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 (3.23)

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: 0000-0002-9490-3061 , Asya Khleborodova [aut], Samuel Gamboa-Tuz [ctb], Marcel Ramos [ctb] ORCID: 0000-0002-3242-0582 , Ludwig Geistlinger [ctb] ORCID: 0000-0002-2495-5464 , Levi Waldron [ctb] ORCID: 0000-0003-2725-0694

Maintainer: Sehyun Oh <shbrief at gmail.com>

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

Installation

To install this package, start R (version "4.6") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Classification, DifferentialExpression, Microbiome, Sequencing, Software, StatisticalMethod
Version	1.19.1
In Bioconductor since	BioC 3.12 (R-4.0) (5 years)
License	Artistic-2.0
Depends	SummarizedExperiment, R (>= 4.5.0)
Imports	coin, MASS, ggplot2, S4Vectors, stats, methods, utils, dplyr, testthat, tibble, tidyr, forcats, stringr, ggtree, BiocGenerics, ape, ggrepel, mia, purrr, tidyselect, treeio
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
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Build Report	Build Report

Package Archives

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

Source Package
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
Package Short Url	https://bioconductor.org/packages/lefser/
Package Downloads Report	Download Stats