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: 1.2.0
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: RELEASE_3_22
git_last_commit: f1af123
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.22
Date/Publication: 2025-10-29
NeedsCompilation: no
Packaged: 2025-10-30 02:53:08 UTC; biocbuild
Author: Qiao Yang [aut, cre] (ORCID: <https://orcid.org/0000-0002-4098-3246>),
  Emmanouil G. Sifakis [aut] (ORCID:
    <https://orcid.org/0000-0001-9919-4471>)
Maintainer: Qiao Yang <yq.kiuo@gmail.com>
