CNVMetrics
This is the development version of CNVMetrics; for the stable release version, see CNVMetrics.
Copy Number Variant Metrics
Bioconductor version: Development (3.20)
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("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 | ||
NEWS | Text |
Details
biocViews | BiologicalQuestion, CopyNumberVariation, Software |
Version | 1.9.0 |
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 |
See More
Suggests | BiocStyle, knitr, rmarkdown, testthat |
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 | CNVMetrics_1.9.0.tar.gz |
Windows Binary | CNVMetrics_1.9.0.zip |
macOS Binary (x86_64) | CNVMetrics_1.9.0.tgz |
macOS Binary (arm64) | CNVMetrics_1.9.0.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 |