exomeCopy

Detection of CNV in exome/targeted sequencing data

Bioconductor version: 2.9

A hidden Markov model for the detection of copy number variants (CNV) in exome/targeted sequencing read depth data. The package 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 <love at molgen.mpg.de>

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	CNV detection in exome sequencing data
PDF		Reference Manual

Details

biocViews	CopyNumberVariants, Sequencing, HighThroughputSequencing, Genetics
Depends	methods, graphics, IRanges, GenomicRanges, Rsamtools(>= 1.4.3)
Imports
Suggests	Biostrings
System Requirements
License	GPL (>= 2)
URL
Depends On Me
Imports Me
Suggests Me
Version	1.0.3
Since	Bioconductor 2.9 (R-2.14)

Package Downloads

Package Source	exomeCopy_1.0.3.tar.gz
Windows Binary	exomeCopy_1.0.3.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	exomeCopy_1.0.3.tgz
Package Downloads Report	Download Stats

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