copynumber
This package is for version 3.9 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: 3.9
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("copynumber")):
Installation
To install this package, start R (version "3.6") 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
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("copynumber")| copynumber.pdf | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | CopyNumberVariation, Genetics, SNP, Software, Visualization, aCGH |
| Version | 1.24.0 |
| In Bioconductor since | BioC 2.12 (R-3.0) (11 years) |
| License | Artistic-2.0 |
| Depends | R (>= 2.10), BiocGenerics |
| Imports | S4Vectors, IRanges, GenomicRanges |
| System Requirements | |
| URL |
See More
| Suggests | |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | PureCN |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | copynumber_1.24.0.tar.gz |
| Windows Binary | copynumber_1.24.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | copynumber_1.24.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/copynumber |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/copynumber |
| Bioc Package Browser | https://code.bioconductor.org/browse/copynumber/ |
| Package Short Url | https://bioconductor.org/packages/copynumber/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |