{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,19]],"date-time":"2026-01-19T14:05:16Z","timestamp":1768831516077,"version":"3.49.0"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"21","license":[{"start":{"date-parts":[[2017,7,14]],"date-time":"2017-07-14T00:00:00Z","timestamp":1499990400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/100000897","name":"Cystic Fibrosis Foundation","doi-asserted-by":"publisher","award":["STANTO15R0"],"award-info":[{"award-number":["STANTO15R0"]}],"id":[{"id":"10.13039\/100000897","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000066","name":"National Institute of Environmental Health Sciences","doi-asserted-by":"publisher","award":["P42 ES007373"],"award-info":[{"award-number":["P42 ES007373"]}],"id":[{"id":"10.13039\/100000066","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Current options to mine publicly available gene expression data deposited in NCBI\u2019s gene expression omnibus (GEO), such as the GEO web portal and related applications, are optimized to reanalyze a single study, or search for a single gene, and therefore require manual intervention to reanalyze multiple studies for user-specified gene sets. ScanGEO is a simple, user-friendly Shiny web application designed to identify differentially expressed genes across all GEO studies matching user-specified criteria, for a flexible set of genes, visualize results and provide summary statistics and other reports using a single command.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The ScanGEO source code is written in R and implemented as a Shiny app that can be freely accessed at http:\/\/scangeo.dartmouth.edu\/ScanGEO\/. For users who would like to run a local instantiation of the app, the R source code is available under a GNU GPLv3 license at https:\/\/github.com\/StantonLabDartmouth\/AppScanGEO.<\/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\/btx452","type":"journal-article","created":{"date-parts":[[2017,7,11]],"date-time":"2017-07-11T19:20:19Z","timestamp":1499800819000},"page":"3500-3501","source":"Crossref","is-referenced-by-count":38,"title":["ScanGEO: parallel mining of high-throughput gene expression data"],"prefix":"10.1093","volume":"33","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1094-0621","authenticated-orcid":false,"given":"Katja","family":"Koeppen","sequence":"first","affiliation":[{"name":"Department of Microbiology and Immunology, The Geisel School of Medicine at Dartmouth, Hanover, NH, USA"}]},{"given":"Bruce A","family":"Stanton","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, The Geisel School of Medicine at Dartmouth, Hanover, NH, USA"}]},{"given":"Thomas H","family":"Hampton","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, The Geisel School of Medicine at Dartmouth, Hanover, NH, USA"}]}],"member":"286","published-online":{"date-parts":[[2017,7,14]]},"reference":[{"key":"2023051506355574800_btx452-B1","doi-asserted-by":"crossref","first-page":"D991","DOI":"10.1093\/nar\/gks1193","article-title":"NCBI GEO: archive for functional genomics data sets \u2013 update","volume":"41","author":"Barrett","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2023051506355574800_btx452-B2","author":"Chang","year":"2017"},{"key":"2023051506355574800_btx452-B3","doi-asserted-by":"crossref","first-page":"3679","DOI":"10.1093\/bioinformatics\/btw519","article-title":"shinyGEO: a web-based application for analyzing gene expression omnibus datasets","volume":"32","author":"Dumas","year":"2016","journal-title":"Bioinforma. 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