compendiumdb: an R package for retrieval and storage of functional genomics data.
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.



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.



p.d.moerland@amc.uva.nl



Supplementary data are available at Bioinformatics online.
Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
Umesh K
UK
Nandal
Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands Biosystems Data Analysis Group, University of Amsterdam, Amsterdam, The Netherlands.
Antoine H C
AH
van Kampen
Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
Perry D
PD
Moerland
D000465:Algorithms; D019295:Computational Biology; D015870:Gene Expression; D015894:Genome, Human; D023281:Genomics; D006801:Humans; D012984:Software; D014584:User-Computer Interface; D064878:Web Browser