CNAnorm

DOI: 10.18129/B9.bioc.CNAnorm    

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see CNAnorm.

A normalization method for Copy Number Aberration in cancer samples

Bioconductor version: 3.7

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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("CNAnorm")

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	1.26.0
In Bioconductor since	BioC 2.9 (R-2.14) (7 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
Links To Me
Build Report

Package Archives

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

Source Package	CNAnorm_1.26.0.tar.gz
Windows Binary	CNAnorm_1.26.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	CNAnorm_1.26.0.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	http://bioconductor.org/packages/CNAnorm/
Package Downloads Report	Download Stats