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RedeR: R/Bioconductor package for representing modular structures, nested networks and multiple levels of hierarchical associations

Mauro AA Castro, Xin Wang, Michael NC Fletcher, Kerstin B Meyer and Florian Markowetz*

Author Affiliations

Cancer Research UK Cambridge Research Institute and Department of Oncology, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK

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Genome Biology 2012, 13:R29  doi:10.1186/gb-2012-13-4-r29

Published: 24 April 2012

Abstract

Visualization and analysis of molecular networks are both central to systems biology. However, there still exists a large technological gap between them, especially when assessing multiple network levels or hierarchies. Here we present RedeR, an R/Bioconductor package combined with a Java core engine for representing modular networks. The functionality of RedeR is demonstrated in two different scenarios: hierarchical and modular organization in gene co-expression networks and nested structures in time-course gene expression subnetworks. Our results demonstrate RedeR as a new framework to deal with the multiple network levels that are inherent to complex biological systems. RedeR is available from http://bioconductor.org/packages/release/bioc/html/RedeR.html webcite.