CNAnorm

This is the released version of CNAnorm; for the devel version, see CNAnorm.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10, 2.9

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 (from within R, enter citation("CNAnorm")):

Stefano Berri, Henry M. Wood, Arief Gusnanto. CNAnorm: A normalization method for Copy Number Aberration in cancer samples. doi:10.18129/B9.bioc.CNAnorm, R package version 1.58.0, https://bioconductor.org/packages/CNAnorm.

Generated from the package metadata; it may differ from the package's own citation.

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	PDF	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

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

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Build Report	Build Report, r-universe

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
Package Short Url	https://bioconductor.org/packages/CNAnorm/
Package Downloads Report	Download Stats