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exomeCopy

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.18 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see exomeCopy.

Copy number variant detection from exome sequencing read depth


Bioconductor version: Release (3.18)

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 (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("exomeCopy")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("exomeCopy")
Copy number variant detection in exome sequencing data PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews CopyNumberVariation, Genetics, Sequencing, Software
Version 1.48.0
In Bioconductor since BioC 2.9 (R-2.14) (12.5 years)
License GPL (>= 2)
Depends R (>= 3.5.0), IRanges(>= 2.5.27), GenomicRanges(>= 1.23.16), Rsamtools
Imports stats4, methods, GenomeInfoDb
System Requirements
URL
See More
Suggests Biostrings
Linking To
Enhances
Depends On Me
Imports Me cn.mops, CNVPanelizer, contiBAIT
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package exomeCopy_1.48.0.tar.gz
Windows Binary exomeCopy_1.48.0.zip
macOS Binary (x86_64) exomeCopy_1.48.0.tgz
macOS Binary (arm64) exomeCopy_1.48.0.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/
Package Downloads Report Download Stats