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 (3.24)
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("oncoscanR")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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")| oncoscanR vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | CopyNumberVariation, Microarray, Software |
| Version | 1.15.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (4 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_1.15.0.tar.gz |
| Windows Binary (x86_64) | oncoscanR_1.15.0.zip |
| macOS Binary (big-sur-x86_64) | oncoscanR_1.15.0.tgz |
| macOS Binary (sonoma-arm64) | oncoscanR_1.15.0.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 |