{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,2]],"date-time":"2026-04-02T08:00:48Z","timestamp":1775116848487,"version":"3.50.1"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2016,10,6]],"date-time":"2016-10-06T00:00:00Z","timestamp":1475712000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institute of Health","doi-asserted-by":"publisher","award":["T32HL094294"],"award-info":[{"award-number":["T32HL094294"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institute of Health","doi-asserted-by":"publisher","award":["R01NS079433"],"award-info":[{"award-number":["R01NS079433"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000968","name":"The American Heart Association","doi-asserted-by":"crossref","award":["15POST25710234"],"award-info":[{"award-number":["15POST25710234"]}],"id":[{"id":"10.13039\/100000968","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Transcriptional profiling using RNA sequencing (RNAseq) has emerged as a powerful methodology to quantify global gene expression patterns in various contexts from single cells to whole tissues. The tremendous amount of data generated by this profiling technology presents a daunting challenge in terms of effectively visualizing and interpreting results. Convenient and intuitive data interfaces are critical for researchers to easily upload, analyze and visualize their RNAseq data. We designed the START (Shiny Transcriptome Analysis Resource Tool) App with these requirements in mind. This application has the power and flexibility to be resident on a local computer or serve as a web-based environment, enabling easy sharing of data between researchers and collaborators.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>Source Code for the START App is written entirely in R and can be freely available to download at https:\/\/github.com\/jminnier\/STARTapp with the code licensed under GPLv3. It can be launched on any system that has R installed. The START App is also hosted on https:\/\/kcvi.shinyapps.io\/START for researchers to temporarily upload their data.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btw624","type":"journal-article","created":{"date-parts":[[2016,9,29]],"date-time":"2016-09-29T19:06:19Z","timestamp":1475175979000},"page":"447-449","source":"Crossref","is-referenced-by-count":91,"title":["The START App: a web-based RNAseq analysis and visualization resource"],"prefix":"10.1093","volume":"33","author":[{"given":"Jonathan W","family":"Nelson","sequence":"first","affiliation":[{"name":"The Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiri","family":"Sklenar","sequence":"additional","affiliation":[{"name":"The Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anthony P","family":"Barnes","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jessica","family":"Minnier","sequence":"additional","affiliation":[{"name":"The Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR, USA"},{"name":"School of Public Health, Oregon Health & Science University, Portland, OR, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2016,10,6]]},"reference":[{"key":"2023020204402960600_btw624-B1","author":"Chang","year":"2016"},{"key":"2023020204402960600_btw624-B2","doi-asserted-by":"crossref","first-page":"2532","DOI":"10.1093\/bioinformatics\/bts477","article-title":"easyRNASeq: a bioconductor package for processing RNA-Seq data","volume":"28","author":"Delhomme","year":"2012","journal-title":"Bioinformatics"},{"key":"2023020204402960600_btw624-B3","first-page":"29","article-title":"Advanced applications of RNA sequencing and challenges","volume":"9","author":"Han","year":"2015","journal-title":"Bioinform. Biol. Insights"},{"key":"2023020204402960600_btw624-B4","doi-asserted-by":"crossref","first-page":"R29.","DOI":"10.1186\/gb-2014-15-2-r29","article-title":"voom: precision weights unlock linear model analysis tools for RNA-seq read counts","volume":"15","author":"Law","year":"2014","journal-title":"Genome Biol"},{"key":"2023020204402960600_btw624-B5","doi-asserted-by":"crossref","first-page":"556","DOI":"10.1016\/j.gde.2013.07.002","article-title":"Chromatin modulators as facilitating factors in cellular reprogramming","volume":"23","author":"Luna-Zurita","year":"2013","journal-title":"Curr. Opin. Genet. Dev"},{"key":"2023020204402960600_btw624-B6","doi-asserted-by":"crossref","first-page":"W566","DOI":"10.1093\/nar\/gkv468","article-title":"ClustVis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap","volume":"43","author":"Metsalu","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023020204402960600_btw624-B7","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1093\/bib\/bbv036","article-title":"Systematically evaluating interfaces for RNA-seq analysis from a life scientist perspective","volume":"17","author":"Poplawski","year":"2016","journal-title":"Brief. Bioinform"},{"key":"2023020204402960600_btw624-B8","author":"R Core Team","year":"2015"},{"key":"2023020204402960600_btw624-B9","doi-asserted-by":"crossref","first-page":"2514","DOI":"10.1093\/bioinformatics\/btu308","article-title":"RNASeqGUI: a GUI for analysing RNA-Seq data","volume":"30","author":"Russo","year":"2014","journal-title":"Bioinformatics"},{"key":"2023020204402960600_btw624-B10","doi-asserted-by":"crossref","first-page":"1001\u20131001.","DOI":"10.1038\/nmeth.3615","article-title":"BrowserGenome.org: web-based RNA-seq data analysis and visualization","volume":"12","author":"Schmid-Burgk","year":"2015","journal-title":"Nat. Methods"},{"key":"2023020204402960600_btw624-B11","doi-asserted-by":"crossref","first-page":"2005","DOI":"10.1056\/NEJMoa1510764","article-title":"Prospective validation of a 21-gene expression assay in breast cancer","volume":"373","author":"Sparano","year":"2015","journal-title":"N. Engl. J. Med"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/3\/447\/49037222\/bioinformatics_33_3_447.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/3\/447\/49037222\/bioinformatics_33_3_447.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T04:41:06Z","timestamp":1675312866000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/3\/447\/2525724"}},"subtitle":[],"editor":[{"given":"Bonnie","family":"Berger","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2016,10,6]]},"references-count":11,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2017,2,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btw624","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2017,2,1]]},"published":{"date-parts":[[2016,10,6]]}}}