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Abstract
Summary
LEfSe is a widely used Python package and Galaxy module for metagenomic biomarker discovery and visualization, utilizing the Kruskal–Wallis test, Wilcoxon Rank-Sum test, and Linear Discriminant Analysis. R/Bioconductor provides a large collection of tools for metagenomic data analysis but has lacked an implementation of this widely used algorithm, hindering benchmarking against other tools and incorporation into R workflows. We present the lefser package to provide comparable functionality within the R/Bioconductor ecosystem of statistical analysis tools, with improvements to the original algorithm for performance, accuracy, and reproducibility. We benchmark the performance of lefser against the original algorithm using human and mouse metagenomic datasets.
Availability and implementation
Our software, lefser, is distributed through the Bioconductor project (https://www.bioconductor.org/packages/release/bioc/html/lefser.html), and all the source code is available in the GitHub repository https://github.com/waldronlab/lefser.
Academic Publication lefser: implementation of metagenomic biomarker discovery tool, LEfSe, in R
Research Abstract & Technology Focus
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What is the core focus of the research titled 'lefser: implementation of metagenomic biomarker discovery tool, LEfSe, in R'?
This literature focuses on: Abstract Summary LEfSe is a widely used Python package and Galaxy module for metagenomic biomarker discovery and visualization, utilizing the Kruskal–Wallis test, Wilcoxon Rank-Sum test, and Line...
Are there open-source GitHub repositories related to lefser: implementation of metagenomic biomarker discovery tool, LEfSe, in R?
Yes, open-source projects like QuipNetwork/xq-rs (A rust implementation of the Quip Network's quantum virtual machine.) are actively building upon these concepts.
What other academic literature is closely related to 'lefser: implementation of metagenomic biomarker discovery tool, LEfSe, in R'?
Yes, highly correlated activity was mapped. An entry titled 'lefser: implementation of metagenomic biomarker discovery tool, LEfSe, in R' discusses this: Abstract Summary LEfSe is a widely used Python package and Galaxy module for metagenomic biomar...
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