exomeCopy

DOI: 10.18129/B9.bioc.exomeCopy    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see exomeCopy.

Copy number variant detection from exome sequencing read depth

Bioconductor version: 3.11

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>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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")

 

PDF	R Script	Copy number variant detection in exome sequencing data
PDF		Reference Manual
Text		NEWS

Details

biocViews	CopyNumberVariation, Genetics, Sequencing, Software
Version	1.34.0
In Bioconductor since	BioC 2.9 (R-2.14) (9 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
Links To Me
Build Report

Package Archives

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

Source Package	exomeCopy_1.34.0.tar.gz
Windows Binary	exomeCopy_1.34.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	exomeCopy_1.34.0.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