{"id":32111450,"url":"https://github.com/benjjneb/decontam","last_synced_at":"2026-02-21T19:33:48.256Z","repository":{"id":37845002,"uuid":"87143734","full_name":"benjjneb/decontam","owner":"benjjneb","description":"Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data","archived":false,"fork":false,"pushed_at":"2025-09-04T21:35:55.000Z","size":1312,"stargazers_count":163,"open_issues_count":97,"forks_count":26,"subscribers_count":10,"default_branch":"master","last_synced_at":"2025-10-20T14:46:17.138Z","etag":null,"topics":["amplicon","bioinformatics","contamination","metabarcoding","metagenomics","microbiome"],"latest_commit_sha":null,"homepage":"https://benjjneb.github.io/decontam/","language":"HTML","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/benjjneb.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":"2017-04-04T03:20:13.000Z","updated_at":"2025-10-14T12:04:14.000Z","dependencies_parsed_at":"2023-10-20T18:22:12.717Z","dependency_job_id":null,"html_url":"https://github.com/benjjneb/decontam","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"purl":"pkg:github/benjjneb/decontam","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/benjjneb%2Fdecontam","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/benjjneb%2Fdecontam/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/benjjneb%2Fdecontam/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/benjjneb%2Fdecontam/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/benjjneb","download_url":"https://codeload.github.com/benjjneb/decontam/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/benjjneb%2Fdecontam/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29691045,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-21T18:18:25.093Z","status":"ssl_error","status_checked_at":"2026-02-21T18:18:22.435Z","response_time":107,"last_error":"SSL_read: 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":["amplicon","bioinformatics","contamination","metabarcoding","metagenomics","microbiome"],"created_at":"2025-10-20T14:30:50.883Z","updated_at":"2026-02-21T19:33:48.251Z","avatar_url":"https://github.com/benjjneb.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"## Documentation\n\n**An [introductory vignette](https://benjjneb.github.io/decontam/vignettes/decontam_intro.html) demonstrating how to use the decontam package to identify contaminants.**\n\n**An [extensive investigation of contamination](https://benjjneb.github.io/DecontamManuscript/Analyses/oral_contamination.html) in an oral mucosal dataset, that includes evaluation of deontam results.**\n\n**The [manuscript introducing decontam](https://doi.org/10.1186/s40168-018-0605-2) with benchmarking demonstrating how `decontam`-inating your data removes reagent sequences, improves accuracy, reduces batch effects, and prevents false-positive associations.**\n\nMore documentation available through the R help interface (e.g. `?isContaminant`) and at [the decontam web site](https://benjjneb.github.io/decontam).\n\n## Installation\n\nThe decontam R package is most easily installed from the Bioconductor repository. To install the most recent version of the decontam package, start R (version \"3.6\") and enter:\n\n```S\nif (!requireNamespace(\"BiocManager\", quietly = TRUE))\n    install.packages(\"BiocManager\")\n\nBiocManager::install(\"decontam\")\n```\n\nSee [the Bioconductor documentation for decontam](https://bioconductor.org/packages/release/bioc/html/decontam.html) for additional information.\n\nThe decontam R package is also available as a source package through github. Installation requires the ability to compile R packages. This means that R and the R tool-chain must be installed, which requires the [Xcode command-line tools](http://railsapps.github.io/xcode-command-line-tools.html) on Mac and [Rtools](https://cran.r-project.org/bin/windows/Rtools/) on Windows.\n\nThe easiest source installation method uses the `devtools` package:\n\n```S\nlibrary(devtools)\ndevtools::install_github(\"benjjneb/decontam\")\n```\n\n## Other Resources\n\nBugs and difficulties in using decontam are welcome on [the issue tracker](https://github.com/benjjneb/decontam/issues).\n\nPlanned feature improvements are also publicly catalogued at on the \"Issues\" page for decontam: https://github.com/benjjneb/decontam/issues\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbenjjneb%2Fdecontam","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbenjjneb%2Fdecontam","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbenjjneb%2Fdecontam/lists"}