To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("CNVrd2")
In most cases, you don't need to download the package archive at all.
CNVrd2
CNVrd2: a read depth-based method to detect and genotype complex common copy number variants from next generation sequencing data.
Bioconductor version: 3.0
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:
source("http://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 | 1.4.0 |
| In Bioconductor since | BioC 2.13 (R-3.0) |
| 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_1.4.0.tar.gz |
| Windows Binary | CNVrd2_1.4.0.zip |
| Mac OS X 10.6 (Snow Leopard) | CNVrd2_1.4.0.tgz |
| Mac OS X 10.9 (Mavericks) | CNVrd2_1.4.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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