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

Research output: Contribution to journalArticleAcademicpeer-review

3 Citations (Scopus)


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
Issue number18
Publication statusPublished - 15 Sept 2016


  • Journal Article

Cite this