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

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.

SUBMITTER: Castro MA

PROVIDER: S-EPMC3446303 | biostudies-literature | 2012 Apr

REPOSITORIES: biostudies-literature

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

Castro Mauro A A MA Wang Xin X Fletcher Michael N C MN Meyer Kerstin B KB Markowetz Florian F

Genome biology 20120424 4

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 i ...[more]

PMID: 22531049

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