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Secondary analyses of CNV data (HRD and more)

Bioconductor version: Release (3.19)

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.

Author: Yann Christinat [aut, cre], Geneva University Hospitals [aut, cph]

Maintainer: Yann Christinat <yann.christinat at>

Citation (from within R, enter citation("oncoscanR")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

oncoscanR vignette HTML R Script
Reference Manual PDF


biocViews CopyNumberVariation, Microarray, Software
Version 1.6.0
In Bioconductor since BioC 3.16 (R-4.2) (1.5 years)
License MIT + file LICENSE
Depends R (>= 4.2), IRanges(>= 2.30.0), GenomicRanges(>= 1.48.0), magrittr
Imports readr, S4Vectors, methods, utils
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Suggests testthat (>= 3.1.4), jsonlite, knitr, rmarkdown, BiocStyle
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Follow Installation instructions to use this package in your R session.

Source Package oncoscanR_1.6.0.tar.gz
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macOS Binary (x86_64) oncoscanR_1.6.0.tgz
macOS Binary (arm64) oncoscanR_1.6.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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