Rcupcake: an R package for querying and analyzing biomedical data through the BD2K PIC-SURE RESTful API

Gutiérrez Sacristán, Alba; Guedj, Romain; Korodi, Gabor; Stedman, Jason; Furlong, Laura I., 1971-; Patel, Chirag J.; Kohane, Isaac S.; Avillach, Paul

doi:http://dx.doi.org/10.1093/bioinformatics/btx788

Rcupcake: an R package for querying and analyzing biomedical data through the BD2K PIC-SURE RESTful API

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Gutiérrez-Sacristán A, Guedj R, Korodi G, Stedman J, Furlong LI, Patel CJ. Rcupcake: an R package for querying and analyzing biomedical data through the BD2K PIC-SURE RESTful API. Bioinformatics. 2018 Apr 15;34(8):1431-1432. DOI: 10.1093/bioinformatics/btx788

Abstract

MOTIVATION: In the era of big data and precision medicine, the number of databases containing clinical, environmental, self-reported and biochemical variables is increasing exponentially. Enabling the experts to focus on their research questions rather than on computational data management, access and analysis is one of the most significant challenges nowadays. RESULTS: We present Rcupcake, an R package that contains a variety of functions for leveraging different databases through the BD2K PIC-SURE RESTful API and facilitating its query, analysis and interpretation. The package offers a variety of analysis and visualization tools, including the study of the phenotype co-occurrence and prevalence, according to multiple layers of data, such as phenome, exposome or genome.