Package: RiskyCNV
Title: Risk Analysis of Genomic Copy Number Variation
Version: 0.1.0
Authors@R: c(
    person("Ashok", "Palaniappan", email = "apalania@scbt.sastra.edu",
           role = c("aut", "cre"),
           comment = c(ORCID = "0000-0003-2841-9527")),
    person("Priyanka", "Ramesh",
           role = "aut"),
    person("Ida", "Titus",
           role = "aut"),
    person("Sangeetha", "Muthamilselvan",
           role = "aut"))
Description: Provides a complete seven-step workflow for copy number variation
    (CNV) analysis applicable to any disease or condition where samples with genomic copy
    number data is available. Supports built-in grading and risk stratification
    presets for seven major cancers (viz. prostate, breast, colorectal, lung,
    cervical, lymphoma, melanoma) based on clinically validated systems including
    ISUP Grade Groups, Nottingham Grading System, Dukes staging, IASLC TNM,
    FIGO, Ann Arbor/Lugano classification, and Breslow depth. Generalizable to other disease types. An automatic mode
    derives a normalised Risk Score from the data using min-max normalisation
    and adaptive binning. Custom user-defined thresholds are supported for
    any other disease type. Downstream functions for CNV aberration detection,
    recurrence analysis, gene annotation, CNV matrix generation, and CNV-RNA
    expression correlation are disease-type agnostic.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 4.1.0)
Imports: dplyr, GenomicRanges, rlang, S4Vectors, stats, tidyr, tools,
        utils
Suggests: BiocManager, knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
RoxygenNote: 7.3.3
biocViews: CopyNumberVariation, GenomicVariation, RNASeq
Config/testthat/edition: 3
NeedsCompilation: no
Packaged: 2026-05-14 08:37:47 UTC; ida_titus
Author: Ashok Palaniappan [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-2841-9527>),
  Priyanka Ramesh [aut],
  Ida Titus [aut],
  Sangeetha Muthamilselvan [aut]
Maintainer: Ashok Palaniappan <apalania@scbt.sastra.edu>
Repository: CRAN
Date/Publication: 2026-06-05 15:00:17 UTC
Built: R 4.6.0; ; 2026-06-05 15:32:40 UTC; unix
