<!-- badges: start --> [](https://github.com/KrasnitzLab/CNVMetrics/actions) [](https://codecov.io/gh/KrasnitzLab/CNVMetrics) [](https://opensource.org/licenses/Artistic-2.0) <!-- badges: end --> <p align="center"> <img src="man/figures/CNVMetrics_text.jpg" alt="CNVMetrics"> <img src="man/figures/CNVMetrics.png" align="right" alt="" width="120" /> </p> The **_CNVMetrics_** package offers multiple quantitative metrics of similarity between copy number profiles. Among these are metrics based on CNV status calls only (amplification/deletion status) or on the level of amplification/deletion. In addition, a visualization tool is provided to explore resulting metrics. ## Citing ## If you use this package for a publication, we would ask you to cite the following: >Belleau P, Deschênes A, Beyaz S et al. CNVMetrics package: Quantifying similarity between copy number profiles [version 1; not peer reviewed]. F1000Research 2021, 10:737 (slides) (doi: 10.7490/f1000research.1118704.1) [F1000Research poster](http://www.doi.org/10.7490/f1000research.1118704.1) ## Authors ## [Astrid Desch&ecirc;nes](http://ca.linkedin.com/in/astriddeschenes "Astrid Desch&ecirc;nes"), [Pascal Belleau](http://ca.linkedin.com/in/pascalbelleau "Pascal Belleau"), [David A. Tuveson](http://tuvesonlab.labsites.cshl.edu/ "David A. Tuveson") and [Alexander Krasnitz](https://www.cshl.edu/research/faculty-staff/alexander-krasnitz/ "Alexander Krasnitz") ## Bioconductor Package ## [](https://bioconductor.org/packages/CNVMetrics) The **_CNVMetrics_** package is now an official package of [Bioconductor](http://bioconductor.org/). The current release can be directly downloaded from their website: [Current release](https://bioconductor.org/packages/CNVMetrics) However, all official releases can be downloaded from this site: [All releases](https://github.com/KrasnitzLab/CNVMetrics/releases) ## Documentation ## [CNVMetrics Website](https://krasnitzlab.github.io/CNVMetrics/) [CNVMetrics Get Started](https://krasnitzlab.github.io/CNVMetrics/articles/CNVMetrics.html) ## Installation ## To install this package from [Bioconductor](https://bioconductor.org/packages/CNVMetrics), start R (version "4.2") and enter: if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") # The following initializes usage of Bioc devel BiocManager::install(version='devel') BiocManager::install("CNVMetrics") To install the latest version accessible using the [devtools](https://cran.r-project.org/web/packages/devtools/index.html) package: ## Load required package library(devtools) ## Install the latest version of CNVMetrics devtools::install_github('KrasnitzLab/CNVMetrics') ## License ## This package and the underlying **_CNVMetrics_** code are distributed under the Artistic license 2.0. You are free to use and redistribute this software. For more information on Artistic 2.0 License see [http://opensource.org/licenses/Artistic-2.0](http://opensource.org/licenses/Artistic-2.0) ## Bugs/Feature requests ## [Please contact us](https://github.com/KrasnitzLab/CNVMetrics/issues) for bug fixes or with feature requests. Thanks!