oncoscanR
Secondary analyses of CNV data (HRD and more)
Bioconductor version: Release (3.20)
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("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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | CopyNumberVariation, Microarray, Software |
| Version | 1.8.0 |
| 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 |
See More
| 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_1.8.0.tar.gz |
| Windows Binary (x86_64) | oncoscanR_1.8.0.zip |
| macOS Binary (x86_64) | oncoscanR_1.8.0.tgz |
| macOS Binary (arm64) | oncoscanR_1.8.0.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 |