To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("copynumber")

In most cases, you don't need to download the package archive at all.

copynumber

 

Segmentation of single- and multi-track copy number data by penalized least squares regression.

Bioconductor version: Release (3.1)

Penalized least squares regression is applied to fit piecewise constant curves to copy number data to locate genomic regions of constant copy number. Procedures are available for individual segmentation of each sample, joint segmentation of several samples and joint segmentation of the two data tracks from SNP-arrays. Several plotting functions are available for visualization of the data and the segmentation results.

Author: Gro Nilsen, Knut Liestoel and Ole Christian Lingjaerde.

Maintainer: Gro Nilsen <gronilse at ifi.uio.no>

Citation (from within R, enter citation("copynumber")):

Installation

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("copynumber")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("copynumber")

 

PDF R Script copynumber.pdf
PDF   Reference Manual
Text   NEWS

Details

biocViews CopyNumberVariation, Genetics, SNP, Software, Visualization, aCGH
Version 1.8.0
In Bioconductor since BioC 2.12 (R-3.0) (2.5 years)
License Artistic-2.0
Depends R (>= 2.10), BiocGenerics
Imports S4Vectors, IRanges, GenomicRanges
LinkingTo
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SystemRequirements
Enhances
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Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source copynumber_1.8.0.tar.gz
Windows Binary copynumber_1.8.0.zip
Mac OS X 10.6 (Snow Leopard) copynumber_1.8.0.tgz
Mac OS X 10.9 (Mavericks) copynumber_1.8.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/copynumber/tree/release-3.1
Package Short Url http://bioconductor.org/packages/copynumber/
Package Downloads Report Download Stats

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