Package: CoreGx
Type: Package
Title: Classes and Functions to Serve as the Basis for Other 'Gx'
        Packages
Version: 2.15.0
Date: 2024-03-11
Authors@R: c(
    person(given="Jermiah", family="Joseph", email="jermiah.joseph@uhn.ca",
        role=c("aut")),
    person(given="Petr", family="Smirnov", email = "petr.smirnov@uhnresearch.ca",
        role = c("aut")),
    person(given="Ian", family="Smith", email = "ianc.smith@mail.utoronto.ca",
        role = c("aut")),
    person(given="Christopher", family="Eeles", email = "christopher.eeles@uhnresearch.ca",
        role = c("aut")),
    person(given="Feifei", family="Li", email="ff.li@mail.utoronto.ca",
        role=c("aut")),
    person("Benjamin", "Haibe-Kains",
        email = "benjamin.haibe.kains@utoronto.ca", role = c("aut", "cre"))
    )
Description: A collection of functions and classes which serve as the
        foundation for our lab's suite of R packages, such as
        'PharmacoGx' and 'RadioGx'. This package was created to
        abstract shared functionality from other lab package releases
        to increase ease of maintainability and reduce code repetition
        in current and future 'Gx' suite programs. Major features
        include a 'CoreSet' class, from which 'RadioSet' and
        'PharmacoSet' are derived, along with get and set methods for
        each respective slot. Additional functions related to fitting
        and plotting dose response curves, quantifying statistical
        correlation and calculating area under the curve (AUC) or
        survival fraction (SF) are included. For more details please
        see the included documentation, as well as: Smirnov, P.,
        Safikhani, Z., El-Hachem, N., Wang, D., She, A., Olsen, C.,
        Freeman, M., Selby, H., Gendoo, D., Grossman, P., Beck, A.,
        Aerts, H., Lupien, M., Goldenberg, A. (2015)
        <doi:10.1093/bioinformatics/btv723>. Manem, V., Labie, M.,
        Smirnov, P., Kofia, V., Freeman, M., Koritzinksy, M., Abazeed,
        M., Haibe-Kains, B., Bratman, S. (2018) <doi:10.1101/449793>.
VignetteBuilder: knitr
VignetteEngine: knitr::rmarkdown
biocViews: Software, Pharmacogenomics, Classification, Survival
Encoding: UTF-8
LazyData: TRUE
Depends: R (>= 4.1), BiocGenerics, SummarizedExperiment
Imports: Biobase, S4Vectors, MultiAssayExperiment, MatrixGenerics,
        piano, BiocParallel, parallel, BumpyMatrix, checkmate, methods,
        stats, utils, graphics, grDevices, lsa, data.table, crayon,
        glue, rlang, bench
Suggests: pander, markdown, BiocStyle, rmarkdown, knitr, formatR,
        testthat
License: GPL (>= 3)
Config/testthat/edition: 3
Roxygen: list(markdown=TRUE, r6=FALSE)
RoxygenNote: 7.3.1
RCollate: 'allGenerics.R' 'immutable-class.R' 'LongTable-class.R'
        'CoreSet-class.R' 'CoreSet-accessors.R' 'CoreSet-utils.R'
        'DataMapper-class.R' 'LongTable-accessors.R'
        'LongTable-utils.R' 'LongTableDataMapper-class.R'
        'LongTableDataMapper-accessors.R'
        'TreatmentResponseExperiment-class.R' 'TREDataMapper-class.R'
        'adaptiveMatthewCor.R' 'aggregate-methods.R'
        'callingWaterfall.R' 'connectivityScore.R' 'cosinePerm.R'
        'datasets.R' 'deprecated.R' 'endoaggregate-methods.R'
        'globals.R' 'gwc.R' 'matthewCor.R' 'mergeAssays-method.R'
        'methods-coerce.R' 'methods-dim.R' 'methods-dimnames.R'
        'methods-drugSensitivitySig.R' 'methods-guessMapping.R'
        'methods-metaConstruct.R' 'methods-subsetTo.R'
        'optimizeCoreGx.R' 'updateObject-methods.R' 'utilities.R'
        'utils-iteration.R' 'utils-messages.R' 'utils-optimization.R'
        'utils-testing.R' 'utils-updateS4.R'
Collate: 'allGenerics.R' 'immutable-class.R' 'LongTable-class.R'
        'CoreSet-class.R' 'CoreSet-accessors.R' 'CoreSet-utils.R'
        'DataMapper-class.R' 'LongTable-accessors.R'
        'LongTable-utils.R' 'LongTableDataMapper-class.R'
        'LongTableDataMapper-accessors.R'
        'TreatmentResponseExperiment-class.R' 'TREDataMapper-class.R'
        'adaptiveMatthewCor.R' 'aggregate-methods.R'
        'callingWaterfall.R' 'connectivityScore.R' 'cosinePerm.R'
        'datasets.R' 'deprecated.R' 'endoaggregate-methods.R'
        'globals.R' 'gwc.R' 'matthewCor.R' 'mergeAssays-method.R'
        'methods-coerce.R' 'methods-dim.R' 'methods-dimnames.R'
        'methods-drugSensitivitySig.R' 'methods-guessMapping.R'
        'methods-metaConstruct.R' 'methods-subsetTo.R'
        'optimizeCoreGx.R' 'updateObject-methods.R' 'utilities.R'
        'utils-iteration.R' 'utils-messages.R' 'utils-optimization.R'
        'utils-testing.R' 'utils-updateS4.R'
Config/pak/sysreqs: libglpk-dev make libicu-dev libxml2-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 14:59:21 UTC
RemoteUrl: https://github.com/bioc/CoreGx
RemoteRef: HEAD
RemoteSha: e18fa8365cb231500ea25d15c0ede92685446aa3
NeedsCompilation: no
Packaged: 2025-11-02 14:46:13 UTC; root
Author: Jermiah Joseph [aut],
  Petr Smirnov [aut],
  Ian Smith [aut],
  Christopher Eeles [aut],
  Feifei Li [aut],
  Benjamin Haibe-Kains [aut, cre]
Maintainer: Benjamin Haibe-Kains <benjamin.haibe.kains@utoronto.ca>
Built: R 4.6.0; ; 2025-11-02 14:49:28 UTC; windows
