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{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:44:57Z","timestamp":1740185097519,"version":"3.37.3"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"14","license":[{"start":{"date-parts":[[2017,3,23]],"date-time":"2017-03-23T00:00:00Z","timestamp":1490227200000},"content-version":"vor","delay-in-days":1,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000268","name":"BBSRC","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,7,15]]},"abstract":"Abstract<\/jats:title>\n \n Motivation<\/jats:title>\n The exponential growth of publicly available RNA-sequencing (RNA-Seq) data poses an increasing challenge to researchers wishing to discover, analyse and store such data, particularly those based in institutions with limited computational resources. EMBL-EBI is in an ideal position to address these challenges and to allow the scientific community easy access to not just raw, but also processed RNA-Seq data. We present a Web service to access the results of a systematically and continually updated standardized alignment as well as gene and exon expression quantification of all public bulk (and in the near future also single-cell) RNA-Seq runs in 264 species in European Nucleotide Archive, using Representational State Transfer.<\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n The RNASeq-er API (Application Programming Interface) enables ontology-powered search for and retrieval of CRAM, bigwig and bedGraph files, gene and exon expression quantification matrices (Fragments Per Kilobase Of Exon Per Million Fragments Mapped, Transcripts Per Million, raw counts) as well as sample attributes annotated with ontology terms. To date over 270 00 RNA-Seq runs in nearly 10 000 studies (1PB of raw FASTQ data) in 264 species in ENA have been processed and made available via the API.<\/jats:p>\n <\/jats:sec>\n \n Availability and Implementation<\/jats:title>\n The RNASeq-er API can be accessed at http:\/\/www.ebi.ac.uk\/fg\/rnaseq\/api. The commands used to analyse the data are available in supplementary materials and at https:\/\/github.com\/nunofonseca\/irap\/wiki\/iRAP-single-library.<\/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\/btx143","type":"journal-article","created":{"date-parts":[[2017,3,20]],"date-time":"2017-03-20T12:13:29Z","timestamp":1490012009000},"page":"2218-2220","source":"Crossref","is-referenced-by-count":27,"title":["The RNASeq-er API\u2014a gateway to systematically updated analysis of public RNA-seq data"],"prefix":"10.1093","volume":"33","author":[{"given":"Robert","family":"Petryszak","sequence":"first","affiliation":[{"name":"Functional Genomics Group, European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK"}]},{"given":"Nuno A","family":"Fonseca","sequence":"additional","affiliation":[{"name":"Functional Genomics Group, European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK"}]},{"given":"Anja","family":"F\u00fcllgrabe","sequence":"additional","affiliation":[{"name":"Functional Genomics Group, European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK"}]},{"given":"Laura","family":"Huerta","sequence":"additional","affiliation":[{"name":"Functional Genomics Group, European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK"}]},{"given":"Maria","family":"Keays","sequence":"additional","affiliation":[{"name":"Functional Genomics Group, European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK"}]},{"given":"Y Amy","family":"Tang","sequence":"additional","affiliation":[{"name":"Functional Genomics Group, European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK"}]},{"given":"Alvis","family":"Brazma","sequence":"additional","affiliation":[{"name":"Functional Genomics Group, European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK"}]}],"member":"286","published-online":{"date-parts":[[2017,3,22]]},"reference":[{"key":"2023051506463208400_btx143-B1","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1093\/bioinformatics\/btu638","article-title":"HTSeq\u2014a Python framework to work with high-throughput sequencing data","volume":"31","author":"Anders","year":"2014","journal-title":"Bioinformatics Print"},{"key":"2023051506463208400_btx143-B2","doi-asserted-by":"crossref","first-page":"2008","DOI":"10.1101\/gr.133744.111","article-title":"Detecting differential usage of exons from RNA-seq data","volume":"22","author":"Anders","year":"2012","journal-title":"Genome Res"},{"key":"2023051506463208400_btx143-B3","doi-asserted-by":"crossref","first-page":"3241","DOI":"10.1093\/bioinformatics\/btt547","article-title":"BioServices: a common Python package to access biological Web Services programmatically","volume":"29","author":"Cokelaer","year":"2013","journal-title":"Bioinformatics"},{"key":"2023051506463208400_btx143-B4","doi-asserted-by":"crossref","first-page":"D662","DOI":"10.1093\/nar\/gku1010","article-title":"Ensembl 2015","volume":"43","author":"Cunningham","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023051506463208400_btx143-B5","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":"2023051506463208400_btx143-B6","doi-asserted-by":"crossref","first-page":"D50","DOI":"10.1093\/nar\/gkt1081","article-title":"Updates to BioSamples database at European Bioinformatics Institute","volume":"42","author":"Faulconbridge","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2023051506463208400_btx143-B7","article-title":"iRAP - 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