CNVrd2
This package is for version 3.11 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: 3.11
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("CNVrd2")
):
Installation
To install this package, start R (version "4.0") 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 | R Script | |
Reference Manual |
Details
biocViews | Clustering., CopyNumberVariation, Coverage, LinkageDisequilibrium, SNP, Sequencing, Software |
Version | 1.26.0 |
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 |
See More
Suggests | knitr |
Linking To | |
Enhances | |
Depends On Me | |
Imports Me | |
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Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | CNVrd2_1.26.0.tar.gz |
Windows Binary | CNVrd2_1.26.0.zip |
macOS 10.13 (High Sierra) | CNVrd2_1.26.0.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 |
Old Source Packages for BioC 3.11 | Source Archive |