Package: BreastSubtypeR
Type: Package
Title: Cohort-aware methods for intrinsic molecular subtyping of breast cancer
Description: BreastSubtypeR provides an assumption-aware, multi-method framework
    for intrinsic molecular subtyping of breast cancer. The package harmonizes
    several published nearest-centroid (NC) and single-sample predictor (SSP)
    classifiers, supplies method-specific preprocessing and robust probe-to-gene
    mapping, and implements a cohort-aware AUTO mode that selectively enables
    classifiers compatible with the cohort composition. A local Shiny app
    (iBreastSubtypeR) is included for interactive analyses and to support users
    without programming experience.
Encoding: UTF-8
Version: 1.3.1
biocViews: RNASeq, Software, GeneExpression, Classification, Preprocessing, Visualization
Authors@R: c(
    person(given = "Qiao", family = "Yang", 
	   role = c("aut", "cre"), 
           email="yq.kiuo@gmail.com", 
           comment = c(ORCID = "0000-0002-4098-3246")),
    person(given = "Emmanouil G.", family = "Sifakis",
           role = c("aut"),
           email = "emmanouil.sifakis@ki.se",
           comment = c(ORCID = "0000-0001-9919-4471"))
 )
Depends:
    R (>= 4.5.0)
Imports:
    methods,
    Biobase,
    tidyselect,
    dplyr,
    ggplot2,
    magrittr,
    rlang,
    stringr,
    withr,
    edgeR,
    ComplexHeatmap,
    impute (>= 1.80.0),
    data.table (>= 1.16.0),
    RColorBrewer (>= 1.1-3),
    circlize (>= 0.4.16),
    ggrepel (>= 0.9.6),
    e1071 (>= 1.7-8),
    SummarizedExperiment,
    utils
Suggests:
    lifecycle,
    tidyverse,
    shiny (>= 1.9.1),
    bslib (>= 0.8.0),
    BiocStyle,
    knitr,
    rmarkdown,
    testthat
URL: https://doi.org/10.18129/B9.bioc.BreastSubtypeR,https://github.com/yqkiuo/BreastSubtypeR,https://github.com/JohanHartmanGroupBioteam/BreastSubtypeR
BugReports: https://github.com/yqkiuo/BreastSubtypeR/issues
License: GPL-3
VignetteBuilder: knitr
Roxygen: list(markdown = TRUE, roclets = c("rd", "namespace", "collate"))
LazyData: FALSE
RoxygenNote: 7.3.3
git_url: https://git.bioconductor.org/packages/BreastSubtypeR
git_branch: devel
git_last_commit: ffbf5d8
git_last_commit_date: 2025-11-23
Repository: Bioconductor 3.23
