DESCRIPTION

Package: microbiomeMarker
Title: microbiome biomarker analysis toolkit
Version: 1.9.0
Authors@R: 
    person(given = "Yang",
           family = "Cao",
           role = c("aut", "cre"),
           email = "caoyang.name@gmail.com")
Description: To date, a number of methods have been developed for microbiome 
    marker discovery based on metagenomic profiles, e.g. LEfSe. However, all of 
    these methods have its own advantages and disadvantages, and none of them is 
    considered standard or universal. Moreover, different programs or softwares 
    may be development using different programming languages, even in different 
    operating systems. Here, we have developed an all-in-one R package 
    microbiomeMarker that integrates commonly used differential analysis 
    methods as well as three machine learning-based approaches, including 
    Logistic regression, Random forest, and Support vector machine, to 
    facilitate the identification of microbiome markers.
License: GPL-3
biocViews: Metagenomics, Microbiome, DifferentialExpression
URL: https://github.com/yiluheihei/microbiomeMarker
BugReports: https://github.com/yiluheihei/microbiomeMarker/issues
Depends: R (>= 4.1.0)
Imports: 
    dplyr,
    phyloseq,
    magrittr,
    purrr,
    MASS,
    utils,
    ggplot2,
    tibble,
    rlang,
    stats,
    coin,
    ggtree,
    tidytree,
    methods,
    IRanges,
    tidyr,
    patchwork,
    ggsignif,
    metagenomeSeq,
    DESeq2,
    edgeR,
    BiocGenerics,
    Biostrings,
    yaml,
    biomformat,
    S4Vectors,
    Biobase,
    ComplexHeatmap,
    ANCOMBC,
    caret,
    limma,
    ALDEx2,
    multtest,
    plotROC,
    vegan,
    pROC,
    BiocParallel
Encoding: UTF-8
RoxygenNote: 7.2.3
Roxygen: list(markdown = TRUE)
Suggests: 
    testthat,
    covr,
    glmnet,
    Matrix,
    kernlab,
    e1071,
    ranger,
    knitr,
    rmarkdown,
    BiocStyle,
    withr
VignetteBuilder: knitr
Config/testthat/edition: 3