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CNAnorm

A normalization method for Copy Number Aberration in cancer samples


Bioconductor version: Release (3.18)

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")):

Installation

To install this package, start R (version "4.3") 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

Details

biocViews CopyNumberVariation, Coverage, DNASeq, GenomicVariation, Normalization, Sequencing, Software, WholeGenome
Version 1.48.0
In Bioconductor since BioC 2.9 (R-2.14) (12.5 years)
License GPL-2
Depends R (>= 2.10.1), methods
Imports DNAcopy
System Requirements
URL http://www.r-project.org
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Package Archives

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

Source Package CNAnorm_1.48.0.tar.gz
Windows Binary CNAnorm_1.48.0.zip
macOS Binary (x86_64) CNAnorm_1.48.0.tgz
macOS Binary (arm64) CNAnorm_1.48.0.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