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BiomMiner: An advanced exploratory microbiome analysis and visualization pipeline

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  • Amirhossein Shamsaddini
  • Kimia Dadkhah
  • Patrick M Gillevet

Abstract

Current microbiome applications require substantial bioinformatics expertise to execute. As microbiome clinical diagnostics are being developed, there is a critical need to implement computational tools and applications that are user-friendly for the medical community to understand microbiome correlation with the health. To address this need, we have developed BiomMiner (pronounced as “biominer”), an automated pipeline that provides a comprehensive analysis of microbiome data. The pipeline finds taxonomic signatures of microbiome data and compiles actionable clinical report that allows clinicians and biomedical scientists to efficiently perform statistical analysis and data mining on the large microbiome datasets. BiomMiner generates web-enabled visualization of the analysis results and is specifically designed to facilitate the use of microbiome datasets in clinical applications.

Suggested Citation

  • Amirhossein Shamsaddini & Kimia Dadkhah & Patrick M Gillevet, 2020. "BiomMiner: An advanced exploratory microbiome analysis and visualization pipeline," PLOS ONE, Public Library of Science, vol. 15(6), pages 1-13, June.
    • Handle: RePEc:plo:pone00:0234860
    DOI: 10.1371/journal.pone.0234860
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    References listed on IDEAS

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    1. Jennifer T. Wolstenholme & Justin M. Saunders & Maren Smith & Jason D. Kang & Phillip B. Hylemon & Javier González-Maeso & Andrew Fagan & Derrick Zhao & Masoumeh Sikaroodi & Jeremy Herzog & Amirhossei, 2022. "Reduced alcohol preference and intake after fecal transplant in patients with alcohol use disorder is transmissible to germ-free mice," Nature Communications, Nature, vol. 13(1), pages 1-14, December.

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