Oxford University Press (OUP), Bioinformatics, 18(32), p. 2856-2857
DOI: 10.1093/bioinformatics/btw335
Full text: Unavailable
Abstract 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. 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. Contact: p.d.moerland@amc.uva.nl Supplementary information: Supplementary data are available at Bioinformatics online.