CNAnorm

DOI: 10.18129/B9.bioc.CNAnorm    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see CNAnorm.

A normalization method for Copy Number Aberration in cancer samples

Bioconductor version: 3.8

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 "3.5") and enter:

if (!requireNamespace("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 1.28.0
In Bioconductor since BioC 2.9 (R-2.14) (7.5 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
Links To Me
Build Report  

Package Archives

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

Source Package CNAnorm_1.28.0.tar.gz
Windows Binary CNAnorm_1.28.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) CNAnorm_1.28.0.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

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