General Information
| Description | An R package for retrieval and storage of functional genomics data |
| Homepage | http://cran.r-project.org/web/packages/compendiumdb/ |
Publications
compendiumdb: an R package for retrieval and storage of functional genomics data
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.
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shinyGEO
Published August 2016
A web-based application for analyzing gene expression omnibus datasets
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