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Network analysis makes it easier to investigate how different populations in a community interact with one another. It offers a range of metrics that outline the social characteristics of each population and the newly formed structural features of the community, addressing new ecological challenges. Using free and open-source tools (R and Gephi) and a publicly available dataset, this chapter walks you through the step-by-step code and instructions for inferring and analyzing an SPIEC-EASI (SParse InversE Covariance Estimation for Ecological Association Inference) network. In addition to providing detailed code and instructions for SPIEC-EASI network analysis, this chapter presents a sophisticated understanding of the social qualities and emerging structural elements of ecological communities, which will help you develop your ecological insights even further. Explore the field of ecological association inference with open-source and free tools.

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Inference and Analysis of SPIEC-EASI Microbiome Networks

  • 章节

  • 发表日期：

    2025年

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  • Muhammad Farooq,
  • Ifra Siddique,
  • Amina Nabi,
  • Muhammad Naseer,
  • Ayesha Younis,
  • Sadia Siddique

摘要

Network analysis makes it easier to investigate how different populations in a community interact with one another. It offers a range of metrics that outline the social characteristics of each population and the newly formed structural features of the community, addressing new ecological challenges. Using free and open-source tools (R and Gephi) and a publicly available dataset, this chapter walks you through the step-by-step code and instructions for inferring and analyzing an SPIEC-EASI (SParse InversE Covariance Estimation for Ecological Association Inference) network. In addition to providing detailed code and instructions for SPIEC-EASI network analysis, this chapter presents a sophisticated understanding of the social qualities and emerging structural elements of ecological communities, which will help you develop your ecological insights even further. Explore the field of ecological association inference with open-source and free tools.