{"id":26447292,"url":"https://github.com/krasnitzlab/cnvmetrics","last_synced_at":"2025-03-18T13:51:39.297Z","repository":{"id":44695951,"uuid":"145624069","full_name":"KrasnitzLab/CNVMetrics","owner":"KrasnitzLab","description":"R Package to compare copy number variant (CNV) results from multiple samples/methods","archived":false,"fork":false,"pushed_at":"2023-07-18T21:43:29.000Z","size":9477,"stargazers_count":4,"open_issues_count":4,"forks_count":2,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-03-18T13:51:37.931Z","etag":null,"topics":["cnv","copy-number-variation","metrics","package","r","r-language","r-package"],"latest_commit_sha":null,"homepage":"https://krasnitzlab.github.io/CNVMetrics/","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/KrasnitzLab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2018-08-21T22:02:49.000Z","updated_at":"2024-06-07T08:41:06.000Z","dependencies_parsed_at":"2022-09-23T04:41:23.815Z","dependency_job_id":"5dc51732-c82d-4017-98e8-767ceb0e9dfe","html_url":"https://github.com/KrasnitzLab/CNVMetrics","commit_stats":null,"previous_names":[],"tags_count":6,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KrasnitzLab%2FCNVMetrics","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KrasnitzLab%2FCNVMetrics/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KrasnitzLab%2FCNVMetrics/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KrasnitzLab%2FCNVMetrics/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/KrasnitzLab","download_url":"https://codeload.github.com/KrasnitzLab/CNVMetrics/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":244236106,"owners_count":20420752,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["cnv","copy-number-variation","metrics","package","r","r-language","r-package"],"created_at":"2025-03-18T13:51:38.336Z","updated_at":"2025-03-18T13:51:39.289Z","avatar_url":"https://github.com/KrasnitzLab.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003c!-- badges: start --\u003e\n[![R-CMD-check-bio](https://github.com/KrasnitzLab/CNVMetrics/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/KrasnitzLab/CNVMetrics/actions)\n[![codecov](https://codecov.io/gh/KrasnitzLab/CNVMetrics/branch/master/graph/badge.svg)](https://codecov.io/gh/KrasnitzLab/CNVMetrics)\n[![License: Artistic-2.0](https://img.shields.io/badge/License-Artistic%202.0-0298c3.svg)](https://opensource.org/licenses/Artistic-2.0)\n\n\n\u003c!-- badges: end --\u003e\n\n\u003cp align=\"center\"\u003e\n\u003cimg src=\"man/figures/CNVMetrics_text.jpg\" alt=\"CNVMetrics\"\u003e \u003cimg src=\"man/figures/CNVMetrics.png\" align=\"right\" alt=\"\" width=\"120\" /\u003e\n\u003c/p\u003e\n\nThe **_CNVMetrics_** package offers multiple quantitative metrics of similarity between copy number profiles.\nAmong 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.\n\n\n## Citing ## \n\nIf you use this package for a publication, we would ask you to cite the following:\n\n\u003eBelleau 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)\n\n[F1000Research poster](http://www.doi.org/10.7490/f1000research.1118704.1)\n\n\n## Authors ##\n\n[Astrid Desch\u0026ecirc;nes](http://ca.linkedin.com/in/astriddeschenes \"Astrid Desch\u0026ecirc;nes\"),\n[Pascal Belleau](http://ca.linkedin.com/in/pascalbelleau \"Pascal Belleau\"),\n[David A. Tuveson](http://tuvesonlab.labsites.cshl.edu/ \"David A. Tuveson\") and \n[Alexander Krasnitz](https://www.cshl.edu/research/faculty-staff/alexander-krasnitz/ \"Alexander Krasnitz\")\n\n\n## Bioconductor Package ##\n\n[![Bioconductor Time](https://bioconductor.org/shields/years-in-bioc/CNVMetrics.svg)](https://bioconductor.org/packages/CNVMetrics)\n\nThe **_CNVMetrics_** package is now an official package of [Bioconductor](http://bioconductor.org/). \n\nThe current release can be directly downloaded from their website:\n[Current release](https://bioconductor.org/packages/CNVMetrics)\n\nHowever, all official releases can be downloaded from this site:\n[All releases](https://github.com/KrasnitzLab/CNVMetrics/releases)\n\n\n## Documentation ##\n\n[CNVMetrics Website](https://krasnitzlab.github.io/CNVMetrics/)\n\n[CNVMetrics Get Started](https://krasnitzlab.github.io/CNVMetrics/articles/CNVMetrics.html)\n\n\n## Installation ##\n\n\nTo install this package from [Bioconductor](https://bioconductor.org/packages/CNVMetrics), start R (version \"4.2\") and enter: \n\n    if (!requireNamespace(\"BiocManager\", quietly = TRUE))\n        install.packages(\"BiocManager\")\n\n    # The following initializes usage of Bioc devel\n    BiocManager::install(version='devel')\n\n    BiocManager::install(\"CNVMetrics\")\n\n\nTo install the latest version accessible using the [devtools](https://cran.r-project.org/web/packages/devtools/index.html) \npackage:\n\n     ## Load required package\n     library(devtools)\n\n     ## Install the latest version of CNVMetrics\n     devtools::install_github('KrasnitzLab/CNVMetrics')\n\n\n## License ##\n\nThis package and the underlying **_CNVMetrics_** code are distributed under \nthe Artistic license 2.0. You are free to use and redistribute this software. \n\nFor more information on Artistic 2.0 License see\n[http://opensource.org/licenses/Artistic-2.0](http://opensource.org/licenses/Artistic-2.0)\n\n\n## Bugs/Feature requests ##\n\n[Please contact us](https://github.com/KrasnitzLab/CNVMetrics/issues) for bug fixes or with feature requests.\n\nThanks!\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkrasnitzlab%2Fcnvmetrics","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fkrasnitzlab%2Fcnvmetrics","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkrasnitzlab%2Fcnvmetrics/lists"}