CNVMetrics

This is the development version of CNVMetrics; for the stable release version, see CNVMetrics.

Copy Number Variant Metrics

Bioconductor version: Development (3.21)

The CNVMetrics package calculates similarity metrics to facilitate copy number variant comparison among samples and/or methods. Similarity metrics can be employed to compare CNV profiles of genetically unrelated samples as well as those with a common genetic background. Some metrics are based on the shared amplified/deleted regions while other metrics rely on the level of amplification/deletion. The data type used as input is a plain text file containing the genomic position of the copy number variations, as well as the status and/or the log2 ratio values. Finally, a visualization tool is provided to explore resulting metrics.

Author: Astrid Deschênes [aut, cre] (ORCID: ), Pascal Belleau [aut] (ORCID: ), David A. Tuveson [aut] (ORCID: ), Alexander Krasnitz [aut]

Maintainer: Astrid Deschênes <adeschen at hotmail.com>

Citation (from within R, enter citation("CNVMetrics")):

Installation

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("CNVMetrics")

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("CNVMetrics")

Copy number variant metrics	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	BiologicalQuestion, CopyNumberVariation, Software
Version	1.11.0
In Bioconductor since	BioC 3.15 (R-4.2) (2.5 years)
License	Artistic-2.0
Depends	R (>= 4.0)
Imports	GenomicRanges, IRanges, S4Vectors, BiocParallel, methods, magrittr, stats, pheatmap, gridExtra, grDevices, rBeta2009
System Requirements
URL	https://github.com/krasnitzlab/CNVMetrics https://krasnitzlab.github.io/CNVMetrics/
Bug Reports	https://github.com/krasnitzlab/CNVMetrics/issues

Suggests	BiocStyle, knitr, rmarkdown, testthat
Linking To
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Build Report	Build Report

Package Archives

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

Source Package	CNVMetrics_1.11.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/CNVMetrics
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/CNVMetrics
Bioc Package Browser	https://code.bioconductor.org/browse/CNVMetrics/
Package Short Url	https://bioconductor.org/packages/CNVMetrics/
Package Downloads Report	Download Stats