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

Genome Biol. 2012 Apr 24;13(4):R29. doi: 10.1186/gb-2012-13-4-r29.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • Computational Biology / methods
  • Computer Simulation
  • Databases, Genetic
  • Gene Expression Profiling / methods*
  • Gene Library
  • Gene Regulatory Networks*
  • Genomics / methods
  • Humans
  • Oligonucleotide Array Sequence Analysis / methods
  • Reproducibility of Results
  • Software*
  • Transcription Initiation Site