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Analyzing Biological Data Using R: Methods for Graphs and Networks

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Bacterial Molecular Networks

Part of the book series: Methods in Molecular Biology ((MIMB,volume 804))

Abstract

R is a powerful language and widely used software tool for the analysis and visualization of data. Its core capabilities can be extended through many different add-on packages. Among the many packages are some which offer a broad range of facilities for analyzing statistical properties of graphs. This chapter provides a practical tutorial covering the use of R methods for graphs and networks to examine biological data and analyze their topological and statistical properties.

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Acknowledgments

Funding for this research was provided by grants from La Ligue Contre Le Cancer (RAB08008NSA; project R08010NS). We also gratefully acknowledge the Instituts national de la santé et de la recherche médicale (INSERM) for supporting this project. Funding for RG was provided by NIH grant P41 HG004059.

The authors would like to thank Wolfgang Huber, Tony Chiang, Shailesh Date and Denise Scholtens for helpful comments and for providing a stimulating research environment that has led to the many tools used here and to the ideas that underlie this research.

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Authors and Affiliations

  1. IRISA, Equipe Symbiose, Université de Rennes I, Rennes, France

    Nolwenn Le Meur

  2. Program in Computational Biology, Fred Hutchinson Cancer Research Center, M2-B876, Seattle, WA, USA

    Robert Gentleman

Authors
  1. Nolwenn Le Meur
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  2. Robert Gentleman
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Corresponding author

Correspondence to Nolwenn Le Meur .

Editor information

Editors and Affiliations

  1. Labo. Bioinformatique des, Génomes et des Réseaux (BiGRe), Université Libre de Bruxelles, bd. du Triomphe, Bruxelles, 1050, Belgium

    Jacques van Helden

  2. Labo. Bioinformatique des, Génomes et des Réseaux (BiGRe), Université Libre de Bruxelles, Bvd. du Triomphe, Bruxelles, 1050, Belgium

    Ariane Toussaint

  3. INSERM 1024, Institut de Biologie de l'Ecole Normale, rue d'Ulm 46, Paris, 75230, France

    Denis Thieffry

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Meur, N.L., Gentleman, R. (2012). Analyzing Biological Data Using R: Methods for Graphs and Networks. In: van Helden, J., Toussaint, A., Thieffry, D. (eds) Bacterial Molecular Networks. Methods in Molecular Biology, vol 804. Springer, New York, NY. https://doi.org/10.1007/978-1-61779-361-5_19

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  • DOI: https://doi.org/10.1007/978-1-61779-361-5_19

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  • Publisher Name: Springer, New York, NY

  • Print ISBN: 978-1-61779-360-8

  • Online ISBN: 978-1-61779-361-5

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