Cyrface: An interface from Cytoscape to R that provides a user interface to R packages.
There is an increasing number of software packages to analyse biological experimental data in the R environment. In particular, Bioconductor, a repository of curated R packages, is one of the most comprehensive resources for bioinformatics and biostatistics. The use of these packages is increasing, but it requires a basic understanding of the R language, as well as the syntax of the specific package used. The availability of user graphical interfaces for these packages would decrease the learning curve and broaden their application. Here, we present a Cytoscape app termed Cyrface that allows Cytoscape apps to connect to any function and package developed in R. Cyrface can be used to run R packages from within the Cytoscape environment making use of a graphical user interface. Moreover, it can link R packages with the capabilities of Cytoscape and its apps, in particular network visualization and analysis. Cyrface's utility has been demonstrated for two Bioconductor packages ( CellNOptR and DrugVsDisease), and here we further illustrate its usage by implementing a workflow of data analysis and visualization. Download links, installation instructions and user guides can be accessed from the Cyrface's homepage ( http://www.ebi.ac.uk/saezrodriguez/cyrface/) and from the Cytoscape app store ( http://apps.cytoscape.org/apps/cyrface).
The European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, CB10 1SD, UK.
Emanuel
E
Gonçalves
The European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, CB10 1SD, UK; University of Applied Science Weihenstephan-Triesdorf, Weidenbach, 91746, Germany.
Franz
F
Mirlach
The European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, CB10 1SD, UK.
Julio
J
Saez-Rodriguez