DOI: 10.18129/B9.bioc.exomeCopy    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see exomeCopy.

Copy number variant detection from exome sequencing read depth

Bioconductor version: 3.12

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")):


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PDF R Script Copy number variant detection in exome sequencing data
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biocViews CopyNumberVariation, Genetics, Sequencing, Software
Version 1.36.0
In Bioconductor since BioC 2.9 (R-2.14) (9.5 years)
License GPL (>= 2)
Depends IRanges(>= 2.5.27), GenomicRanges(>= 1.23.16), Rsamtools
Imports stats4, methods, GenomeInfoDb
Suggests Biostrings
Depends On Me
Imports Me cn.mops, CNVPanelizer, contiBAIT, Rariant, SomaticCancerAlterations
Suggests Me
Links To Me
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Source Package exomeCopy_1.36.0.tar.gz
Windows Binary exomeCopy_1.36.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra) exomeCopy_1.36.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/exomeCopy
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/exomeCopy
Package Short Url https://bioconductor.org/packages/exomeCopy/
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