oncoscanR

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see oncoscanR.

Secondary analyses of CNV data (HRD and more)

Bioconductor version: 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")):

Installation

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


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

oncoscanR vignette HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews CopyNumberVariation, Microarray, Software

Version 1.6.0

In Bioconductor since BioC 3.16 (R-4.2) (2 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

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_1.6.0.tar.gz

Windows Binary (x86_64) oncoscanR_1.6.0.zip

macOS Binary (x86_64) oncoscanR_1.6.0.tgz

macOS Binary (arm64) oncoscanR_1.6.0.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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