CNAnorm
This is the released version of CNAnorm; for the devel version, see CNAnorm.
A normalization method for Copy Number Aberration in cancer samples
Bioconductor version: Release (3.23)
Performs ratio, GC content correction and normalization of data obtained using low coverage (one read every 100-10,000 bp) high troughput sequencing. It performs a "discrete" normalization looking for the ploidy of the genome. It will also provide tumour content if at least two ploidy states can be found.
Author: Stefano Berri <sberri at illumina.com>, Henry M. Wood <H.M.Wood at leeds.ac.uk>, Arief Gusnanto <a.gusnanto at leeds.ac.uk>
Maintainer: Stefano Berri <sberri at illumina.com>
citation("CNAnorm")):
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")
BiocManager::install("CNAnorm")
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("CNAnorm")| CNAnorm.pdf | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | CopyNumberVariation, Coverage, DNASeq, GenomicVariation, Normalization, Sequencing, Software, WholeGenome |
| Version | 1.58.0 |
| In Bioconductor since | BioC 2.9 (R-2.14) (15 years) |
| License | GPL-2 |
| Depends | R (>= 2.10.1), methods |
| Imports | DNAcopy |
| System Requirements | |
| URL | http://www.r-project.org |
See More
| Suggests | |
| 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 | CNAnorm_1.58.0.tar.gz |
| Windows Binary (x86_64) | CNAnorm_1.58.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | CNAnorm_1.58.0.tgz |
| macOS Binary (sonoma-arm64) | CNAnorm_1.58.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/CNAnorm |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CNAnorm |
| Bioc Package Browser | https://code.bioconductor.org/browse/CNAnorm/ |
| Package Short Url | https://bioconductor.org/packages/CNAnorm/ |
| Package Downloads Report | Download Stats |