To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("CNVrd2")

In most cases, you don't need to download the package archive at all.

CNVrd2

This package is for version 3.0 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: 3.0

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>

Citation (from within R, enter citation("CNVrd2")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("CNVrd2")

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 1.4.0
In Bioconductor since BioC 2.13 (R-3.0) (2.5 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
Build Report

Package Archives

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

Package Source CNVrd2_1.4.0.tar.gz
Windows Binary CNVrd2_1.4.0.zip
Mac OS X 10.6 (Snow Leopard) CNVrd2_1.4.0.tgz
Mac OS X 10.9 (Mavericks) CNVrd2_1.4.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/CNVrd2/tree/release-3.0
Package Short Url http://bioconductor.org/packages/CNVrd2/
Package Downloads Report Download Stats

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