Abstract
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).
Highlights
The availability of high-throughput experimental data has led to the development of multiple computational methods to analyse these data
Multiple R packages for computational biology and bioinformatics are available in various resources such as the Comprehensive R Archive Network (CRAN)
Here, we present Cyrface; a bioinformatics Java library that provides a general interaction between Cytoscape and R
Summary
This article is included in the Cytoscape gateway. We thank the reviewers for the helpful suggestions and comments that improved both our work and our manuscript. The major differences are: (i) Cyrface is compatible with Cytoscape 3; (ii) the manuscript was adapted and some parts re-written to address the reviewer’s suggestions; (iii) Rserve is automatically installed and configured. This greatly simplifies the usage of Cyrface, since it saves the users of having to open R and manually initialising Rserve
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