{"id":15704339,"url":"https://github.com/poisonalien/beadanalyze","last_synced_at":"2025-05-12T16:43:57.163Z","repository":{"id":182576270,"uuid":"65260802","full_name":"PoisonAlien/beadAnalyze","owner":"PoisonAlien","description":"Automated differential expression analysis for Illumina beadarrays (HT12 V4 arrays).","archived":false,"fork":false,"pushed_at":"2016-08-09T04:11:46.000Z","size":225,"stargazers_count":8,"open_issues_count":0,"forks_count":2,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-04-01T00:41:20.259Z","etag":null,"topics":["differential-expression","idat","illumina-beadarrays","microarry"],"latest_commit_sha":null,"homepage":null,"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/PoisonAlien.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":"2016-08-09T03:46:00.000Z","updated_at":"2019-09-25T09:33:43.000Z","dependencies_parsed_at":null,"dependency_job_id":"524ce328-5cfc-4bce-9510-344c26d64daf","html_url":"https://github.com/PoisonAlien/beadAnalyze","commit_stats":null,"previous_names":["poisonalien/beadanalyze"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PoisonAlien%2FbeadAnalyze","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PoisonAlien%2FbeadAnalyze/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PoisonAlien%2FbeadAnalyze/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PoisonAlien%2FbeadAnalyze/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/PoisonAlien","download_url":"https://codeload.github.com/PoisonAlien/beadAnalyze/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":253778473,"owners_count":21962874,"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":["differential-expression","idat","illumina-beadarrays","microarry"],"created_at":"2024-10-03T20:11:26.586Z","updated_at":"2025-05-12T16:43:57.145Z","avatar_url":"https://github.com/PoisonAlien.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# beadAnalyze\nAutomated differential expression analysis for Illumina beadarrays (HT12 V4 arrays).\n\nThis R script performs automated differential analysis from Illumina's expression  [idat](https://www.bioconductor.org/packages/devel/bioc/vignettes/illuminaio/inst/doc/EncryptedFormat.pdf) files. By default this script assumes idat files are from HT12 V4 arrays, but with little modification it should work with any arrays.\n\nMake sure you have the following dependencies installed:\n\n[beadarray](https://www.bioconductor.org/packages/release/bioc/html/beadarray.html), [illuminaHumanv4.db](http://bioconductor.org/packages/release/data/annotation/html/illuminaHumanv4.db.html), [limma](https://bioconductor.org/packages/release/bioc/html/limma.html), ggplot2, ggrepel\n\n###Usage:\nClone this repo and source `analyzeBead.R`\n\nArguments:\n\n`idats` = input IDAT files\n\n`names` = Sample names for each idat file\n\n`condition` = Sample conditions for each idat file\n\n`ref.condition` = reference condition. \n\n`fdr` = FDR cutoff. Default 0.05\n\n`pltPCA` = If TRUE performs PCA\n\n\n```{r}\n#Example usage with four idat files (2 control and 2 treated).\nsource(\"AnalyzeBead.R\")\nbead.results = beadAnalyze(idats = c(\"file1.idat\",\"file2.idat\",\"file3.idat\",\"file4.idat\"), \n  names = c(\"control1\",\"control2\",\"treated1\",\"treated2\"), \n  condition = c(\"control\",\"control\",\"treated\",\"treated\"), \n  ref.condition = \"treated\",\n  fdr = 0.05, plotPCA = T) \n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpoisonalien%2Fbeadanalyze","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpoisonalien%2Fbeadanalyze","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpoisonalien%2Fbeadanalyze/lists"}