Package: nipalsMCIA
Title: Multiple Co-Inertia Analysis via the NIPALS Method
Version: 1.9.0
Authors@R: c(
    person("Maximilian", "Mattessich",
            email = "maximilian.mattessich@northwestern.edu",
            role = "cre", comment = c(ORCID = "0000-0002-1233-1240")),
    person("Joaquin", "Reyna", email = "joreyna@live.com",
            role = "aut", comment = c(ORCID = "0000-0002-8468-2840")),
    person("Edel", "Aron", email = "edel.aron@yale.edu",
            role = "aut", comment = c(ORCID = "0000-0002-8683-4772")),
    person("Ferhat", "Ay", email = "ferhatay@lji.org",
            role = "aut", comment = c(ORCID = "0000-0002-0708-6914")),
    person("Steven", "Kleinstein", email = "steven.kleinstein@yale.edu",
            role = "aut", comment = c(ORCID = "0000-0003-4957-1544")),
    person("Anna", "Konstorum", email = "konstorum.anna@gmail.com",
            role = "aut", comment = c(ORCID = "0000-0003-4024-2058")))
Description: Computes Multiple Co-Inertia Analysis (MCIA), a
    dimensionality reduction (jDR) algorithm, for a multi-block dataset
    using a modification to the Nonlinear Iterative Partial Least Squares
    method (NIPALS) proposed in (Hanafi et. al, 2010). Allows multiple
    options for row- and table-level preprocessing, and speeds up
    computation of variance explained. Vignettes detail application to
    bulk- and single cell- multi-omics studies.
License: GPL-3
URL: https://github.com/Muunraker/nipalsMCIA
BugReports: https://github.com/Muunraker/nipalsMCIA/issues
Depends:
    R (>= 4.3.0)
Imports:
    ComplexHeatmap,
    dplyr,
    fgsea,
    ggplot2 (>= 3.0.0),
    graphics,
    grid,
    methods,
    MultiAssayExperiment,
    SummarizedExperiment,
    pracma,
    rlang,
    RSpectra,
    scales,
    stats
Suggests:
    BiocFileCache,
    BiocStyle,
    circlize,
    ggpubr,
    KernSmooth,
    knitr,
    piggyback,
    reshape2,
    rmarkdown,
    rpart,
    Seurat (>= 4.0.0),
    spatstat.explore,
    stringr,
    survival,
    tidyverse,
    testthat (>= 3.0.0)
VignetteBuilder:
    knitr
biocViews: Software, Clustering, Classification, MultipleComparison,
    Normalization, Preprocessing, SingleCell
Encoding: UTF-8
RoxygenNote: 7.3.2
Config/testthat/edition: 3
git_url: https://git.bioconductor.org/packages/nipalsMCIA
git_branch: devel
git_last_commit: 9adbe20
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
