CNVrd2

DOI: 10.18129/B9.bioc.CNVrd2    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see CNVrd2.

CNVrd2: a read depth-based method to detect and genotype complex common copy number variants from next generation sequencing data.

Bioconductor version: 3.8

CNVrd2 uses next-generation sequencing data to measure human gene copy number for multiple samples, indentify SNPs tagging copy number variants and detect copy number polymorphic genomic regions.

Author: Hoang Tan Nguyen, Tony R Merriman and Mik Black

Maintainer: Hoang Tan Nguyen <hoangtannguyenvn at gmail.com>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("CNVrd2")

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("CNVrd2")

 

PDF	R Script	A Markdown Vignette with knitr
PDF		Reference Manual

Details

biocViews	Clustering., CopyNumberVariation, Coverage, LinkageDisequilibrium, SNP, Sequencing, Software
Version	1.20.0
In Bioconductor since	BioC 2.13 (R-3.0) (5.5 years)
License	GPL-2
Depends	R (>= 3.0.0), methods, VariantAnnotation, parallel, rjags, ggplot2, gridExtra
Imports	DNAcopy, IRanges, Rsamtools
LinkingTo
Suggests	knitr
SystemRequirements
Enhances
URL	https://github.com/hoangtn/CNVrd2
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	CNVrd2_1.20.0.tar.gz
Windows Binary	CNVrd2_1.20.0.zip
Mac OS X 10.11 (El Capitan)	CNVrd2_1.20.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/CNVrd2
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/CNVrd2
Package Short Url	http://bioconductor.org/packages/CNVrd2/
Package Downloads Report	Download Stats