Package: RadioGx
Type: Package
Title: Analysis of Large-Scale Radio-Genomic Data
Version: 2.14.0
Date: 2023-04-19
Authors@R: c(
  person("Venkata","Manem", email = "mail2mvskumar@gmail.com",
    role = c("aut")),
  person("Petr","Smirnov", email = "petr.smirnov@uhnresearch.ca",
    role = c("aut")),
  person("Ian","Smith", email = "ianc.smith@mail.utoronto.ca",
    role = c("aut")),
  person("Meghan","Lambie", email = "megan.lambie@mail.utoronto.ca",
    role = c("aut")),
  person("Christopher","Eeles", email = "christopher.eeles@uhnresearch.ca",
    role = c("aut")),
  person("Scott", "Bratman", email = "scott.bratman@rmp.uhn.ca",
    role = c("aut")),
  person("Jermiah", "Joseph", email = "jermiah.joseph@uhn.ca",
    role = c("aut")),  
  person("Benjamin","Haibe-Kains", email = "benjamin.haibe.kains@utoronto.ca",
    role = c("aut","cre"))
  )
Description: Computational tool box for radio-genomic analysis which
        integrates radio-response data, radio-biological modelling and
        comprehensive cell line annotations for hundreds of cancer cell
        lines. The 'RadioSet' class enables creation and manipulation
        of standardized datasets including information about cancer
        cells lines, radio-response assays and dose-response
        indicators. Included methods allow fitting and plotting
        dose-response data using established radio-biological models
        along with quality control to validate results. 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, references,
        as well as: Manem, V. et al (2018) <doi:10.1101/449793>.
License: GPL-3
VignetteBuilder: knitr
VignetteEngine: knitr::rmarkdown
Encoding: UTF-8
LazyData: true
Depends: R (>= 4.1), CoreGx
Imports: SummarizedExperiment, BiocGenerics, data.table, S4Vectors,
        Biobase, parallel, BiocParallel, RColorBrewer, caTools,
        magicaxis, methods, reshape2, scales, grDevices, graphics,
        stats, utils, assertthat, matrixStats, downloader
Suggests: rmarkdown, BiocStyle, knitr, pander, markdown
biocViews: Software, Pharmacogenetics, QualityControl, Survival,
        Pharmacogenomics, Classification
RoxygenNote: 7.2.3
Collate: 'OERmodel.R' 'RadioSet-class.R' 'RadioSet-accessors.R'
        'computeAUC.R' 'computeD10.R' 'computeSF2.R'
        'computeSensitivity.R' 'datasets.R' 'doseResponseCurve.R'
        'downloadRSet.R' 'geneDrugSensitivity.R' 'linearQuadratic.R'
        'linearQuadraticInv.R' 'linearQuadraticModel.R'
        'makeGrittyGuess.R' 'plotCurve.R' 'radSensitivitySig.R'
        'rankGeneRadSensitivity.R' 'signatureClass.R'
        'subsetTo-methods.R' 'summarizeMolecularProfiles-methods.R'
        'summarizeSensitivityProfiles-methods.R'
        'updateObject-methods.R' 'utilities.R' 'zzz.R'
Config/pak/sysreqs: libglpk-dev make libicu-dev libxml2-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:00:09 UTC
RemoteUrl: https://github.com/bioc/RadioGx
RemoteRef: RELEASE_3_22
RemoteSha: 060523930469e89864d47c3af5f2e52fc8e63b5f
NeedsCompilation: no
Packaged: 2025-11-11 16:45:24 UTC; root
Author: Venkata Manem [aut],
  Petr Smirnov [aut],
  Ian Smith [aut],
  Meghan Lambie [aut],
  Christopher Eeles [aut],
  Scott Bratman [aut],
  Jermiah Joseph [aut],
  Benjamin Haibe-Kains [aut, cre]
Maintainer: Benjamin Haibe-Kains <benjamin.haibe.kains@utoronto.ca>
Built: R 4.5.2; ; 2025-11-11 16:52:54 UTC; windows
