To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

exomeCopy

Copy number variant detection from exome sequencing read depth

Bioconductor version: Release (2.14)

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>

Citation (from within R, enter citation("exomeCopy")):

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 CopyNumberVariation, Genetics, Sequencing, Software
Version 1.10.0
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 Rariant, SomaticCancerAlterations
Suggests Me

Package Archives

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

Package Source exomeCopy_1.10.0.tar.gz
Windows Binary exomeCopy_1.10.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) exomeCopy_1.10.0.tgz
Mac OS X 10.9 (Mavericks) exomeCopy_1.10.0.tgz
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