DOI: 10.18129/B9.bioc.oncoscanR  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see oncoscanR.

Secondary analyses of CNV data (HRD and more)

Bioconductor version: 3.16

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")):


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biocViews CopyNumberVariation, Microarray, Software
Version 1.0.0
In Bioconductor since BioC 3.16 (R-4.2) (< 6 months)
License MIT + file LICENSE
Depends R (>= 4.2), IRanges(>= 2.30.0), GenomicRanges(>= 1.48.0), magrittr
Imports readr, S4Vectors, methods, utils
Suggests testthat (>= 3.1.4), jsonlite, knitr, rmarkdown
URL https://github.com/yannchristinat/oncoscanR
BugReports https://github.com/yannchristinat/oncoscanR/issues
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Source Package oncoscanR_1.0.0.tar.gz
Windows Binary oncoscanR_1.0.0.zip
macOS Binary (x86_64) oncoscanR_1.0.0.tgz
macOS Binary (arm64) oncoscanR_1.0.0.tgz
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Bioc Package Browser https://code.bioconductor.org/browse/oncoscanR/
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