exomeCopy
This package is for version 3.9 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: 3.9
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("exomeCopy")):
Installation
To install this package, start R (version "3.6") 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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | CopyNumberVariation, Genetics, Sequencing, Software |
| Version | 1.30.0 |
| In Bioconductor since | BioC 2.9 (R-2.14) (12.5 years) |
| License | GPL (>= 2) |
| Depends | 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, Rariant, SomaticCancerAlterations |
| 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_1.30.0.tar.gz |
| Windows Binary | exomeCopy_1.30.0.zip |
| Mac OS X 10.11 (El Capitan) | exomeCopy_1.30.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/exomeCopy |
| Source Repository (Developer Access) | git clone [email protected]:packages/exomeCopy |
| Bioc Package Browser | https://code.bioconductor.org/browse/exomeCopy/ |
| Package Short Url | https://bioconductor.org/packages/exomeCopy/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |