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NetCoMi: network construction and comparison for microbiome data in R.

Stefanie Peschel1, Christian L Müller2,3,4, Erika von Mutius1,5,6

  • 1Institute for Asthma and Allergy Prevention, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany.

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Summary

This study introduces NetCoMi, an R package for constructing and comparing microbial association networks from sequencing data. NetCoMi provides a unified workflow for analyzing microbial community interactions and their differences across conditions.

Keywords:
compositional datadifferential associationmicrobial association estimationnetwork analysisnetwork comparisonsample similarity network

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Area of Science:

  • Microbiology
  • Bioinformatics
  • Computational Biology

Background:

  • Microbial association networks are crucial for understanding microbial community dynamics.
  • Existing methods for network construction and comparison are fragmented.
  • A unified computational tool is needed for comprehensive microbiome network analysis.

Purpose of the Study:

  • To introduce NetCoMi, an R package for microbial association network analysis.
  • To provide a reproducible workflow for constructing, analyzing, and comparing microbial networks.
  • To enable the identification of differential microbial associations between groups.

Main Methods:

  • Development of the NetCoMi R package.
  • Integration of methods for zero handling, data normalization, and association computation.
  • Implementation of functions for single network analysis, differential network construction, and dissimilarity network analysis.

Main Results:

  • NetCoMi offers a comprehensive workflow for microbial network analysis.
  • The package facilitates the construction and comparison of microbial association networks.
  • NetCoMi can identify differential associations between microbial taxa and changes in network structure.

Conclusions:

  • NetCoMi provides a valuable tool for microbiome researchers.
  • The package enhances the ability to study microbial community interactions and differences.
  • NetCoMi supports reproducible and integrated analysis of microbiome sequencing data.