exomeCopy

Copy number variant detection from exome sequencing read depth

Bioconductor version: Development (3.0)

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>

To install this package, start R and enter:

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

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

    citation("exomeCopy")

Documentation

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

Details

biocViews CopyNumberVariation, Genetics, Sequencing, Software
Version 1.11.0
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 Downloads

Package Source exomeCopy_1.11.0.tar.gz
Windows Binary exomeCopy_1.11.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) exomeCopy_1.11.0.tgz
Mac OS X 10.9 (Mavericks)
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