CNAnorm

A normalization method for Copy Number Aberration in cancer samples

Bioconductor version: 2.10

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 <s.berri at leeds.ac.uk>, Henry M. Wood <H.M.Wood at leeds.ac.uk>, Arief Gusnanto <a.gusnanto at leeds.ac.uk>

Maintainer: Stefano Berri <s.berri at leeds.ac.uk>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("CNAnorm")

To cite this package in a publication, start R and enter:

    citation("CNAnorm")

Documentation

PDF R Script CNAnorm.pdf
PDF   Reference Manual
Text   NEWS

Details

biocViews Bioinformatics, Cancer, CopyNumberVariants, HighThroughputSequencing, Lung, Sequencing, Software
Depends R (>= 2.10.1), DNAcopy, methods
Imports methods
Suggests
System Requirements
License GPL-2
URL http://www.r-project.org,
Depends On Me
Imports Me
Suggests Me
Version 1.2.0
Since Bioconductor 2.9 (R-2.14)

Package Downloads

Package Source CNAnorm_1.2.0.tar.gz
Windows Binary CNAnorm_1.2.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary CNAnorm_1.2.0.tgz
Package Downloads Report Download Stats

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Fred Hutchinson Cancer Research Center