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DESCRIPTION
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DESCRIPTION
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Package: MiscMetabar
Type: Package
Title: Miscellaneous Functions for Metabarcoding Analysis
Version: 0.9.2
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