CNAnorm
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see CNAnorm.
A normalization method for Copy Number Aberration in cancer samples
Bioconductor version: 3.9
Performs ratio, GC content correction and normalization of data obtained using low coverage (one read every 100-10,000 bp) high troughput sequencing. It performs a "discrete" normalization looking for the ploidy of the genome. It will also provide tumour content if at least two ploidy states can be found.
Author: Stefano Berri <sberri at illumina.com>, Henry M. Wood <H.M.Wood at leeds.ac.uk>, Arief Gusnanto <a.gusnanto at leeds.ac.uk>
Maintainer: Stefano Berri <sberri at illumina.com>
citation("CNAnorm")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("CNAnorm")
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("CNAnorm")| CNAnorm.pdf | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | CopyNumberVariation, Coverage, DNASeq, GenomicVariation, Normalization, Sequencing, Software, WholeGenome |
| Version | 1.30.0 |
| In Bioconductor since | BioC 2.9 (R-2.14) (12.5 years) |
| License | GPL-2 |
| Depends | R (>= 2.10.1), methods |
| Imports | DNAcopy |
| System Requirements | |
| URL | http://www.r-project.org |
See More
| Suggests | |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | CNAnorm_1.30.0.tar.gz |
| Windows Binary | CNAnorm_1.30.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | CNAnorm_1.30.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/CNAnorm |
| Source Repository (Developer Access) | git clone [email protected]:packages/CNAnorm |
| Bioc Package Browser | https://code.bioconductor.org/browse/CNAnorm/ |
| Package Short Url | https://bioconductor.org/packages/CNAnorm/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |