lefser

DOI: 10.18129/B9.bioc.lefser    

R implementation of the LEfSE method for microbiome biomarker discovery

Bioconductor version: Release (3.12)

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 "4.0") and enter:

if (!requireNamespace("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 1.0.0
In Bioconductor since BioC 3.12 (R-4.0) (< 6 months)
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
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package lefser_1.0.0.tar.gz
Windows Binary lefser_1.0.0.zip
macOS 10.13 (High Sierra) lefser_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/lefser
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/lefser
Package Short Url https://bioconductor.org/packages/lefser/
Package Downloads Report Download Stats

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