Rcupcake: an R package for querying and analyzing biomedical data through the BD2K PIC-SURE RESTful API.
Bioinformatics
; 34(8): 1431-1432, 2018 04 15.
Article
em En
| MEDLINE
| ID: mdl-29267850
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. Availability and implementation The package is implemented in R and is available under Mozilla v2 license from GitHub (https//github.com/hms-dbmi/Rcupcake). Two reproducible case studies are also available (https//github.com/hms-dbmi/Rcupcake-case-studies/blob/master/SSCcaseStudy_v01.ipynb, https//github.com/hms-dbmi/Rcupcake-case-studies/blob/master/NHANEScaseStudy_v01.ipynb). Contact paul_avillach@hms.harvard.edu. Supplementary information Supplementary data are available at Bioinformatics online.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Fenótipo
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Software
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Genoma Humano
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Biologia Computacional
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Medicina de Precisão
Tipo de estudo:
Prognostic_studies
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Risk_factors_studies
Limite:
Humans
Idioma:
En
Revista:
Bioinformatics
Assunto da revista:
INFORMATICA MEDICA
Ano de publicação:
2018
Tipo de documento:
Article
País de afiliação:
Estados Unidos