{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,20]],"date-time":"2026-05-20T03:53:31Z","timestamp":1779249211620,"version":"3.51.4"},"reference-count":3,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2018,10,10]],"date-time":"2018-10-10T00:00:00Z","timestamp":1539129600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000054","name":"NCI","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01CA190766"],"award-info":[{"award-number":["R01CA190766"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000092","name":"NLM","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000092","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Institute of Health","award":["R21LM012752"],"award-info":[{"award-number":["R21LM012752"]}]},{"DOI":"10.13039\/501100001809","name":"National Nature Science Foundation of China","doi-asserted-by":"crossref","award":["11701391"],"award-info":[{"award-number":["11701391"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>The rapid advances of omics technologies have generated abundant genomic data in public repositories and effective analytical approaches are critical to fully decipher biological knowledge inside these data. Meta-analysis combines multiple studies of a related hypothesis to improve statistical power, accuracy and reproducibility beyond individual study analysis. To date, many transcriptomic meta-analysis methods have been developed, yet few thoughtful guidelines exist. Here, we introduce a comprehensive analytical pipeline and browser-based software suite, called MetaOmics, to meta-analyze multiple transcriptomic studies for various biological purposes, including quality control, differential expression analysis, pathway enrichment analysis, differential co-expression network analysis, prediction, clustering and dimension reduction. The pipeline includes many public as well as &amp;gt;10 in-house transcriptomic meta-analytic methods with data-driven and biological-aim-driven strategies, hands-on protocols, an intuitive user interface and step-by-step instructions.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>MetaOmics is freely available at https:\/\/github.com\/metaOmics\/metaOmics.<\/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\/bty825","type":"journal-article","created":{"date-parts":[[2018,9,19]],"date-time":"2018-09-19T20:32:35Z","timestamp":1537389155000},"page":"1597-1599","source":"Crossref","is-referenced-by-count":29,"title":["MetaOmics: analysis pipeline and browser-based software suite for transcriptomic meta-analysis"],"prefix":"10.1093","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3605-0811","authenticated-orcid":false,"given":"Tianzhou","family":"Ma","sequence":"first","affiliation":[{"name":"Department of Epidemiology and Biostatistics, University of Maryland, College Park, MD, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhiguang","family":"Huo","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, University of Florida, Gainesville, FL, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anche","family":"Kuo","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, Graduate School of Public Health University of Pittsburgh, Pittsburgh, PA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Li","family":"Zhu","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, Graduate School of Public Health University of Pittsburgh, Pittsburgh, PA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhou","family":"Fang","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, Graduate School of Public Health University of Pittsburgh, Pittsburgh, PA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiangrui","family":"Zeng","sequence":"additional","affiliation":[{"name":"School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chien-Wei","family":"Lin","sequence":"additional","affiliation":[{"name":"Division of Biostatistics, Medical College of Wisconsin, Milwaukee, WI, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Silvia","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lin","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Statistics, Capital University of Economics and Business, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peng","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, Graduate School of Public Health University of Pittsburgh, Pittsburgh, PA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tanbin","family":"Rahman","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, Graduate School of Public Health University of Pittsburgh, Pittsburgh, PA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lun-Ching","family":"Chang","sequence":"additional","affiliation":[{"name":"Department of Mathematical Sciences, Florida Atlantic University, Boca Raton, FL, 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University of Pittsburgh, Pittsburgh, PA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Etienne","family":"Sibille","sequence":"additional","affiliation":[{"name":"Centre for Addiction and Mental Health, University of Toronto, Toronto, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5447-1014","authenticated-orcid":false,"given":"George C","family":"Tseng","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, Graduate School of Public Health University of Pittsburgh, Pittsburgh, PA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2018,10,10]]},"reference":[{"key":"2023012806482392600_bty825-B1","doi-asserted-by":"crossref","first-page":"1665","DOI":"10.1093\/bioinformatics\/btl163","article-title":"Integrative array analyzer: a software package for analysis of cross-platform and cross-species microarray 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