lefser

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see lefser.

R implementation of the LEfSE method for microbiome biomarker discovery


Bioconductor version: 3.15

lefser is an implementation in R of the popular "LDA Effect Size (LEfSe)" method for microbiome biomarker discovery. It uses the Kruskal-Wallis test, Wilcoxon-Rank Sum test, and Linear Discriminant Analysis to find biomarkers of groups and sub-groups.

Author: Asya Khleborodova [cre, aut], Ludwig Geistlinger [ctb], Marcel Ramos [ctb] , Levi Waldron [ctb]

Maintainer: Asya Khleborodova <asya.bioconductor at gmail.com>

Citation (from within R, enter citation("lefser")):

Installation

To install this package, start R (version "4.2") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("lefser")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("lefser")
Introduction to the lefser R implementation of the popular LEfSE software for biomarker discovery in microbiome analysis. HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Classification, DifferentialExpression, Microbiome, Sequencing, Software, StatisticalMethod
Version 1.6.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License Artistic-2.0
Depends SummarizedExperiment, R (>= 4.0.0)
Imports coin, MASS, ggplot2, stats, methods
System Requirements
URL https://github.com/waldronlab/lefser
Bug Reports https://github.com/waldronlab/lefser/issues
See More
Suggests knitr, rmarkdown, curatedMetagenomicData, BiocStyle, testthat, pkgdown, covr, withr
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Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package lefser_1.6.0.tar.gz
Windows Binary lefser_1.6.0.zip (64-bit only)
macOS Binary (x86_64) lefser_1.6.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/lefser
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/lefser
Bioc Package Browser https://code.bioconductor.org/browse/lefser/
Package Short Url https://bioconductor.org/packages/lefser/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.15 Source Archive