DESCRIPTION

Package: MiscMetabar
Type: Package
Title: Miscellaneous Functions for Metabarcoding Analysis
Version: 0.9.1
Authors@R: person("Adrien", "Taudière", email = "adrien.taudiere@zaclys.net",
  role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0003-1088-1182"))
Description: Facilitate the description, transformation, exploration, and reproducibility of metabarcoding analyses. 'MiscMetabar' is mainly built on top of the 'phyloseq', 'dada2' and 'targets' R packages. It helps to build reproducible and robust bioinformatics pipelines in R. 'MiscMetabar' makes ecological analysis of alpha and beta-diversity easier, more reproducible and more powerful by integrating a large number of tools. Important features are described in Taudière A. (2023) <doi:10.21105/joss.06038>.
License: AGPL-3
Encoding: UTF-8
LazyData: true
Depends:
    R (>= 3.5.0),
    phyloseq,
    ggplot2 (>= 3.5.0),
    dada2,
    dplyr,
    purrr
Suggests: 
    adespatial,
    ANCOMBC,
    BiocManager,
    Biostrings,
    circlize,
    ComplexUpset,
    DECIPHER,
    DESeq2,
    devtools,
    DT,
    edgeR,
    formattable,
    ggalluvial,
    ggfittext,
    gghalves,
    ggh4x,
    ggstatsplot,
    ggridges,
    ggVennDiagram,
    glmulti,
    gtsummary,
    grDevices,
    grid,
    gridExtra,
    here,
    httr,
    iNEXT,
    indicspecies,
    jsonlite,
    knitr,
    magrittr,
    metacoder,
    methods,
    mia,
    mixtools,
    multcompView,
    networkD3,
    pak,
    patchwork,
    permute,
    phangorn,
    phyloseqGraphTest,
    pbapply,
    plotly,
    plyr,
    reshape2,
    rmarkdown,
    rotl,
    Rtsne,
    scales,
    seqinr,
    SRS,
    stringr,
    SummarizedExperiment,
    testthat (>= 3.0.0),
    tibble,
    tidyr,
    treemapify,
    vegan,
    venneuler,
    vctrs,
    viridis,
    withr
RoxygenNote: 7.3.1
URL: https://github.com/adrientaudiere/MiscMetabar,
    https://adrientaudiere.github.io/MiscMetabar/
biocViews: Sequencing, Microbiome, Metagenomics,
    Clustering, Classification, Visualization
BugReports: https://github.com/adrientaudiere/MiscMetabar/issues
Roxygen: list(markdown = TRUE)
Imports: 
    ape,
    lifecycle,
    rlang,
    stats
Config/testthat/edition: 3
Config/testthat/parallel: true
VignetteBuilder: knitr
Language: en-US