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DESCRIPTION
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DESCRIPTION
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Package: lefser
Type: Package
Title: R implementation of the LEfSE method for microbiome biomarker discovery
Description: 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.
Version: 1.15.0
Date: 2024-04-27
Authors@R: c(
person("Asya", "Khleborodova", , "asya.bioconductor@gmail.com", c("cre", "aut")),
person("Ludwig", "Geistlinger", , "Ludwig.Geistlinger@sph.cuny.edu", "ctb"),
person("Marcel", "Ramos", , "marcel.ramos@roswellpark.org", "ctb", c(ORCID = "0000-0002-3242-0582")),
person("Samuel", "Gamboa-Tuz", , "Samuel.Gamboa.Tuz@gmail.com", "ctb"),
person("Levi", "Waldron", , "levi.waldron@sph.cuny.edu", "ctb"),
person("Sehyun", "Oh", , "Sehyun.Oh@sph.cuny.edu", "ctb")
)
License: Artistic-2.0
Depends:
SummarizedExperiment,
R (>= 4.0.0)
Imports:
coin,
MASS,
ggplot2,
S4Vectors,
stats,
methods,
utils,
dplyr
Suggests:
knitr,
rmarkdown,
curatedMetagenomicData,
BiocStyle,
phyloseq,
testthat,
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: 7.3.1
Roxygen: list(markdown = TRUE)