{"id":14235521,"url":"https://github.com/thierrygosselin/radiator","last_synced_at":"2025-08-11T00:31:50.165Z","repository":{"id":38420062,"uuid":"94663323","full_name":"thierrygosselin/radiator","owner":"thierrygosselin","description":"RADseq Data Exploration, Manipulation and Visualization using R","archived":false,"fork":false,"pushed_at":"2024-11-06T16:57:51.000Z","size":10439,"stargazers_count":59,"open_issues_count":5,"forks_count":23,"subscribers_count":13,"default_branch":"master","last_synced_at":"2024-11-06T17:48:54.710Z","etag":null,"topics":["artifacts-detection","batch-effects","filter","gbs","genetics","genomic-data-analysis","genomics","genomics-visualization","genotype-likelihoods","genotyping-by-sequencing","heterozygosity","imputation","missingness","normalization","outliers","outliers-detection","paralogs","radseq","radseq-data","visualization"],"latest_commit_sha":null,"homepage":"https://thierrygosselin.github.io/radiator/","language":"HTML","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/thierrygosselin.png","metadata":{"files":{"readme":"README.Rmd","changelog":"NEWS.md","contributing":"docs/contributing.md","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":"2017-06-18T03:45:14.000Z","updated_at":"2024-11-06T16:57:56.000Z","dependencies_parsed_at":"2023-01-21T13:02:30.389Z","dependency_job_id":"20c57eb2-760d-4720-96a6-129abe9d42a2","html_url":"https://github.com/thierrygosselin/radiator","commit_stats":null,"previous_names":[],"tags_count":11,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/thierrygosselin%2Fradiator","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/thierrygosselin%2Fradiator/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/thierrygosselin%2Fradiator/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/thierrygosselin%2Fradiator/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/thierrygosselin","download_url":"https://codeload.github.com/thierrygosselin/radiator/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":229478668,"owners_count":18079371,"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":["artifacts-detection","batch-effects","filter","gbs","genetics","genomic-data-analysis","genomics","genomics-visualization","genotype-likelihoods","genotyping-by-sequencing","heterozygosity","imputation","missingness","normalization","outliers","outliers-detection","paralogs","radseq","radseq-data","visualization"],"created_at":"2024-08-20T21:02:02.026Z","updated_at":"2025-08-11T00:31:50.129Z","avatar_url":"https://github.com/thierrygosselin.png","language":"HTML","funding_links":[],"categories":["R"],"sub_categories":[],"readme":"---\noutput: github_document\n---\n\n\n# radr \u003ca href='http://thierrygosselin.github.io/radr/'\u003e\u003cimg src='man/figures/logo.png' align=\"right\" height=\"160\" /\u003e\u003c/a\u003e\n\n\n```{r, echo = FALSE}\ndescription \u003c- readLines(\"DESCRIPTION\")\nrvers \u003c- stringr::str_match(grep(\"R \\\\(\", description, value = TRUE), \"[0-9]{1,4}\\\\.[0-9]{1,4}\\\\.[0-9]{1,4}\")[1,1]\nversion \u003c- gsub(\" \", \"\", gsub(\"Version:\", \"\", grep(\"Version:\", description, value = TRUE)))\n```\n\n\u003c!-- badges: start --\u003e\n[![lifecycle](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://tidyverse.org/lifecycle/#maturing)\n[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)\n[![packageversion](https://img.shields.io/badge/Package%20version-`r version`-orange.svg)](commits/master)\n[![Last-changedate](https://img.shields.io/badge/last%20change-`r gsub('-', '--', Sys.Date())`-brightgreen.svg)](/commits/master)\n[![R-CMD-check](https://github.com/thierrygosselin/radiator/workflows/R-CMD-check/badge.svg)](https://github.com/thierrygosselin/radiator/actions)\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3687060.svg)](https://doi.org/10.5281/zenodo.3687060)\n\u003c!-- badges: end --\u003e\n\n```{r, echo = FALSE}\nknitr::opts_chunk$set(\n  collapse = TRUE,\n  comment = \"#\u003e\",\n  fig.path = \"README-\"\n)\n```\n# radiator: an R package for RADseq Data Exploration, Manipulation and Visualization\n\nMost genomic analysis look for patterns and trends with various statistics. \nBias, noise and outliers can have bounded influence on estimators and interfere\nwith polymorphism discovery. Avoid bad data exploration and control the impact\nof filters on your downstream genetic analysis. Use radiator to: import, explore,\nmanipulate, visualize, filter, impute and export your GBS/RADseq data.\n\n**radiator** is designed and optimized for fast computations of diploid data \nusing Genomic Data Structure [GDS](https://github.com/zhengxwen/gdsfmt) file \nformat and data science packages in \n[tidyverse](https://www.tidyverse.org). **radiator** handles VCF files with millions of\nSNPs and files of several GB.\n\n## Installation\nTo try out the dev version of **radiator**, copy/paste the code below:\n\n```{r eval = FALSE}\nif (!require(\"devtools\")) install.packages(\"devtools\")\ndevtools::install_github(\"thierrygosselin/radiator\")\nlibrary(radiator)\n```\n\n**Note** \n\nSome Windows OS and Linux OS recently experienced some problems during installations,\nlinked to CRAN \u0026 Bioconductor tango problems:\n\n- If you're experiencing problems with radiator installation see \n[troubleshooting section](https://thierrygosselin.github.io/radiator/articles/rad_genomics_computer_setup.html)\nand try the lines below.\n\n- Verify that installing **radiator** also installed the \n[Bioconductor](https://www.bioconductor.org/packages/release/bioc/html/SeqArray.html) \npackages: `gdsfmt` and \n[SeqArray](https://github.com/zhengxwen/SeqArray) with version \u003e= 1.28.1.\n\n```{r eval = FALSE}\ndevtools::package_info(pkgs = \"SeqArray\") # to verify version\n\n# If manually installing SeqArray is necessary\ninstall.packages(\"BiocManager\")\nBiocManager::install(\"SeqArray\")\n```\n\n\nWeb site with additional info: [https://thierrygosselin.github.io/radiator/](https://thierrygosselin.github.io/radiator/)\n\n* [Computer setup and troubleshooting](https://thierrygosselin.github.io/radiator/articles/rad_genomics_computer_setup.html)\n* [Learning radiator](https://thierrygosselin.github.io/radiator/articles/get_started.html) and [Overview of features](https://thierrygosselin.github.io/radiator/articles/get_started.html#overview)\n* [Vignettes](https://thierrygosselin.github.io/radiator/articles/index.html)\n\n## [Life cycle](https://thierrygosselin.github.io/radiator/articles/life_cycle.html)\n\nradiator is maturing, but in order to make the package better, changes are \ninevitable. Experimental functions will change, argument names will change.\nYour codes and workflows might break from time to time until radiator is stable. \nConsequently, depending on your tolerance to change, radiator might not be for you.\nAvoid using radiator if you suffer from the Semmelweis reflex. \nPhilosophy, major changes and deprecated functions/arguments are documented in\nlife cycle section of functions. \n\n* The latest changes are documented ([here](https://thierrygosselin.github.io/radiator/articles/life_cycle.html)) and\nin [changelog, versions, new features and bug history](https://thierrygosselin.github.io/radiator/news/index.html)\n* Question(s) or problem(s) with radiator, open an [issue](https://github.com/thierrygosselin/radiator/issues/new/choose)\n* [Contributions are welcomed](https://github.com/thierrygosselin/radiator/issues/new/choose)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fthierrygosselin%2Fradiator","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fthierrygosselin%2Fradiator","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fthierrygosselin%2Fradiator/lists"}