Package: ClassifyR
Type: Package
Title: A framework for cross-validated classification problems, with
        applications to differential variability and differential
        distribution testing
Version: 3.13.4
Date: 2025-04-13
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: 2025-08-13 21:55:45 UTC; biocbuild
RoxygenNote: 7.3.2
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/
git_url: https://git.bioconductor.org/packages/ClassifyR
git_branch: devel
git_last_commit: 4aa8cd6
git_last_commit_date: 2025-08-13
Repository: Bioconductor 3.22
Date/Publication: 2025-08-13
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>
Built: R 4.5.1; x86_64-w64-mingw32; 2025-08-14 12:36:19 UTC; windows
Archs: x64
