CNVMetrics
This is the released version of CNVMetrics; for the devel version, see CNVMetrics.
Copy Number Variant Metrics
Bioconductor version: Release (3.23)
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>
citation("CNVMetrics")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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")| Copy number variant metrics | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BiologicalQuestion, CopyNumberVariation, Software |
| Version | 1.16.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (4.5 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, XVector |
| 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_1.16.0.tar.gz |
| Windows Binary (x86_64) | CNVMetrics_1.16.0.zip |
| macOS Binary (big-sur-x86_64) | CNVMetrics_1.16.0.tgz |
| macOS Binary (sonoma-arm64) | CNVMetrics_1.16.0.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 |