DESCRIPTION

Package: ranomaly
Title: An R package grouping ANOMALY worflow functions
Version: 1.2.0
Authors@R:
    c(person("Sebastien", "Theil", , "sebastien.theil@inrae.fr", role = c("aut")),
    person("Etienne", "Rifa", , "etienne.rifa@insa-toulouse.fr", role = c("cre", "aut")))
Description: rANOMALY use Amplicon Sequence Variant (ASV from Dada2
    package) as taxonomic unit, allowing an easy and relevant sequence
    tracking between different environments and/or projects.  Decontam
    package is included for an accurate and consistent detection of
    contaminant ASV and taxonomic assignment step relies on IDTAXA method.
    Our workflow is able to merge and check annotations from two taxonomic
    databases to unravel misannotation, discordance or inconsistency. The
    well known Phyloseq package provides the most common graphical
    representation, with additional statistics to assess significant
    impact of tested factors on microbial communities. The workflow
    incorporate multiple differential analyses (DESeq2 etc...)  to reveal
    thin community contrast between conditions.
License: GPL (>= 3) + file LICENSE
Depends:
    R (>= 4.3.0),
    phyloseq
Imports:
    bold,
    cluster,
    ComplexHeatmap,
    dada2,
    DECIPHER,
    decontam,
    DESeq2,
    doParallel,
    foreach,
    futile.logger,
    GenomicAlignments,
    ggplot2,
    htmlwidgets,
    metacoder,
    metagenomeSeq,
    mixOmics,
    nlme,
    phangorn,
    pkgndep,
    plotly (>= 4.10.4),
    psadd,
    Rhtslib,
    Rsamtools,
    ShortRead,
    stats,
    stringr,
    taxize,
    tools,
    utils,
    venn,
    VennDiagram,
    vroom
Remotes:
    ropensci/bold,
    ropensci/taxize,
    cpauvert/psadd,
    grunwaldlab/metacoder,
    HCBravoLab/metagenomeSeq,
    mikelove/DESeq2
Suggests:
    readxl,
    scales,
    microbiome,
    testthat (>= 3.0.0),
    knitr,
    rmarkdown
Author@R: c(person(given = "Sebastien", family = "Theil", role = c("aut",
    "cre"), email = "sebastien.theil@inrae.fr"), person(given = "Etienne",
    family = "Rifa", role = "aut", email = "etienne.rifa@inrae.fr"))
Config/testthat/edition: 3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.3.2
VignetteBuilder: knitr