{"id":26675329,"url":"https://github.com/krasnitzlab/raids","last_synced_at":"2025-04-12T08:11:09.045Z","repository":{"id":50547963,"uuid":"478687408","full_name":"KrasnitzLab/RAIDS","owner":"KrasnitzLab","description":"Accurate and robust inference of genetic ancestry from cancer-derived molecular data across genomic platforms","archived":false,"fork":false,"pushed_at":"2025-04-10T00:15:46.000Z","size":8523,"stargazers_count":5,"open_issues_count":0,"forks_count":4,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-04-10T00:28:17.792Z","etag":null,"topics":["ancestry","cancer-genomics","exome-sequencing","genomics","inference","r-language","r-package","rna-seq","rna-sequencing","whole-genome-sequencing"],"latest_commit_sha":null,"homepage":"https://krasnitzlab.github.io/RAIDS/","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","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":"LICENSE.md","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2022-04-06T18:47:59.000Z","updated_at":"2025-04-09T23:58:24.000Z","dependencies_parsed_at":"2024-08-17T02:41:24.798Z","dependency_job_id":"64e091f4-e21b-4871-9d7d-5ba35022ba64","html_url":"https://github.com/KrasnitzLab/RAIDS","commit_stats":null,"previous_names":[],"tags_count":9,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KrasnitzLab%2FRAIDS","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KrasnitzLab%2FRAIDS/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KrasnitzLab%2FRAIDS/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KrasnitzLab%2FRAIDS/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/KrasnitzLab","download_url":"https://codeload.github.com/KrasnitzLab/RAIDS/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248537131,"owners_count":21120710,"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":["ancestry","cancer-genomics","exome-sequencing","genomics","inference","r-language","r-package","rna-seq","rna-sequencing","whole-genome-sequencing"],"created_at":"2025-03-26T03:17:41.835Z","updated_at":"2025-04-12T08:11:09.036Z","avatar_url":"https://github.com/KrasnitzLab.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003c!-- badges: start --\u003e\n[![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)\n[![codecov](https://codecov.io/gh/krasnitzlab/RAIDS/branch/main/graph/badge.svg?token=LPFLOMUDVT)](https://codecov.io/gh/krasnitzlab/RAIDS)\n[![R-CMD-check-bioc](https://github.com/krasnitzlab/RAIDS/actions/workflows/check-bioc.yaml/badge.svg)](https://github.com/krasnitzlab/RAIDS/actions/workflows/check-bioc.yaml)\n\u003c!-- badges: end --\u003e\n\n\n# Robust genetic ancestry inference from challenging molecular data with **RAIDS** #\n\nThe Robust Ancestry Inference using Data Synthesis (**RAIDS**) package \nenables accurate and robust inference of genetic \nancestry from various types of molecular data, including whole-genome, \nwhole-exome, targeted gene panels and RNA sequences, as described in our \nmanuscript. Our tools retain high accuracy in presence of somatic \nalterations, such as those caused by cancer.\n\n**This code and analysis pipeline were designed and developed for the following publication:**\n\n\u003e  Pascal Belleau, Astrid Deschênes, Nyasha Chambwe, David A. Tuveson, Alexander Krasnitz; Genetic Ancestry Inference from Cancer-Derived Molecular Data across Genomic and Transcriptomic Platforms. Cancer Res 1 January 2023; 83 (1): 49–58. https://doi.org/10.1158/0008-5472.CAN-22-0682\n\n\n## Authors ##\n\n[Pascal Belleau](http://ca.linkedin.com/in/pascalbelleau \"Pascal Belleau\"),\n[Astrid Desch\u0026ecirc;nes](https://www.linkedin.com/in/astriddeschenes \"Astrid Desch\u0026ecirc;nes\"),\n[David A. Tuveson](https://tuvesonlab.labsites.cshl.edu/) and\n[Alexander Krasnitz](https://www.cshl.edu/research/faculty-staff/alexander-krasnitz/ \"Alexander Krasnitz\")\n\n\n## Citing ##\n\nIf you use the **RAIDS** package for a publication, we would ask you to cite \nthe following:\n\n\u003e  Pascal Belleau, Astrid Deschênes, Nyasha Chambwe, David A. Tuveson, Alexander Krasnitz; Genetic Ancestry Inference from Cancer-Derived Molecular Data across Genomic and Transcriptomic Platforms. Cancer Res 1 January 2023; 83 (1): 49–58. https://doi.org/10.1158/0008-5472.CAN-22-0682\n\n\n## Bioconductor Package ##\n\n[![Bioconductor Time](https://bioconductor.org/shields/years-in-bioc/RAIDS.svg)](https://bioconductor.org/packages/RAIDS)\n\nThe **RAIDS** package is now an official package \nof [Bioconductor](http://bioconductor.org/). \n\nThe current Bioconductor release can be directly downloaded from their website:\n[Current release](https://bioconductor.org/packages/RAIDS)\n\n\n## Installation ##\n\nTo install this package \nfrom [Bioconductor](https://bioconductor.org/packages/RAIDS), start R \n(version \"4.3\" or later) and enter: \n\n    if (!requireNamespace(\"BiocManager\", quietly = TRUE))\n        install.packages(\"BiocManager\")\n\n    BiocManager::install(\"RAIDS\")\n    \n\nTo install the latest version accessible from Github, \nthe [devtools](https://cran.r-project.org/web/packages/devtools/index.html) \npackage is required.\n\n     ## Load required package\n     library(devtools)\n\n     ## Install the latest version of RAIDS\n     devtools::install_github('KrasnitzLab/RAIDS')\n\n\n## Documentation ##\n\n[RAIDS Website](https://krasnitzlab.github.io/RAIDS/)\n\n[RAIDS Get Started](https://krasnitzlab.github.io/RAIDS/articles/RAIDS.html)\n\n\n## License ##\n\nThis package and the underlying **RAIDS** code are distributed under \nthe Apache-2.0 license. You are free to use and redistribute this software. \n\nFor more information on Apache-2.0 License see\n[https://opensource.org/licenses/Apache-2.0](https://opensource.org/licenses/Apache-2.0)\n\n\n\n## Maintainer\n\n[Pascal Belleau](https://github.com/belleau/ \"Pascal Belleau\")\n\n\n## Bugs/Feature requests ##\n\n[Please contact us](https://github.com/KrasnitzLab/RAIDS/issues) for bug fixes or with feature requests. \n\nThanks!\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkrasnitzlab%2Fraids","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fkrasnitzlab%2Fraids","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkrasnitzlab%2Fraids/lists"}