copynumber

DOI: 10.18129/B9.bioc.copynumber  

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.17 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see copynumber.

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

Bioconductor version: 3.17

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>

Installation

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

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("copynumber")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF		Reference Manual

Details

biocViews	CopyNumberVariation, Genetics, SNP, Software, Visualization, aCGH
Version	1.40.0
In Bioconductor since	BioC 2.12 (R-3.0) (10.5 years)
License	Artistic-2.0
Depends	R (>= 2.10), BiocGenerics
Imports	S4Vectors, IRanges, GenomicRanges
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Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/copynumber
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/copynumber
Package Short Url	https://bioconductor.org/packages/copynumber/
Package Downloads Report	Download Stats