Package: ClassifyR
Type: Package
Title: A framework for cross-validated classification problems, with
        applications to differential variability and differential
        distribution testing
Version: 3.17.0
Date: 2025-10-08
Authors@R: 
    c(
    person(given = "Dario", family = "Strbenac", email = "dario.strbenac@sydney.edu.au", role = c("aut", "cre")),
    person(given = "Ellis", family = "Patrick", role = "aut"),
    person(given = "Sourish", family = "Iyengar", role = "aut"),
    person(given = "Harry", family = "Robertson", role = "aut"),
    person(given = "Andy", family = "Tran", role = "aut"),
    person(given = "John", family = "Ormerod", role = "aut"),
    person(given = "Graham", family = "Mann", role = "aut"),
    person(given = "Jean", family = "Yang", email = "jean.yang@sydney.edu.au", role = "aut")
    )
VignetteBuilder: knitr
Encoding: UTF-8
biocViews: Classification, Survival
Depends: R (>= 4.1.0), generics, methods, S4Vectors,
        MultiAssayExperiment, BiocParallel, survival
Imports: grid, genefilter, utils, dplyr, tidyr, rlang, ranger, ggplot2
        (>= 3.5.0), ggpubr, reshape2, ggupset, broom, dcanr
Suggests: limma, edgeR, car, Rmixmod, gridExtra (>= 2.0.0), cowplot,
        BiocStyle, pamr, PoiClaClu, knitr, htmltools, gtable, scales,
        e1071, rmarkdown, IRanges, robustbase, glmnet, class,
        randomForestSRC, MatrixModels, xgboost, data.tree, ggnewscale,
        TOP, BiocNeighbors
Description: The software formalises a framework for classification and
        survival model evaluation in R. There are four stages; Data
        transformation, feature selection, model training, and
        prediction. The requirements of variable types and variable
        order are fixed, but specialised variables for functions can
        also be provided. The framework is wrapped in a driver loop
        that reproducibly carries out a number of cross-validation
        schemes. Functions for differential mean, differential
        variability, and differential distribution are included.
        Additional functions may be developed by the user, by creating
        an interface to the framework.
License: GPL-3
Packaged: 2026-06-23 15:48:41 UTC; root
RoxygenNote: 7.3.3
NeedsCompilation: yes
Collate: 'ROCplot.R' 'available.R' 'classes.R' 'calcPerformance.R'
        'constants.R' 'crissCrossValidate.R' 'crossValidate.R' 'data.R'
        'distribution.R' 'edgesToHubNetworks.R' 'featureSetSummary.R'
        'getLocationsAndScales.R' 'interactorDifferences.R'
        'interfaceClassify.R' 'interfaceCoxPH.R' 'interfaceCoxnet.R'
        'interfaceDLDA.R' 'interfaceFisherDiscriminant.R'
        'interfaceGLM.R' 'interfaceKNN.R' 'interfaceKTSPclassifier.R'
        'interfaceMerge.R' 'interfaceMixModels.R' 'interfaceNSC.R'
        'interfaceNaiveBayesKernel.R' 'interfacePCA.R'
        'interfacePenalisedGLM.R' 'interfacePrevalidation.R'
        'interfaceRandomForest.R' 'interfaceRandomForestSurvival.R'
        'interfaceSVM.R' 'interfaceXGB.R' 'performancePlot.R'
        'plotFeatureClasses.R' 'precisionPathways.R' 'prepareData.R'
        'previousSelection.R' 'previousTrained.R' 'randomSelection.R'
        'rankingBartlett.R' 'rankingCoxPH.R' 'rankingDMD.R'
        'rankingDifferentMeans.R' 'rankingEdgeR.R'
        'rankingKolmogorovSmirnov.R' 'rankingKullbackLeibler.R'
        'rankingLevene.R' 'rankingLikelihoodRatio.R' 'rankingLimma.R'
        'rankingPairsDifferences.R' 'rankingPlot.R' 'runTest.R'
        'runTests.R' 'samplesMetricMap.R' 'selectMulti.R'
        'selectionPlot.R' 'simpleParams.R' 'subtractFromLocation.R'
        'utilities.R'
URL: https://sydneybiox.github.io/ClassifyR/
Config/pak/sysreqs: cmake libglpk-dev make libicu-dev libpng-dev
        libxml2-dev libssl-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:39:30 UTC
RemoteUrl: https://github.com/bioc/ClassifyR
RemoteRef: HEAD
RemoteSha: 8497bd6bd2eebb60652180ecd0bb87f30d674ffc
Author: Dario Strbenac [aut, cre],
  Ellis Patrick [aut],
  Sourish Iyengar [aut],
  Harry Robertson [aut],
  Andy Tran [aut],
  John Ormerod [aut],
  Graham Mann [aut],
  Jean Yang [aut]
Maintainer: Dario Strbenac <dario.strbenac@sydney.edu.au>