title: FirebrowseR: an R client to the Broad Institute's Firehose Pipeline.
abstract: With its Firebrowse service (http://firebrowse.org/) the Broad Institute is making large-scale multi-platform omics data analysis results publicly available through a Representational State Transfer (REST) Application Programmable Interface (API). Querying this database through an API client from an arbitrary programming environment is an essential task, allowing other developers and researchers to focus on their analysis and avoid data wrangling. Hence, as a first result, we developed a workflow to automatically generate, test and deploy such clients for rapid response to API changes. Its underlying infrastructure, a combination of free and publicly available web services, facilitates the development of API clients. It decouples changes in server software from the client software by reacting to changes in the RESTful service and removing direct dependencies on a specific implementation of an API. As a second result, FirebrowseR, an R client to the Broad Institute's RESTful Firehose Pipeline, is provided as a working example, which is built by the means of the presented workflow. The package's features are demonstrated by an example analysis of cancer gene expression data.Database URL: https://github.com/mariodeng/.
authors.affiliation: Pathology of the University Medical Center Schleswig-Holstein, Campus Luebeck and the Research Center Borstel, Leibniz Center for Medicine and Biosciences, 23538 Luebeck and 23845 Borstel, Germany.
authors.forename: Mario
authors.initials: M
authors.lastname: Deng
authors.affiliation: Molecular Pathology & Department of Translational Genomics, University Hospital Cologne, Weyertal 115b, Cologne, 50931, Germany.
authors.forename: Johannes
authors.initials: J
authors.lastname: Brägelmann
authors.affiliation: Department of Biochemistry and Molecular Biology and Alberta Children's Hospital Research Institute Calgary Biochemistry and Molecular Biology Doctoral Program in Bioinformatics, University of Calgary, Cumming School of Medicine, Alberta, Canada.
authors.forename: Ivan
authors.initials: I
authors.lastname: Kryukov
authors.affiliation: Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal and.|Departamento de Informática, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal.
authors.forename: Nuno
authors.initials: N
authors.lastname: Saraiva-Agostinho
authors.affiliation: Pathology of the University Medical Center Schleswig-Holstein, Campus Luebeck and the Research Center Borstel, Leibniz Center for Medicine and Biosciences, 23538 Luebeck and 23845 Borstel, Germany.
authors.forename: Sven
authors.initials: S
authors.lastname: Perner
mesh_terms: D000818:Animals; D030541:Databases, Genetic; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D020407:Internet; D009369:Neoplasms / Q000235:genetics / Q000378:metabolism; D011381:Programming Languages; D014584:User-Computer Interface