Tools for Retrieval and Storage of Functional Genomics Data

Description

Public repositories such as the Gene Expression Omnibus (GEO) contain thousands of high-throughput functional genomics datasets. These datasets are a rich source of useful biological information. Extraction of meaningful information often requires the integration of a large number of datasets from different studies and platforms. The package compendiumdb provides a flexible platform for the systematic retrieval and storage of functional genomics data downloaded from GEO in the form of a MySQL database accessed via R functions. It provides functions to (i) download data from GEO, (ii) store data in the database and (iii) retrieve data from the database.

Details

Package: compendiumdb
Type: Package
Version: 1.0.3
Date: 2015-10-12
License: GPL (>= 2)
LazyLoad: yes

Author(s)

Umesh K. Nandal <u.k.nandal@amc.uva.nl> and Perry D. Moerland <p.d.moerland@amc.uva.nl>