MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis (original) (raw)

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>.

Version:	0.14.2
Depends:	R (≥ 4.1.0), phyloseq, ggplot2 (≥ 3.5.0), dada2, dplyr, purrr
Imports:	ape, lifecycle, rlang, stats
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, spelling
Published:	2025-03-20
DOI:	10.32614/CRAN.package.MiscMetabar
Author:	Adrien Taudière [aut, cre, cph]
Maintainer:	Adrien Taudière <adrien.taudiere at zaclys.net>
BugReports:	https://github.com/adrientaudiere/MiscMetabar/issues
License:	AGPL-3
URL:	https://github.com/adrientaudiere/MiscMetabar,https://adrientaudiere.github.io/MiscMetabar/
NeedsCompilation:	no
Language:	en-US
Materials:	README NEWS
CRAN checks:	MiscMetabar results [issues need fixing before 2025-06-20]

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