lefser

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see lefser.

R implementation of the LEfSE method for microbiome biomarker discovery

Bioconductor version: 3.19

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], Sehyun Oh [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")
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Classification, DifferentialExpression, Microbiome, Sequencing, Software, StatisticalMethod

Version 1.14.0

In Bioconductor since BioC 3.12 (R-4.0) (4 years)

License Artistic-2.0

Depends SummarizedExperiment, R (>= 4.0.0)

Imports coin, MASS, ggplot2, S4Vectors, stats, methods, utils, dplyr

System Requirements

URL https://github.com/waldronlab/lefser

Bug Reports https://github.com/waldronlab/lefser/issues

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

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Package Archives

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

Source Package lefser_1.14.0.tar.gz

Windows Binary (x86_64) lefser_1.14.0.zip

macOS Binary (x86_64) lefser_1.14.0.tgz

macOS Binary (arm64) lefser_1.14.0.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/

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