RedeR - bridging the gap between functional analyses and hierarchical network visualization
RedeR is an R-based package combined with a stand-alone Java application for dynamic network visualization and manipulation. It implements a callback engine by using a low-level R-to-Java interface to build and run common plugins. In this sense, RedeR takes advantage of R to run robust statistics, while the R-to-Java interface bridges the gap between network analysis and visualization: for R Developers, it allows the development of Java plug-ins exclusively using R codes; for Java Users, it runs R methods implemented in a stand-alone application, and for R Users RedeR interactively displays R graphs using a robust Java graphic engine embedded in this package.
RedeR presents the following main features:
- dynamic network visualization
- network manipulation (dynamic and static layout algorithms)
- sub-network representation and clustering
- nested network layouts
- network attributes overlayed onto dynamic topology (e.g. time-course interactions, edge-weight and pairwise-similarity)
- fully interactive
- xml / xgmml as standard data format
- files saved/exported as TIF, BMP, JPG, PDF, postscript, interaction matrix (among other formats)
- able to be called from external enviroments (e.g. R-packages)
Download
RedeR is available from BioConductor at http://bioconductor.org/packages/devel/bioc/html/RedeR.html
References
- RedeR - bridging the gap between network analysis and visualization
M.A.A. Castro et al, Journal Paper (in preparation), 2011.
