{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,31]],"date-time":"2026-03-31T02:41:26Z","timestamp":1774924886380,"version":"3.50.1"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2019,11,15]],"date-time":"2019-11-15T00:00:00Z","timestamp":1573776000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Operational Programme of Youth Employment"},{"DOI":"10.13039\/501100004895","name":"European Social Fund","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004895","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100002854","name":"ESF","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100002854","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Junta de Castilla y Leon"},{"DOI":"10.13039\/501100014180","name":"JCyL","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100014180","id-type":"DOI","asserted-by":"crossref"}]},{"name":"PTA fellowship","award":["PTA2015-10483-I"],"award-info":[{"award-number":["PTA2015-10483-I"]}]},{"DOI":"10.13039\/501100010198","name":"Ministry of Economy, Industry and Competitiveness","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100010198","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003329","name":"MINECO","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003329","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>RaNA-Seq is a cloud platform for the rapid analysis and visualization of RNA-Seq data. It performs a full analysis in minutes by quantifying FASTQ files, calculating quality control metrics, running differential expression analyses and enabling the explanation of results with functional analyses. Our analysis pipeline applies generally accepted and reproducible protocols that can be applied with two simple steps in its web interface. Analysis results are presented as interactive graphics and reports, ready for their interpretation and publication.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>RaNA-Seq web service is freely available online at https:\/\/ranaseq.eu.<\/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\/btz854","type":"journal-article","created":{"date-parts":[[2019,11,13]],"date-time":"2019-11-13T12:10:43Z","timestamp":1573647043000},"page":"1955-1956","source":"Crossref","is-referenced-by-count":132,"title":["RaNA-Seq: interactive RNA-Seq analysis from FASTQ files to functional analysis"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8178-9768","authenticated-orcid":false,"given":"Carlos","family":"Prieto","sequence":"first","affiliation":[{"name":"Bioinformatics Service, Nucleus, University of Salamanca , Salamanca 37007, Spain"}]},{"given":"David","family":"Barrios","sequence":"additional","affiliation":[{"name":"Bioinformatics Service, Nucleus, University of Salamanca , Salamanca 37007, Spain"}]}],"member":"286","published-online":{"date-parts":[[2019,11,15]]},"reference":[{"key":"2023060911585898900_btz854-B1","doi-asserted-by":"crossref","first-page":"566","DOI":"10.1038\/nbt.4163","article-title":"KBase: the United States Department of Energy Systems Biology Knowledgebase","volume":"36","author":"Arkin","year":"2018","journal-title":"Nat. Biotechnol"},{"key":"2023060911585898900_btz854-B2","doi-asserted-by":"crossref","DOI":"10.1002\/minf.201700090","article-title":"RJSplot: interactive Graphs with R","volume":"37","author":"Barrios","year":"2018","journal-title":"Mol. Inform"},{"key":"2023060911585898900_btz854-B3","doi-asserted-by":"crossref","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"Fastp: an ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"2023060911585898900_btz854-B4","doi-asserted-by":"crossref","first-page":"D492","DOI":"10.1093\/nar\/gkp858","article-title":"The NCBI BioSystems database","volume":"38","author":"Geer","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"2023060911585898900_btz854-B5","doi-asserted-by":"crossref","first-page":"397","DOI":"10.1186\/1471-2164-14-397","article-title":"Web-based visual analysis for high-throughput genomics","volume":"14","author":"Goecks","year":"2013","journal-title":"BMC Genomics"},{"key":"2023060911585898900_btz854-B6","author":"Lachmann","year":"2018"},{"key":"2023060911585898900_btz854-B7","doi-asserted-by":"crossref","first-page":"1366","DOI":"10.1038\/s41467-018-03751-6","article-title":"Massive mining of publicly available RNA-seq data from human and mouse","volume":"9","author":"Lachmann","year":"2018","journal-title":"Nat. Commun"},{"key":"2023060911585898900_btz854-B8","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":"2023060911585898900_btz854-B9","author":"Love","year":"2014"},{"key":"2023060911585898900_btz854-B10","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1038\/nmeth.4197","article-title":"Salmon provides fast and bias-aware quantification of transcript expression","volume":"14","author":"Patro","year":"2017","journal-title":"Nat. Methods"},{"key":"2023060911585898900_btz854-B11","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":"2023060911585898900_btz854-B12","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","article-title":"edgeR: a Bioconductor package for differential expression analysis of digital gene expression data","volume":"26","author":"Robinson","year":"2010","journal-title":"Bioinformatics"},{"key":"2023060911585898900_btz854-B13","doi-asserted-by":"crossref","first-page":"524","DOI":"10.1186\/1471-2164-13-524","article-title":"SERE: single-parameter quality control and sample comparison for RNA-Seq","volume":"13","author":"Schulze","year":"2012","journal-title":"BMC Genomics"},{"key":"2023060911585898900_btz854-B14","author":"Sergushichev","year":"2016"},{"key":"2023060911585898900_btz854-B15","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1093\/bib\/bbt086","article-title":"Comparison of software packages for detecting differential expression in RNA-seq studies","volume":"16","author":"Seyednasrollah","year":"2015","journal-title":"Brief. Bioinform"},{"key":"2023060911585898900_btz854-B16","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1186\/1471-2105-14-91","article-title":"A comparison of methods for differential expression analysis of RNA-seq data","volume":"14","author":"Soneson","year":"2013","journal-title":"BMC Bioinformatics"},{"key":"2023060911585898900_btz854-B17","doi-asserted-by":"crossref","first-page":"556","DOI":"10.1016\/j.cels.2018.10.007","article-title":"BioJupies: automated generation of interactive notebooks for RNA-seq data analysis in the cloud","volume":"7","author":"Torre","year":"2018","journal-title":"Cell Syst"},{"key":"2023060911585898900_btz854-B18","first-page":"1","article-title":"Goseq\u202f: gene ontology testing for RNA-seq datasets reading data","author":"Young","year":"2010","journal-title":"Gene"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btz854\/30795576\/btz854.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/6\/1955\/50553495\/bioinformatics_36_6_1955.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/6\/1955\/50553495\/bioinformatics_36_6_1955.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,9]],"date-time":"2023-06-09T12:00:47Z","timestamp":1686312047000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/36\/6\/1955\/5626181"}},"subtitle":[],"editor":[{"given":"Bonnie","family":"Berger","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2019,11,15]]},"references-count":18,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2020,3,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btz854","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2020,3,15]]},"published":{"date-parts":[[2019,11,15]]}}}