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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

Reference Manual PDF

Details

biocViews Classification, DifferentialExpression, Microbiome, Sequencing, Software, StatisticalMethod
Version 1.13.4
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
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Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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/
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