Package: CoreGx
Type: Package
Title: Classes and Functions to Serve as the Basis for Other 'Gx'
        Packages
Version: 1.4.1
Date: 2021-05-27
Authors@R: c(
    person("Petr","Smirnov", email = "petr.smirnov@uhnresearch.ca", role = c("aut")),
    person("Ian","Smith", email = "ianc.smith@mail.utoronto.ca", role = c("aut")),
    person("Christopher", "Eeles", , email = "christopher.eeles@uhnresearch.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, methods, stats, utils, graphics,
        grDevices, lsa, data.table, crayon, glue, rlang
Suggests: pander, markdown, BiocStyle, rmarkdown, knitr, formatR,
        testthat
License: GPL-3
Roxygen: list(markdown = TRUE, r6=FALSE)
RoxygenNote: 7.1.1
Collate: 'allGenerics.R' 'LongTable-class.R' 'CoreSet-class.R'
        'CoreSet-accessors.R' 'DataMapper-class.R'
        'LongTable-accessors.R' 'LongTableDataMapper-class.R'
        'adaptiveMatthewCor.R' 'callingWaterfall.R'
        'connectivityScore.R' 'cosinePerm.R' 'datasets.R' 'globals.R'
        'gwc.R' 'matthewCor.R' 'methods-$.R' 'methods-[.R'
        'methods-[[.R' 'methods-assay.R' 'methods-assayNames.R'
        'methods-assays.R' 'methods-buildLongTable.R'
        'methods-coerce.R' 'methods-colData.R' 'methods-dim.R'
        'methods-dimnames.R' 'methods-drugSensitivitySig.R'
        'methods-getIntern.R' 'methods-guessMapping.R'
        'methods-intersect.R' 'methods-metaConstruct.R'
        'methods-metadata.R' 'methods-reindex.R' 'methods-rowData.R'
        'methods-subset.R' 'methods-subsetTo.R' 'utilities.R'
        'utils-iteration.R' 'utils-messages.R' 'utils-updateS4.R'
git_url: https://git.bioconductor.org/packages/CoreGx
git_branch: RELEASE_3_13
git_last_commit: 1bc1d98
git_last_commit_date: 2021-05-31
Date/Publication: 2021-06-01
NeedsCompilation: no
Packaged: 2021-06-01 15:07:57 UTC; biocbuild
Author: Petr Smirnov [aut],
  Ian Smith [aut],
  Christopher Eeles [aut],
  Benjamin Haibe-Kains [aut, cre]
Maintainer: Benjamin Haibe-Kains <benjamin.haibe.kains@utoronto.ca>
Built: R 4.1.0; ; 2021-06-03 18:14:02 UTC; unix
