Package: MiscMetabar
Type: Package
Title: Miscellaneous Functions for Metabarcoding Analysis
Version: 0.16.8
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, 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
Imports: ape, Biostrings, cli, dada2, divent, lifecycle, purrr, rlang,
        stats, XVector
Config/testthat/edition: 3
Config/testthat/parallel: true
VignetteBuilder: knitr
Language: en-US
NeedsCompilation: no
Packaged: 2026-06-08 13:42:57 UTC; adrien
Author: Adrien Taudière [aut, cre, cph] (ORCID:
    <https://orcid.org/0000-0003-1088-1182>)
Maintainer: Adrien Taudière <adrien.taudiere@zaclys.net>
Repository: CRAN
Date/Publication: 2026-06-08 14:30:02 UTC
Built: R 4.5.3; ; 2026-06-09 23:51:13 UTC; windows
