exomeCopy

CNV detection from exome sequencing read depth

Bioconductor version: 2.10

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 <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
Text   NEWS

Details

biocViews CopyNumberVariants, Genetics, HighThroughputSequencing, Sequencing, Software
Depends IRanges, GenomicRanges, Rsamtools
Imports stats4, methods
Suggests Biostrings
System Requirements
License GPL (>= 2)
URL
Depends On Me
Imports Me
Suggests Me
Version 1.2.0
Since Bioconductor 2.9 (R-2.14)

Package Downloads

Package Source exomeCopy_1.2.0.tar.gz
Windows Binary exomeCopy_1.2.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary exomeCopy_1.2.0.tgz
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