CNAnorm
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see CNAnorm.
A normalization method for Copy Number Aberration in cancer samples
Bioconductor version: 3.19
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 "4.4") 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 | 1.50.0 |
In Bioconductor since | BioC 2.9 (R-2.14) (13 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 | |
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Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | CNAnorm_1.50.0.tar.gz |
Windows Binary (x86_64) | CNAnorm_1.50.0.zip |
macOS Binary (x86_64) | CNAnorm_1.50.0.tgz |
macOS Binary (arm64) | CNAnorm_1.50.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/CNAnorm |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CNAnorm |
Bioc Package Browser | https://code.bioconductor.org/browse/CNAnorm/ |
Package Short Url | https://bioconductor.org/packages/CNAnorm/ |
Package Downloads Report | Download Stats |