Package: MiscMetabar
Type: Package
Title: Miscellaneous Functions for Metabarcoding Analysis
Version: 0.17.0.9000
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 (>= 4.1.0), phyloseq, ggplot2 (>= 3.5.0), dplyr
Suggests: adespatial, ALDEx2, ANCOMBC, BiocManager, circlize,
        ComplexUpset, DECIPHER, DESeq2, devtools, DT, edgeR,
        formattable, ggalluvial, ggfittext, ggh4x, ggnetwork,
        ggstatsplot, ggridges, ggVennDiagram, glmulti, gtsummary,
        grDevices, grid, gridExtra, here, httr, igraph, iNEXT,
        indicspecies, IRanges, jsonlite, knitr, lefser, magrittr,
        methods, mia, metagenomeSeq, mixtools, multcompView, networkD3,
        pak, patchwork, pbapply, permute, phangorn, phyloseqGraphTest,
        pkgnet, plotly, plyr, reshape2, rmarkdown, rotl, Rtsne, scales,
        seqinr, SRS, stringr, SummarizedExperiment, testthat (>=
        3.0.0), tibble, tidyr, treemapify, umap, uwot, vegan,
        venneuler, vctrs, viridis, withr, writexl, spelling
RoxygenNote: 8.0.0
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, Biostrings, cli, dada2, divent, lifecycle, purrr, rlang,
        stats, XVector
Config/testthat/edition: 3
Config/testthat/parallel: true
VignetteBuilder: knitr
Language: en-US
Config/pak/sysreqs: cmake libglpk-dev make libbz2-dev libicu-dev
        libjpeg-dev liblzma-dev libpng-dev libxml2-dev xz-utils
        zlib1g-dev
Repository: https://adrientaudiere.r-universe.dev
Date/Publication: 2026-07-07 19:58:16 UTC
RemoteUrl: https://github.com/adrientaudiere/miscmetabar
RemoteRef: HEAD
RemoteSha: bb1bf8099f7544432980725d387859327bdac49f
NeedsCompilation: no
Packaged: 2026-10-05 11:03:14 UTC; root
Author: Adrien Taudière [aut, cre, cph] (ORCID:
    <https://orcid.org/0000-0003-1088-1182>)
Maintainer: Adrien Taudière <adrien.taudiere@zaclys.net>