Package: MiscMetabar
Type: Package
Title: Miscellaneous Functions for Metabarcoding Analysis
Version: 0.12.1
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 (>= 4.1.0), 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,
        IRanges, jsonlite, knitr, magrittr, methods, mia, 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
RoxygenNote: 7.3.2
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, lifecycle, rlang, stats
Config/testthat/edition: 3
Config/testthat/parallel: true
VignetteBuilder: knitr
Language: en-US
NeedsCompilation: no
Packaged: 2025-01-29 08:12:01 UTC; adrien
Author: Adrien Taudière [aut, cre, cph]
    (<https://orcid.org/0000-0003-1088-1182>)
Maintainer: Adrien Taudière <adrien.taudiere@zaclys.net>
Repository: CRAN
Date/Publication: 2025-01-29 08:40:02 UTC
Built: R 4.4.1; ; 2025-01-29 09:13:53 UTC; unix
