copynumber

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

Bioconductor version: Development (3.0)

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>

To install this package, start R and enter:

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

To cite this package in a publication, start R and enter:

    citation("copynumber")

Documentation

PDF R Script copynumber.pdf
PDF   Reference Manual
Text   NEWS

Details

biocViews CopyNumberVariation, Genetics, SNP, Software, Visualization, aCGH
Version 1.5.0
In Bioconductor since BioC 2.12 (R-3.0)
License Artistic-2.0
Depends R (>= 2.10), BiocGenerics
Imports GenomicRanges, IRanges
Suggests
System Requirements
URL
Depends On Me
Imports Me
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Package Downloads

Package Source copynumber_1.5.0.tar.gz
Windows Binary copynumber_1.5.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) copynumber_1.5.0.tgz
Mac OS X 10.9 (Mavericks)
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