Package: DspikeIn
Type: Package
Title: Estimating Absolute Abundance from Microbial Spike-in Controls
Version: 1.0.0
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
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libfribidi-dev libglpk-dev make
        libharfbuzz-dev libicu-dev libjpeg-dev libpng-dev libtiff-dev
        libwebp-dev libxml2-dev libssl-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:39:12 UTC
RemoteUrl: https://github.com/bioc/DspikeIn
RemoteRef: RELEASE_3_22
RemoteSha: 8a427ff4e61cba46ede54bf23612f02693d70288
Packaged: 2026-01-24 20:38:11 UTC; root
Author: Mitra Ghotbi [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-9185-9993>),
  Marjan Ghotbi [ctb] (ORCID: <https://orcid.org/0000-0003-4655-6445>)
Maintainer: Mitra Ghotbi <mitra.ghotbi@gmail.com>
Built: R 4.5.2; ; 2026-01-24 20:41:23 UTC; windows
