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Inference and Analysis of SPIEC-EASI Microbiome Networks

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The Plant Microbiome

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2232))

Abstract

Network analysis facilitates examination of the interactions between different populations in a community. It can provide a range of metrics describing the social characteristics of each population and emergent structural properties of the community, which may be used to address novel ecological questions. Using a publicly available dataset, this chapter provides point-by-point code and instructions to infer and analyze a SPIEC-EASI (SParse InversE Covariance Estimation for Ecological Association Inference) network using free, open source software (R and Gephi).

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Authors and Affiliations

  1. School of Earth and Environmental Sciences, The University of Queensland, Brisbane, QLD, Australia

    Henry W. G. Birt & Paul G. Dennis

Authors
  1. Henry W. G. Birt
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  2. Paul G. Dennis
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Corresponding author

Correspondence to Paul G. Dennis .

Editor information

Editors and Affiliations

  1. Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia

    Lilia C. Carvalhais

  2. School of Earth and Environmental Sciences, The University of Queensland, Brisbane, QLD, Australia

    Paul G. Dennis

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Birt, H.W.G., Dennis, P.G. (2021). Inference and Analysis of SPIEC-EASI Microbiome Networks. In: Carvalhais, L.C., Dennis, P.G. (eds) The Plant Microbiome. Methods in Molecular Biology, vol 2232. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1040-4_14

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  • DOI: https://doi.org/10.1007/978-1-0716-1040-4_14

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1039-8

  • Online ISBN: 978-1-0716-1040-4

  • eBook Packages: Springer Protocols

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