","volume":"19","author":"Wolf","year":"2018","journal-title":"Genome Biol"},{"key":"2023051706062656200_btaa836-B6","author":"Wyman","year":"2019"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaa836\/34463328\/btaa836.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/9\/1322\/50359663\/btaa836.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/9\/1322\/50359663\/btaa836.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,17]],"date-time":"2023-05-17T02:11:39Z","timestamp":1684289499000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/37\/9\/1322\/5912931"}},"subtitle":[],"editor":[{"given":"Inanc","family":"Birol","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2020,11,23]]},"references-count":6,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2021,6,9]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaa836","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2020.06.09.143024","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":[[2021,5,1]]},"published":{"date-parts":[[2020,11,23]]}}}