CNVMetrics

DOI: 10.18129/B9.bioc.CNVMetrics  

Copy Number Variant Metrics

Bioconductor version: Release (3.16)

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

Maintainer: Astrid Deschênes <adeschen at hotmail.com>

Installation

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

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

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")

 

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

Details

biocViews	BiologicalQuestion, CopyNumberVariation, Software
Version	1.2.0
In Bioconductor since	BioC 3.15 (R-4.2) (1 year)
License	Artistic-2.0
Depends	R (>= 4.1)
Imports	GenomicRanges, IRanges, S4Vectors, BiocParallel, methods, magrittr, stats, pheatmap, gridExtra, grDevices
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, testthat
SystemRequirements
Enhances
URL	https://github.com/krasnitzlab/CNVMetrics https://krasnitzlab.github.io/CNVMetrics/
BugReports	https://github.com/krasnitzlab/CNVMetrics/issues
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	CNVMetrics_1.2.0.tar.gz
Windows Binary	CNVMetrics_1.2.0.zip
macOS Binary (x86_64)	CNVMetrics_1.2.0.tgz
macOS Binary (arm64)	CNVMetrics_1.2.0.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