Package: lefser
Type: Package
Title: R implementation of the LEfSE method for microbiome biomarker
        discovery
Description: 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).
Version: 1.23.0
Date: 2026-04-22
Authors@R: c(
    person("Sehyun", "Oh", , "shbrief@gmail.com", role = c("cre", "ctb"),
           comment = c(ORCID = "0000-0002-9490-3061")),
    person("Asya", "Khleborodova", , "asya.bioconductor@gmail.com", role = "aut"),
    person("Samuel", "Gamboa-Tuz", , "Samuel.Gamboa.Tuz@gmail.com", role = "ctb"),
    person("Marcel", "Ramos", , "marcel.ramos@sph.cuny.edu", role = "ctb",
           comment = c(ORCID = "0000-0002-3242-0582")),
    person("Ludwig", "Geistlinger", , "Ludwig.Geistlinger@sph.cuny.edu", role = "ctb",
           comment = c(ORCID = "0000-0002-2495-5464")),
    person("Levi", "Waldron", , "levi.waldron@sph.cuny.edu", role = "ctb",
           comment = c(ORCID = "0000-0003-2725-0694")),
    person("NCI", role = "fnd",
           comment = c(GrantNo. = "R01CA230551"))
  )
License: Artistic-2.0
Depends: SummarizedExperiment, R (>= 4.5.0)
Imports: coin, MASS, ggplot2 (>= 3.4.0), S4Vectors, stats, methods,
        utils, dplyr, testthat, tibble, tidyr, forcats, stringr,
        ggtree, BiocGenerics, ape, ggrepel, mia, purrr, tidyselect,
        treeio
Suggests: knitr, rmarkdown, curatedMetagenomicData, BiocStyle,
        phyloseq, pkgdown, covr, withr
Encoding: UTF-8
BugReports: https://github.com/waldronlab/lefser/issues
URL: https://github.com/waldronlab/lefser
VignetteBuilder: knitr
biocViews: Software, Sequencing, DifferentialExpression, Microbiome,
        StatisticalMethod, Classification
RoxygenNote: 7.3.3
Roxygen: list(markdown = TRUE)
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libfribidi-dev libglpk-dev make libgsl0-dev
        libharfbuzz-dev libicu-dev libjpeg-dev libpng-dev libtiff-dev
        libuv1-dev libwebp-dev libxml2-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-05-14 20:56:18 UTC
RemoteUrl: https://github.com/bioc/lefser
RemoteRef: HEAD
RemoteSha: a0a8ddd4c8818b5c93a6b67bf75b3eee145526b4
NeedsCompilation: no
Packaged: 2026-06-14 10:03:46 UTC; root
Author: Sehyun Oh [cre, ctb] (ORCID: <https://orcid.org/0000-0002-9490-3061>),
  Asya Khleborodova [aut],
  Samuel Gamboa-Tuz [ctb],
  Marcel Ramos [ctb] (ORCID: <https://orcid.org/0000-0002-3242-0582>),
  Ludwig Geistlinger [ctb] (ORCID:
    <https://orcid.org/0000-0002-2495-5464>),
  Levi Waldron [ctb] (ORCID: <https://orcid.org/0000-0003-2725-0694>),
  NCI [fnd] (GrantNo.: R01CA230551)
Maintainer: Sehyun Oh <shbrief@gmail.com>