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This is the development version of oncoscanR; for the stable release version, see oncoscanR.

Secondary analyses of CNV data (HRD and more)

Bioconductor version: Development (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 hcuge.ch>

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


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

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

# The following initializes usage of Bioc devel


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 1.5.0
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
System Requirements
URL https://github.com/yannchristinat/oncoscanR
Bug Reports https://github.com/yannchristinat/oncoscanR/issues
See More
Suggests testthat (>= 3.1.4), jsonlite, knitr, rmarkdown, BiocStyle
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package oncoscanR_1.5.0.tar.gz
Windows Binary oncoscanR_1.5.0.zip
macOS Binary (x86_64) oncoscanR_1.5.0.tgz
macOS Binary (arm64) oncoscanR_1.5.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/oncoscanR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/oncoscanR
Bioc Package Browser https://code.bioconductor.org/browse/oncoscanR/
Package Short Url https://bioconductor.org/packages/oncoscanR/
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