DNAcopy

DOI: 10.18129/B9.bioc.DNAcopy  

DNA copy number data analysis

Bioconductor version: Release (3.16)

Implements the circular binary segmentation (CBS) algorithm to segment DNA copy number data and identify genomic regions with abnormal copy number.

Author: Venkatraman E. Seshan, Adam Olshen

Maintainer: Venkatraman E. Seshan <seshanv at mskcc.org>

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("DNAcopy")

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("DNAcopy")

 

PDF	R Script	DNAcopy
PDF		Reference Manual

Details

biocViews	CopyNumberVariation, Microarray, Software
Version	1.72.3
In Bioconductor since	BioC 1.6 (R-2.1) or earlier (> 18 years)
License	GPL (>= 2)
Depends
Imports
LinkingTo
Suggests
SystemRequirements
Enhances
URL
Depends On Me	CGHcall, cghMCR, Clonality, CRImage, PureCN
Imports Me	ADaCGH2, AneuFinder, ChAMP, cn.farms, CNAnorm, CNVrd2, contiBAIT, conumee, CopywriteR, GWASTools, maftools, MDTS, MEDIPS, MethCP, MinimumDistance, QDNAseq, rCGH, Repitools, SCOPE, snapCGH
Suggests Me	beadarraySNP, cn.mops, CopyNumberPlots, fastseg, nullranges, sesame
Links To Me
Build Report

Package Archives

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

Source Package	DNAcopy_1.72.3.tar.gz
Windows Binary	DNAcopy_1.72.3.zip (64-bit only)
macOS Binary (x86_64)	DNAcopy_1.72.3.tgz
macOS Binary (arm64)	DNAcopy_1.72.3.tgz
Source Repository	git clone https://git.bioconductor.org/packages/DNAcopy
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/DNAcopy
Bioc Package Browser	https://code.bioconductor.org/browse/DNAcopy/
Package Short Url	https://bioconductor.org/packages/DNAcopy/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.16	Source Archive