https://github.com/krasnitzlab/cnvmetrics

R Package to compare copy number variant (CNV) results from multiple samples/methods
https://github.com/krasnitzlab/cnvmetrics

cnv copy-number-variation metrics package r r-language r-package

Last synced: 9 months ago
JSON representation

R Package to compare copy number variant (CNV) results from multiple samples/methods

• Host: GitHub
• URL: https://github.com/krasnitzlab/cnvmetrics
• Owner: KrasnitzLab
• Created: 2018-08-21T22:02:49.000Z (over 7 years ago)
• Default Branch: master
• Last Pushed: 2023-07-18T21:43:29.000Z (over 2 years ago)
• Last Synced: 2025-03-18T13:51:37.931Z (9 months ago)
• Topics: cnv, copy-number-variation, metrics, package, r, r-language, r-package
• Language: R
• Homepage: https://krasnitzlab.github.io/CNVMetrics/
• Size: 9.04 MB
• Stars: 4
• Watchers: 1
• Forks: 2
• Open Issues: 4
• Metadata Files:
  • Readme: README.md

Awesome Lists containing this project

README

          

[![R-CMD-check-bio](https://github.com/KrasnitzLab/CNVMetrics/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/KrasnitzLab/CNVMetrics/actions)

[![codecov](https://codecov.io/gh/KrasnitzLab/CNVMetrics/branch/master/graph/badge.svg)](https://codecov.io/gh/KrasnitzLab/CNVMetrics)

[![License: Artistic-2.0](https://img.shields.io/badge/License-Artistic%202.0-0298c3.svg)](https://opensource.org/licenses/Artistic-2.0)



 



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 CNVMetrics package: Quantifying similarity between copy number profiles [version 1; not peer reviewed].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 Deschênes](http://ca.linkedin.com/in/astriddeschenes "Astrid Deschênes"),

[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 ##

[![Bioconductor Time](https://bioconductor.org/shields/years-in-bioc/CNVMetrics.svg)](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!