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

exomeCopy

Copy number variant detection from exome sequencing read depth

Bioconductor version: 2.13

Detection of copy number variants (CNV) from exome sequencing samples, including unpaired samples. The package implements a hidden Markov model which uses positional covariates, such as background read depth and GC-content, to simultaneously normalize and segment the samples into regions of constant copy count.

Author: Michael Love

Maintainer: Michael Love <michaelisaiahlove at gmail.com>

Installation

To install this package, start R and enter:

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("exomeCopy")

 

PDF	R Script	Copy number variant detection in exome sequencing data
PDF		Reference Manual
Text		NEWS

Details

biocViews	CopyNumberVariants, Genetics, HighThroughputSequencing, Sequencing, Software
Version	1.8.1
In Bioconductor since	BioC 2.9 (R-2.14)
License	GPL (>= 2)
Depends	IRanges, GenomicRanges, Rsamtools
Imports	stats4, methods
Suggests	Biostrings
System Requirements
URL
Depends On Me
Imports Me	SomaticCancerAlterations
Suggests Me

Package Archives

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

Package Source	exomeCopy_1.8.1.tar.gz
Windows Binary	exomeCopy_1.8.1.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	exomeCopy_1.8.1.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats