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CNVMetrics

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

Copy Number Variant Metrics


Bioconductor version: Development (3.19)

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 DeschĂȘnes [aut, cre] , Pascal Belleau [aut] , David A. Tuveson [aut] , Alexander Krasnitz [aut]

Maintainer: Astrid DeschĂȘnes <adeschen at hotmail.com>

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

Installation

To install this package, start R (version "4.4") 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

Details

biocViews BiologicalQuestion, CopyNumberVariation, Software
Version 1.7.0
In Bioconductor since BioC 3.15 (R-4.2) (2 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
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Suggests BiocStyle, knitr, rmarkdown, testthat
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Package Archives

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

Source Package CNVMetrics_1.7.0.tar.gz
Windows Binary CNVMetrics_1.7.0.zip
macOS Binary (x86_64) CNVMetrics_1.7.0.tgz
macOS Binary (arm64) CNVMetrics_1.7.0.tgz
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