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Oxford University Press (OUP), Bioinformatics, 18(32), p. 2856-2857

DOI: 10.1093/bioinformatics/btw335

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

Journal article published in 2016 by Umesh K. Nandal, Antoine H. C. van Kampen, Perry D. Moerland ORCID
This paper was not found in any repository, but could be made available legally by the author.
This paper was not found in any repository, but could be made available legally by the author.

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Data provided by SHERPA/RoMEO

Abstract

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.