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oncoscanR

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16

Secondary analyses of CNV data (HRD and more)

DOI: 10.18129/B9.bioc.oncoscanR

Bioconductor version: Development (3.24)

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")):

Yann Christinat, Geneva University Hospitals. oncoscanR: Secondary analyses of CNV data (HRD and more). doi:10.18129/B9.bioc.oncoscanR, R package version 1.15.0, https://bioconductor.org/packages/oncoscanR.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

BiocManager::install("oncoscanR")

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

Documentation

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

browseVignettes("oncoscanR")

Details

Package Archives

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