CNVrd2

This is the released version of CNVrd2; for the devel version, see CNVrd2.

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

Platform availability badge Ranking badge Support activity badge Years in BioConductor badge Build results badge Last commit badge Dependency count badge

DOI: 10.18129/B9.bioc.CNVrd2

Bioconductor version: Release (3.22)

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 "4.5") and enter:


if (!require("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")

A Markdown Vignette with knitr PDF R Script

Reference Manual PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Clustering., CopyNumberVariation, Coverage, LinkageDisequilibrium, SNP, Sequencing, Software

Version 1.48.0

In Bioconductor since BioC 2.13 (R-3.0) (12 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

Suggests knitr

Linking To

Enhances

Depends On Me

Imports Me

Suggests Me

Links To Me

Build Report Build Report

Package Archives

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

Source Package CNVrd2_1.48.0.tar.gz

Windows Binary (x86_64) CNVrd2_1.48.0.zip

macOS Binary (x86_64) CNVrd2_1.48.0.tgz

macOS Binary (arm64) CNVrd2_1.48.0.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