Compendiumdb: An R package for retrieval and storage of functional genomics data

Umesh K. Nandal, Antoine H.C. Van Kampen, Perry D. Moerland

Research output: Contribution to journalArticlepeer-review

3 Scopus citations

Abstract

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.

Original languageEnglish
Pages (from-to)2856-2857
Number of pages2
JournalBioinformatics
Volume32
Issue number18
DOIs
StatePublished - Sep 15 2016

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