To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("CNVrd2")
In most cases, you don't need to download the package archive at all.
CNVrd2
|
This package is for version 3.1 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: 3.1
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 and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("CNVrd2")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("CNVrd2")
| R Script | A Markdown Vignette with knitr | |
| Reference Manual |
Details
| biocViews | Clustering., CopyNumberVariation, Coverage, LinkageDisequilibrium, SNP, Sequencing, Software |
| Version | 1.6.0 |
| In Bioconductor since | BioC 2.13 (R-3.0) (2.5 years) |
| License | GPL-2 |
| Depends | R (>= 3.0.0), methods, VariantAnnotation, parallel, rjags, ggplot2, gridExtra |
| Imports | DNAcopy, IRanges, Rsamtools |
| LinkingTo | |
| Suggests | knitr |
| SystemRequirements | |
| Enhances | |
| URL | https://github.com/hoangtn/CNVrd2 |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | CNVrd2_1.6.0.tar.gz |
| Windows Binary | CNVrd2_1.6.0.zip |
| Mac OS X 10.6 (Snow Leopard) | CNVrd2_1.6.0.tgz |
| Mac OS X 10.9 (Mavericks) | CNVrd2_1.6.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/CNVrd2/tree/release-3.1 |
| Package Short Url | http://bioconductor.org/packages/CNVrd2/ |
| Package Downloads Report | Download Stats |
Documentation »
Bioconductor
- Package vignettes and manuals.
- Workflows for learning and use.
- Course and conference material.
- Videos.
- Community resources and tutorials.
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations:
- Support site - for questions about Bioconductor packages
- Bioc-devel mailing list - for package developers
