lefser

DOI: 10.18129/B9.bioc.lefser  

R implementation of the LEfSE method for microbiome biomarker discovery

Bioconductor version: Release (3.16)

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>

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")

 

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

Details

biocViews	Classification, DifferentialExpression, Microbiome, Sequencing, Software, StatisticalMethod
Version	1.8.0
In Bioconductor since	BioC 3.12 (R-4.0) (2.5 years)
License	Artistic-2.0
Depends	SummarizedExperiment, R (>= 4.0.0)
Imports	coin, MASS, ggplot2, stats, methods
LinkingTo
Suggests	knitr, rmarkdown, curatedMetagenomicData, BiocStyle, testthat, pkgdown, covr, withr
SystemRequirements
Enhances
URL	https://github.com/waldronlab/lefser
BugReports	https://github.com/waldronlab/lefser/issues
Depends On Me
Imports Me	ggpicrust2
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	lefser_1.8.0.tar.gz
Windows Binary	lefser_1.8.0.zip
macOS Binary (x86_64)	lefser_1.8.0.tgz
macOS Binary (arm64)	lefser_1.8.0.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