Package: SwitchClass
Title: Label-Switch Classification for Baseline- and
        Perturbation-Aligned Features
Version: 0.99.1
Description: Quantifies baseline-aligned and perturbation-aligned
        molecular features across biological perturbations using a
        label-switch classification framework. Provides a unified
        workflow for identifying changes in molecular-feature alignment
        in longitudinal or comparative omics datasets. Includes tools
        for classification, visualization, dimension reduction, and
        pathway enrichment.
Authors@R: c(
    person("Di", "Xiao", role = c("aut", "cre"),
        email = "d.xiao@sydney.edu.au"),
    person("Pengyi", "Yang", role = "aut",
        email = "pyang@cmri.org.au")
    )
License: MIT + file LICENSE
URL: https://github.com/PYangLab/SwitchClass
BugReports: https://github.com/PYangLab/SwitchClass/issues
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
biocViews: Software, Classification, FeatureExtraction, GeneExpression,
        Proteomics, Transcriptomics, SingleCell, Pathways
Depends: R (>= 4.5.0)
Imports: randomForest, uwot, ggplot2, ggrepel, PhosR, pheatmap, dplyr,
        RColorBrewer, ggpubr, parallel
Suggests: BiocStyle, knitr, rmarkdown, limma, matrixStats, patchwork,
        clusterProfiler, glmnet, reactome.db, org.Hs.eg.db, msigdbr,
        testthat (>= 3.0.0)
VignetteBuilder: knitr
Config/testthat/edition: 3
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: cmake libglpk-dev make libicu-dev libjpeg-dev
        libpng-dev libxml2-dev libssl-dev zlib1g-dev
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-08-04 23:40:27 UTC
RemoteUrl: https://github.com/BiocStaging/SwitchClass
RemoteRef: HEAD
RemoteSha: 106a48d8112ce92b1a01dad1dc2a9b9069d01b08
NeedsCompilation: no
Packaged: 2026-09-18 10:30:03 UTC; root
Author: Di Xiao [aut, cre],
  Pengyi Yang [aut]
Maintainer: Di Xiao <d.xiao@sydney.edu.au>