Package: DspikeIn
Type: Package
Title: Estimating Absolute Abundance from Microbial Spike-in Controls
Version: 1.1.0
Authors@R: c(
    person("Mitra", "Ghotbi", , "mitra.ghotbi@gmail.com", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0001-9185-9993")),
    person("Marjan", "Ghotbi", , "ghotbi.marjan@gmail.com", role = "ctb",
           comment = c(ORCID = "0000-0003-4655-6445"))
  )
Description: Provides a reproducible and modular workflow for absolute microbial 
    quantification using spike-in controls. Supports both single spike-in taxa 
    and synthetic microbial communities with user-defined spike-in volumes and 
    genome copy numbers. Compatible with 'phyloseq' and 'TreeSummarizedExperiment' 
    (TSE) data structures. The package implements methods for spike-in validation, 
    preprocessing, scaling factor estimation, absolute abundance conversion, 
    bias correction, and normalization. Facilitates downstream statistical 
    analyses with 'DESeq2', 'edgeR', and other Bioconductor-compatible methods. 
    Visualization tools are provided via 'ggplot2', 'ggtree', and related packages. 
    Includes detailed vignettes, case studies, and function-level documentation 
    to guide users through experimental design, quantification, and interpretation.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
LazyDataCompression: xz
Depends: 
    R (>= 4.1.0)
Imports:
    ape,
    Biostrings,
    data.table,
    DECIPHER,
    DESeq2,
    dplyr,
    edgeR,
    flextable,
    ggalluvial,
    ggnewscale,
    ggplot2,
    ggpubr,
    ggraph,
    ggrepel,
    ggridges,
    ggtree,
    ggtreeExtra,
    graphics,
    grDevices,
    igraph,
    limma,
    matrixStats,
    methods,
    microbiome,
    officer,
    grid,
    reshape2,
    patchwork,
    phangorn,
    phyloseq,
    randomForest,
    RColorBrewer,
    rlang,
    S4Vectors,
    scales,
    stats,
    tibble,
    tidyr,
    SummarizedExperiment,
    TreeSummarizedExperiment,
    utils,
    msa,
    xml2,
    ggstar
Suggests:
    Biobase,
        mia,
    BiocGenerics,
    magrittr,
    BiocManager,
    cluster,
    devtools,
    DT,
    e1071,
    foreach,
    ggtext,
    intergraph,
    knitr,
    optparse,
    plyr,
    preprocessCore,
    qpdf,
    remotes,
    rmarkdown,
    ShortRead,
    testthat (>= 3.0.0),
    vegan,
    viridis
biocViews: 
    Microbiome, 
    Preprocessing, 
    QualityControl, 
    DifferentialExpression, 
    Normalization, 
    Sequencing, 
    Visualization, 
    Phylogenetics, 
    ExperimentalDesign, 
    DataImport, 
    Software
URL: https://github.com/mghotbi/DspikeIn
BugReports: https://github.com/mghotbi/DspikeIn/issues
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
VignetteBuilder: knitr
NeedsCompilation: no
git_url: https://git.bioconductor.org/packages/DspikeIn
git_branch: devel
git_last_commit: 18fc5b8
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
