CNViz

DOI: 10.18129/B9.bioc.CNViz  

Copy Number Visualization

Bioconductor version: Release (3.16)

CNViz takes probe, gene, and segment-level log2 copy number ratios and launches a Shiny app to visualize your sample's copy number profile. You can also integrate loss of heterozygosity (LOH) and single nucleotide variant (SNV) data.

Author: Rebecca Greenblatt [aut, cre]

Maintainer: Rebecca Greenblatt <rebecca.greenblatt at gmail.com>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("CNViz")

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("CNViz")

 

HTML	R Script	CNViz
PDF		Reference Manual
Text		NEWS

Details

biocViews	CopyNumberVariation, DNASeq, Sequencing, Software, Visualization
Version	1.6.0
In Bioconductor since	BioC 3.13 (R-4.1) (2 years)
License	Artistic-2.0
Depends	R (>= 4.0), shiny (>= 1.5.0)
Imports	dplyr, stats, utils, grDevices, plotly, karyoploteR, CopyNumberPlots, GenomicRanges, magrittr, DT, scales, graphics
LinkingTo
Suggests	rmarkdown, knitr
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	CNViz_1.6.0.tar.gz
Windows Binary	CNViz_1.6.0.zip
macOS Binary (x86_64)	CNViz_1.6.0.tgz
macOS Binary (arm64)	CNViz_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/CNViz
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/CNViz
Bioc Package Browser	https://code.bioconductor.org/browse/CNViz/
Package Short Url	https://bioconductor.org/packages/CNViz/
Package Downloads Report	Download Stats