CNVrd2
This package is for version 3.7 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: 3.7
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 "3.5") 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 | R Script | |
| Reference Manual |
Details
| biocViews | Clustering., CopyNumberVariation, Coverage, LinkageDisequilibrium, SNP, Sequencing, Software |
| Version | 1.18.0 |
| 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 | |
| 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_1.18.0.tar.gz |
| Windows Binary | CNVrd2_1.18.0.zip |
| Mac OS X 10.11 (El Capitan) | CNVrd2_1.18.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/CNVrd2 |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CNVrd2 |
| Package Short Url | https://bioconductor.org/packages/CNVrd2/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.7 | Source Archive |