CNAnorm

DOI: 10.18129/B9.bioc.CNAnorm    

A normalization method for Copy Number Aberration in cancer samples

Bioconductor version: Release (3.14)

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>

Installation

To install this package, start R (version "4.1") 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")

 

PDF	R Script	CNAnorm.pdf
PDF		Reference Manual
Text		NEWS

Details

biocViews	CopyNumberVariation, Coverage, DNASeq, GenomicVariation, Normalization, Sequencing, Software, WholeGenome
Version	1.40.0
In Bioconductor since	BioC 2.9 (R-2.14) (10.5 years)
License	GPL-2
Depends	R (>= 2.10.1), methods
Imports	DNAcopy
LinkingTo
Suggests
SystemRequirements
Enhances
URL	http://www.r-project.org
Depends On Me
Imports Me
Suggests Me
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Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	CNAnorm_1.40.0.tar.gz
Windows Binary	CNAnorm_1.40.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	CNAnorm_1.40.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/CNAnorm
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/CNAnorm
Package Short Url	https://bioconductor.org/packages/CNAnorm/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.14	Source Archive