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Bioconductor - lefser

lefser

This is the released version of lefser; for the devel version, see lefser.

R implementation of the LEfSE method for microbiome biomarker discovery

Bioconductor version: Release (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: 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 "4.5") 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")
Details biocViews Classification, DifferentialExpression, Microbiome, Sequencing, Software, StatisticalMethod Version 1.18.0 In Bioconductor since BioC 3.12 (R-4.0) (4.5 years) License Artistic-2.0 Depends R (>= 4.1.0), SummarizedExperiment 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 See More Package Archives

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

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