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:
Maintainer: Astrid Deschênes <adeschen at hotmail.com>
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 | ||
| NEWS | Text |
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 |
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_1.11.0.tar.gz |
| Windows Binary (x86_64) | CNVMetrics_1.11.0.zip |
| macOS Binary (x86_64) | CNVMetrics_1.11.0.tgz |
| 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 |