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oncoscanR

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")):

Installation

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


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

# The following initializes usage of Bioc devel
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")
oncoscanR vignette HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

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

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/
Package Downloads Report Download Stats