CNVrd2
This is the released version of CNVrd2; for the devel 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: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.50.0 |
| In Bioconductor since | BioC 2.13 (R-3.0) (13 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_1.50.0.tar.gz |
| Windows Binary (x86_64) | CNVrd2_1.50.0.zip |
| macOS Binary (big-sur-x86_64) | CNVrd2_1.50.0.tgz |
| macOS Binary (sonoma-arm64) | CNVrd2_1.50.0.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 |