{"id":32111098,"url":"https://github.com/uds-helms/beclear","last_synced_at":"2026-02-20T15:32:58.627Z","repository":{"id":91809336,"uuid":"150225223","full_name":"uds-helms/BEclear","owner":"uds-helms","description":"Correction of batch effects in DNA methylation data","archived":false,"fork":false,"pushed_at":"2026-01-17T17:34:54.000Z","size":1151,"stargazers_count":5,"open_issues_count":10,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2026-01-26T16:20:23.989Z","etag":null,"topics":["batch-effects","bioconductor-package","dna-methylation","latent-factor-model","methylation","missing-data","missing-values","rpackage","stochastic-gradient-descent"],"latest_commit_sha":null,"homepage":"https://bioconductor.org/packages/release/bioc/html/BEclear.html","language":"R","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/uds-helms.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2018-09-25T07:33:03.000Z","updated_at":"2026-01-17T17:34:58.000Z","dependencies_parsed_at":null,"dependency_job_id":"d45c5a7a-ea06-464a-8acc-76f29354322e","html_url":"https://github.com/uds-helms/BEclear","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/uds-helms/BEclear","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/uds-helms%2FBEclear","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/uds-helms%2FBEclear/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/uds-helms%2FBEclear/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/uds-helms%2FBEclear/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/uds-helms","download_url":"https://codeload.github.com/uds-helms/BEclear/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/uds-helms%2FBEclear/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29655307,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-20T09:27:29.698Z","status":"ssl_error","status_checked_at":"2026-02-20T09:26:12.373Z","response_time":59,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"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":["batch-effects","bioconductor-package","dna-methylation","latent-factor-model","methylation","missing-data","missing-values","rpackage","stochastic-gradient-descent"],"created_at":"2025-10-20T14:14:06.161Z","updated_at":"2026-02-20T15:32:58.615Z","avatar_url":"https://github.com/uds-helms.png","language":"R","readme":"# BEclear\n\n## Description\n\nThis package provides functions to detect and correct for batch effects in\nDNA methylation data. The core function for the data imputation is based on \nlatent factor models and can also be used to predict missing values in any other \nmatrix containing real numbers.\n\n## Installation\n\n```r\n# Installation from Bioconductor\nif (!requireNamespace(\"BiocManager\", quietly = TRUE))\n    install.packages(\"BiocManager\")\nBiocManager::install(\"BEclear\")\n```\n\n```r\n# Installation of the development version from GitHub\nif (!requireNamespace(\"devtools\", quietly = TRUE))\n    install.packages(\"devtools\")\ndevtools::install_github(\"uds-helms/BEclear\", build_opts = c())\n```\n\n## Usage example\n\nFor example code you can either read the [vignette](https://bioconductor.org/packages/devel/bioc/vignettes/BEclear/inst/doc/BEclear.html) on Bioconductor. Or you can open it local, after you installed the BEclear package with following command:\n\n```r\nbrowseVignettes(\"BEclear\")\n```\n\n## Planned features\n\n- [Treating Data-Sets Without Batches](https://github.com/uds-helms/BEclear/issues/22)\n- [Make Saving Temporary Data Optional](https://github.com/uds-helms/BEclear/issues/21)\n- [Bias Modelling](https://github.com/uds-helms/BEclear/issues/18)\n- [ALS](https://github.com/uds-helms/BEclear/issues/19)\n- [Test For Convergence Durin Epochs](https://github.com/uds-helms/BEclear/issues/23)\n- [Testing BEclear on other data-sets](https://github.com/uds-helms/BEclear/issues/24)\n- [After Merging Blocks Continue GD](https://github.com/uds-helms/BEclear/issues/25)\n\nIf you have a suggestion\nyou could either open an [issue](https://github.com/uds-helms/BEclear/issues) or \nwrite an email under the following address: [Livia.Rasp at gmail.com](mailto:Livia.Rasp@gmail.com)\n\n\n## Citation\n\nAkulenko, R., Merl, M., \u0026 Helms, V. (2016). BEclear: Batch effect detection and \nadjustment in DNA methylation data. PLoS ONE, 11(8), 1–17.\nhttps://doi.org/10.1371/journal.pone.0159921\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fuds-helms%2Fbeclear","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fuds-helms%2Fbeclear","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fuds-helms%2Fbeclear/lists"}