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Assisted Selection of Biomarkers by Linear Discriminant Analysis Effect Size (LEfSe) in Microbiome Data
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JoVE 杂志 遗传学
Assisted Selection of Biomarkers by Linear Discriminant Analysis Effect Size (LEfSe) in Microbiome Data

Assisted Selection of Biomarkers by Linear Discriminant Analysis Effect Size (LEfSe) in Microbiome Data

DOI:
10.3791/61715-v

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04:57 min

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May 16, 2022

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, ,
1Marine Resources Research Centre,Tianjin Research Institute for Water Transport Engineering, M.O.T., 2Key Laboratory of Regional Energy Systems Optimization, Ministry of Education, College of Environmental Science and Engineering,North China Electric Power University, 3School of Environmental Science and Engineering,Huazhong University of Science and Technology

Chapters

  • 00:04Introduction
  • 00:39Linear Discriminant Analysis Effect Size (LEfSe) Native Analysis
  • 01:49LEfSe Online Analysis (Galaxy)
  • 03:05Results: Representative Microbiome LEfSe Characterization
  • 04:21Conclusion

Summary

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LEfSe (LDA Effect Size) is a tool for high-dimensional biomarker mining to identify genomic features (such as genes, pathways, and taxonomies) that significantly characterize two or more groups in microbiome data.

Tags

BiomarkerLinear Discriminant AnalysisEffect SizeLEfSeMicrobiomeBiologic GroupsStatistical DifferencesGenomic BiomarkersConda EnvironmentData FormatLDA CalculationBiomarker PlotCladogramSingle Biomarker PlotGalaxy Server

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