CNVrd2

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

Bioconductor version: Release (2.14)

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 MA Black

Maintainer: Hoang Tan Nguyen <hoangtannguyenvn at gmail.com>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("CNVrd2")

To cite this package in a publication, start R and enter:

    citation("CNVrd2")

Documentation

PDF R Script A Markdown Vignette with knitr
PDF   Reference Manual

Details

biocViews CNV, High Throughput Sequencing, SNP., Software
Version 1.2.0
In Bioconductor since BioC 2.13 (R-3.0)
License GPL-2
Depends R (>= 3.0.0), DNAcopy, methods, Rsamtools, VariantAnnotation, parallel, rjags, ggplot2, gridExtra
Imports IRanges
Suggests knitr
System Requirements
URL https://github.com/hoangtn/CNVrd2
Depends On Me
Imports Me
Suggests Me

Package Downloads

Package Source CNVrd2_1.2.0.tar.gz
Windows Binary CNVrd2_1.2.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) CNVrd2_1.2.0.tgz
Mac OS X 10.9 (Mavericks)
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