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Bioconductor - CNVrd2 (development version)

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 (3.22)

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")

# 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")
Details biocViews Clustering., CopyNumberVariation, Coverage, LinkageDisequilibrium, SNP, Sequencing, Software Version 1.47.0 In Bioconductor since BioC 2.13 (R-3.0) (11.5 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 See More 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.

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