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 (3.21)

lefser is the R implementation of the popular microbiome biomarker discovery too, LEfSe. It uses the Kruskal-Wallis test, Wilcoxon-Rank Sum test, and Linear Discriminant Analysis to find biomarkers from two-level classes (and optional sub-classes).

Author: Sehyun Oh [cre, ctb] (ORCID: ), Asya Khleborodova [aut], Samuel Gamboa-Tuz [ctb], Marcel Ramos [ctb] (ORCID: ), Ludwig Geistlinger [ctb] (ORCID: ), Levi Waldron [ctb] (ORCID: )

Maintainer: Sehyun Oh <shbrief at gmail.com>

Citation (from within R, enter citation("lefser")):

Installation

To install this package, start R (version "4.5") 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")

Quickstart	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	1.17.0
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, testthat, tibble, tidyr, forcats, stringr, ggtree
System Requirements
URL	https://github.com/waldronlab/lefser
Bug Reports	https://github.com/waldronlab/lefser/issues

Suggests	knitr, rmarkdown, curatedMetagenomicData, BiocStyle, phyloseq, 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_1.17.0.tar.gz
Windows Binary (x86_64)
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
Bioc Package Browser	https://code.bioconductor.org/browse/lefser/
Package Short Url	https://bioconductor.org/packages/lefser/
Package Downloads Report	Download Stats