DESCRIPTION

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: 1.17.6
Date: 2024-12-16
Authors@R: c(
  person("Sehyun", "Oh", , "shbrief@gmail.com", c("cre", "ctb"), c(ORCID = "0000-0002-9490-3061")),
  person("Asya", "Khleborodova", , "asya.bioconductor@gmail.com", "aut"),
  person("Samuel", "Gamboa-Tuz", , "Samuel.Gamboa.Tuz@gmail.com", "ctb"),
  person("Marcel", "Ramos", , "marcel.ramos@roswellpark.org", "ctb", c(ORCID = "0000-0002-3242-0582")),
  person("Ludwig", "Geistlinger", , "Ludwig.Geistlinger@sph.cuny.edu", "ctb", c(ORCID = "0000-0002-2495-5464")),
  person("Levi", "Waldron", , "levi.waldron@sph.cuny.edu", "ctb", c(ORCID = "0000-0003-2725-0694"))
  )
License: Artistic-2.0
Depends:
  SummarizedExperiment,
  R (>= 4.0.0)
Imports:
    coin,
    MASS,
    ggplot2,
    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: 7.3.2
Roxygen: list(markdown = TRUE)