Package: oncoscanR
Type: Package
Title: Secondary analyses of CNV data (HRD and more)
Version: 1.15.0
Authors@R: c(person("Yann", "Christinat", email = "yann.christinat@hcuge.ch", 
                  role = c("aut", "cre")),
             person("Geneva University Hospitals", role=c("aut", "cph")))
Description: The software uses the copy number segments from a text
        file and identifies all chromosome arms that are globally
        altered and computes various genome-wide scores. The following
        HRD scores (characteristic of BRCA-mutated cancers) are
        included: LST, HR-LOH, nLST and gLOH. the package is tailored
        for the ThermoFisher Oncoscan assay analyzed with their
        Chromosome Alteration Suite (ChAS) but can be adapted to any
        input.
License: MIT + file LICENSE
Date: 2025-06-27
Encoding: UTF-8
VignetteBuilder: knitr
biocViews: CopyNumberVariation, Microarray, Software
Imports: readr, S4Vectors, methods, utils
RoxygenNote: 7.3.2
Depends: R (>= 4.2), IRanges (>= 2.30.0), GenomicRanges (>= 1.48.0),
        magrittr
Suggests: testthat (>= 3.1.4), jsonlite, knitr, rmarkdown, BiocStyle
URL: https://github.com/yannchristinat/oncoscanR
BugReports: https://github.com/yannchristinat/oncoscanR/issues
LazyData: true
Config/pak/sysreqs: libx11-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:58:48 UTC
RemoteUrl: https://github.com/bioc/oncoscanR
RemoteRef: HEAD
RemoteSha: 74407d7cd88ef1665e19c7847bbe2bbf79a6fc40
NeedsCompilation: no
Packaged: 2026-07-04 23:25:48 UTC; root
Author: Yann Christinat [aut, cre],
  Geneva University Hospitals [aut, cph]
Maintainer: Yann Christinat <yann.christinat@hcuge.ch>