lefser
This is thereleased version of lefser; for the devel version, seelefser.
R implementation of the LEfSE method for microbiome biomarker discovery
Bioconductor version: Release (3.22)
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("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 appropriateBioconductor 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 | ||
| NEWS | Text |
Details
| biocViews | Classification,DifferentialExpression,Microbiome,Sequencing,Software,StatisticalMethod |
| Version | 1.20.2 |
| 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 |
See More
| Suggests | knitr,rmarkdown,curatedMetagenomicData,BiocStyle,phyloseq,pkgdown,covr,withr |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | dar,curatedMetagenomicData,ggpicrust2 |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | lefser_1.20.2.tar.gz |
| Windows Binary (x86_64) | lefser_1.20.2.zip |
| 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 |
| Old Source Packages for BioC 3.22 | Source Archive |