DNAcopy

This is the development version of DNAcopy; for the stable release version, see DNAcopy.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10, 2.9, 2.8, 2.7, 2.6, 2.5

DNA Copy Number Data Analysis

Bioconductor version: Development (3.24)

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>

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

Venkatraman E. Seshan, Adam Olshen. DNAcopy: DNA Copy Number Data Analysis. doi:10.18129/B9.bioc.DNAcopy, R package version 1.87.0, https://bioconductor.org/packages/DNAcopy.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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")

DNAcopy	PDF	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	CopyNumberVariation, Microarray, Software
Version	1.87.0
In Bioconductor since	BioC 1.6 (R-2.1) or earlier (> 21.5 years)
License	GPL (>= 2)
Depends
Imports
System Requirements
URL

Suggests
Linking To
Enhances
Depends On Me	CGHcall, cghMCR, CRImage, CSclone, ParDNAcopy, PureCN
Imports Me	ADaCGH2, ChAMP, cn.farms, CNAnorm, CNVrd2, conumee, GWASTools, jointseg, maftools, MDTS, MEDIPS, MinimumDistance, PSCBS, QDNAseq, rCGH, SCOPE, wavFeatExt
Suggests Me	ACNE, aroma.cn, aroma.core, bcp, calmate, cn.mops, CopyNumberPlots, fastseg, nullranges, sesame
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	DNAcopy_1.87.0.tar.gz
Windows Binary (x86_64)	DNAcopy_1.87.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	DNAcopy_1.87.0.tgz
macOS Binary (sonoma-arm64)	DNAcopy_1.87.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/DNAcopy
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/DNAcopy
Package Short Url	https://bioconductor.org/packages/DNAcopy/
Package Downloads Report	Download Stats