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lefser

This is the development version of lefser; for the stable release version, see lefser.

R implementation of the LEfSE method for microbiome biomarker discovery


Bioconductor version: Development (3.19)

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] , Samuel Gamboa-Tuz [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 "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.13.1
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, S4Vectors, stats, methods, utils
System Requirements
URL https://github.com/waldronlab/lefser
Bug Reports https://github.com/waldronlab/lefser/issues
See More
Suggests knitr, rmarkdown, curatedMetagenomicData, BiocStyle, phyloseq, testthat, pkgdown, covr, withr
Linking To
Enhances
Depends On Me
Imports Me ggpicrust2
Suggests Me dar
Links To Me
Build Report Build Report

Package Archives

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

Source Package lefser_1.13.1.tar.gz
Windows Binary lefser_1.13.1.zip
macOS Binary (x86_64) lefser_1.13.1.tgz
macOS Binary (arm64) lefser_1.13.1.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