{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,5,25]],"date-time":"2025-05-25T12:27:02Z","timestamp":1748176022463},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"18","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Currently, the Gene Expression Omnibus (GEO) contains public data of over 1 million samples from more than 40 000 microarray-based functional genomics experiments. This provides a rich source of information for novel biological discoveries. However, unlocking this potential often requires retrieving and storing a large number of expression profiles from a wide range of different studies and platforms. The compendiumdb R package provides an environment for downloading functional genomics data from GEO, parsing the information into a local or remote database and interacting with the database using dedicated R functions, thus enabling seamless integration with other tools available in R\/Bioconductor.<\/jats:p>\n               <jats:p>Availability and Implementation: The compendiumdb package is written in R, MySQL and Perl. Source code and binaries are available from CRAN (http:\/\/cran.r-project.org\/web\/packages\/compendiumdb\/) for all major platforms (Linux, MS Windows and OS X) under the GPLv3 license.<\/jats:p>\n               <jats:p>Contact: \u00a0p.d.moerland@amc.uva.nl<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw335","type":"journal-article","created":{"date-parts":[[2016,6,10]],"date-time":"2016-06-10T00:56:16Z","timestamp":1465520176000},"page":"2856-2857","source":"Crossref","is-referenced-by-count":6,"title":["compendiumdb: an R package for retrieval and storage of functional genomics data"],"prefix":"10.1093","volume":"32","author":[{"given":"Umesh K.","family":"Nandal","sequence":"first","affiliation":[{"name":"1 Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands"}]},{"given":"Antoine H. C.","family":"van Kampen","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands"},{"name":"2 Biosystems Data Analysis Group, University of Amsterdam, Amsterdam, The Netherlands"}]},{"given":"Perry D.","family":"Moerland","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands"}]}],"member":"286","published-online":{"date-parts":[[2016,6,9]]},"reference":[{"key":"2023020113392778600_btw335-B1","doi-asserted-by":"crossref","first-page":"528","DOI":"10.1186\/1471-2105-11-528","article-title":"PathEx: a novel multi factors based datasets selector web tool","volume":"11","author":"Bareke","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2023020113392778600_btw335-B2","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":"2023020113392778600_btw335-B3","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1186\/1471-2105-11-421","article-title":"Microarray meta-analysis database (M2DB): a uniformly pre-processed, quality controlled, and manually curated human clinical microarray database","volume":"11","author":"Cheng","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2023020113392778600_btw335-B4","doi-asserted-by":"crossref","first-page":"R104","DOI":"10.1186\/gb-2012-13-11-r104","article-title":"InSilico DB genomic datasets hub: an efficient starting point for analyzing genome-wide studies in GenePattern, Integrative Genomics Viewer, and R\/Bioconductor","volume":"13","author":"Coletta","year":"2012","journal-title":"Genome Biol"},{"key":"2023020113392778600_btw335-B5","doi-asserted-by":"crossref","first-page":"1846","DOI":"10.1093\/bioinformatics\/btm254","article-title":"GEOquery: a bridge between the gene expression omnibus (GEO) and BioConductor","volume":"23","author":"Davis","year":"2007","journal-title":"Bioinformatics"},{"key":"2023020113392778600_btw335-B6","doi-asserted-by":"crossref","first-page":"709","DOI":"10.1016\/j.jbi.2010.04.007","article-title":"DSGeo: software tools for cross-platform analysis of gene expression data in GEO","volume":"43","author":"Lacson","year":"2010","journal-title":"J. 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