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

Umesh K. Nandal | Zendy; Antoine H. C. van Kampen | Zendy; Perry D. Moerland | Zendy

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

Author(s) -

Umesh K. Nandal,

Antoine H. C. van Kampen,

Perry D. Moerland

Publication year - 2016

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btw335

Subject(s) - computer science , r package , functional genomics , information retrieval , genomics , computational biology , biology , programming language , genome , genetics , gene

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.

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