Cyrface: An interface from Cytoscape to R that provides a user interface to R packages [v1; ref status: indexed, http://f1000r.es/1tv]
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,...
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doaj-d7fcce7444c847ee91e17d99b15bec122020-11-25T03:30:21ZengF1000 Research LtdF1000Research2046-14022013-09-01210.12688/f1000research.2-192.v12371Cyrface: An interface from Cytoscape to R that provides a user interface to R packages [v1; ref status: indexed, http://f1000r.es/1tv]Emanuel Gonçalves0Julio Saez-Rodriguez1The European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, CB10 1SD, UKThe European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, CB10 1SD, UKThere 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 plug-in termed Cyrface that allows Cytoscape plug-ins 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 links the R packages with the capabilities of Cytoscape and its plug-ins, 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 homepage (http://www.ebi.ac.uk/saezrodriguez/cyrface/).http://f1000research.com/articles/2-192/v1Bioinformatics |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Emanuel Gonçalves Julio Saez-Rodriguez |
spellingShingle |
Emanuel Gonçalves Julio Saez-Rodriguez Cyrface: An interface from Cytoscape to R that provides a user interface to R packages [v1; ref status: indexed, http://f1000r.es/1tv] F1000Research Bioinformatics |
author_facet |
Emanuel Gonçalves Julio Saez-Rodriguez |
author_sort |
Emanuel Gonçalves |
title |
Cyrface: An interface from Cytoscape to R that provides a user interface to R packages [v1; ref status: indexed, http://f1000r.es/1tv] |
title_short |
Cyrface: An interface from Cytoscape to R that provides a user interface to R packages [v1; ref status: indexed, http://f1000r.es/1tv] |
title_full |
Cyrface: An interface from Cytoscape to R that provides a user interface to R packages [v1; ref status: indexed, http://f1000r.es/1tv] |
title_fullStr |
Cyrface: An interface from Cytoscape to R that provides a user interface to R packages [v1; ref status: indexed, http://f1000r.es/1tv] |
title_full_unstemmed |
Cyrface: An interface from Cytoscape to R that provides a user interface to R packages [v1; ref status: indexed, http://f1000r.es/1tv] |
title_sort |
cyrface: an interface from cytoscape to r that provides a user interface to r packages [v1; ref status: indexed, http://f1000r.es/1tv] |
publisher |
F1000 Research Ltd |
series |
F1000Research |
issn |
2046-1402 |
publishDate |
2013-09-01 |
description |
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 plug-in termed Cyrface that allows Cytoscape plug-ins 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 links the R packages with the capabilities of Cytoscape and its plug-ins, 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 homepage (http://www.ebi.ac.uk/saezrodriguez/cyrface/). |
topic |
Bioinformatics |
url |
http://f1000research.com/articles/2-192/v1 |
work_keys_str_mv |
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