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CNVrd2

This is the development version of CNVrd2; for the stable 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: Development (3.19)

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 (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
A Markdown Vignette with knitr PDF R Script
Reference Manual PDF

Details

biocViews Clustering., CopyNumberVariation, Coverage, LinkageDisequilibrium, SNP, Sequencing, Software
Version 1.41.0
In Bioconductor since BioC 2.13 (R-3.0) (10.5 years)
License GPL-2
Depends R (>= 3.0.0), methods, VariantAnnotation, parallel, rjags, ggplot2, gridExtra
Imports DNAcopy, IRanges, Rsamtools
System Requirements
URL https://github.com/hoangtn/CNVrd2
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Package Archives

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

Source Package CNVrd2_1.41.0.tar.gz
Windows Binary CNVrd2_1.41.0.zip
macOS Binary (x86_64) CNVrd2_1.41.0.tgz
macOS Binary (arm64) CNVrd2_1.41.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/CNVrd2
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CNVrd2
Bioc Package Browser https://code.bioconductor.org/browse/CNVrd2/
Package Short Url https://bioconductor.org/packages/CNVrd2/
Package Downloads Report Download Stats