lefser
R implementation of the LEfSE method for microbiome biomarker discovery
Bioconductor version: Release (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("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 | ||
| NEWS | Text |
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 |
See More
| 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 | |
| Build Report | Build Report |
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/ |
| Package Downloads Report | Download Stats |