Type: Package
Package: DspikeIn
Title: Estimating Absolute Abundance from Microbial Spike-in Controls
Version: 0.99.15
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 gene copy numbers. Compatible with 'phyloseq' and
    'TreeSummarizedExperiment' (TSE) data structures. The package
    implements core methods for spike-in validation, scaling factor
    estimation, absolute abundance conversion, and bias correction.
    Visualization tools are provided via 'ggplot2', 'ggtree', and related
    packages. This streamlined version focuses on core functionality and
    quantification. For helper utilities and extended pipelines, refer to
    the 'MGhotbi' branch on GitHub.
License: MIT + file LICENSE
URL: https://github.com/mghotbi/DspikeIn
BugReports: https://github.com/mghotbi/DspikeIn/issues
Depends: R (>= 4.5.0)
Imports: ape, Biostrings, data.table, DECIPHER, DESeq2, dplyr, edgeR,
        flextable, ggalluvial, ggnewscale, ggplot2, ggpubr, ggstar,
        ggtree, ggtreeExtra, graphics, grDevices, grid, limma,
        matrixStats, methods, microbiome, msa, officer, phangorn,
        phyloseq, randomForest, RColorBrewer, S4Vectors, scales, stats,
        SummarizedExperiment, tibble, tidyr, TreeSummarizedExperiment,
        utils
Suggests: mia, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), vegan
VignetteBuilder: knitr
biocViews: Microbiome, Preprocessing, QualityControl,
        DifferentialExpression, Normalization,
        Sequencing,Classification, Visualization, Phylogenetics,
        ExperimentalDesign, DataImport, Software
Encoding: UTF-8
LazyData: true
LazyDataCompression: xz
NeedsCompilation: no
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Packaged: 2025-07-23 22:24:11 UTC; pkgbuild
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>
