To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("exomeCopy")

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

exomeCopy

DOI: 10.18129/B9.bioc.exomeCopy

Copy number variant detection from exome sequencing read depth

Bioconductor version: Release (3.5)

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:

## try http:// if https:// URLs are not supported
source("https://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 1.22.0
In Bioconductor since BioC 2.9 (R-2.14) (6 years)
License GPL (>= 2)
Depends IRanges(>= 2.5.27), GenomicRanges(>= 1.23.16), Rsamtools
Imports stats4, methods, GenomeInfoDb
LinkingTo
Suggests Biostrings
SystemRequirements
Enhances
URL
Depends On Me
Imports Me cn.mops, CNVPanelizer, contiBAIT, Rariant, SomaticCancerAlterations
Suggests Me
Build Report

Package Archives

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

Source Package exomeCopy_1.22.0.tar.gz
Windows Binary exomeCopy_1.22.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) exomeCopy_1.22.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/exomeCopy
Package Short Url http://bioconductor.org/packages/exomeCopy/
Package Downloads Report Download Stats

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