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
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

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/
Package Downloads Report	Download Stats