{"id":28190297,"url":"https://github.com/microbiome/rpa","last_synced_at":"2025-05-16T10:12:33.228Z","repository":{"id":147861245,"uuid":"110440529","full_name":"microbiome/RPA","owner":"microbiome","description":"Robust Probabilistic Averaging","archived":false,"fork":false,"pushed_at":"2025-01-31T06:59:41.000Z","size":1132,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":5,"default_branch":"master","last_synced_at":"2025-01-31T07:33:03.599Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"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/microbiome.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,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2017-11-12T14:45:46.000Z","updated_at":"2022-09-29T17:08:28.000Z","dependencies_parsed_at":"2023-06-26T02:08:19.747Z","dependency_job_id":null,"html_url":"https://github.com/microbiome/RPA","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/microbiome%2FRPA","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/microbiome%2FRPA/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/microbiome%2FRPA/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/microbiome%2FRPA/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/microbiome","download_url":"https://codeload.github.com/microbiome/RPA/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":254509444,"owners_count":22082896,"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":[],"created_at":"2025-05-16T10:12:32.836Z","updated_at":"2025-05-16T10:12:33.223Z","avatar_url":"https://github.com/microbiome.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"RPA\n===\n\nRobust Probabilistic Averaging (RPA) is a Bioconductor R package for\nprobe-level preprocessing and analysis of short oligonucleotide\narrays. The tools are generic but special wrappers are available for\nAffymetrix gene expression arrays as well as phylogenetic microarrays\n(HITChip in particular). \n\nThis Github repository is the home for the latest development version.\nFor the release version, see [RPA Bioconductor\npage](http://bioconductor.org/packages/release/bioc/html/RPA.html)\n\n\n### Installation and use\n\nThe installation instructions and working examples are in\n[RPA wiki](https://github.com/antagomir/RPA/wiki).\n\n\n### Contents of this directory\n\nThis directory contains the following:\n\n * The R package structure (development version)\n * [inst/extras/misc](inst/extras/misc) Miscellaneous development and test code\n * [inst/extras/NAR2013](inst/extras/NAR2013) Some scripts used for the [NAR 2013](http://nar.oxfordjournals.org/content/41/10/e110) paper\n\n### Citing RPA\n\nThe work has been documented in these two publications. Kindly cite if\nappropriate:\n\n * [A fully scalable online pre-processing algorithm for short oligonucleotide microarray atlases](http://nar.oxfordjournals.org/content/41/10/e110) Leo Lahti, Aurora Torrente, Laura L Elo, Alvis Brazma, Johan Rung. _Nucleic Acids Research'_ 41(10):e110, 2013. \n\n * [Probabilistic analysis of probe reliability in differential gene expression studies with short oligonucleotide arrays](https://www.researchgate.net/publication/224439493_Probabilistic_Analysis_of_Probe_Reliability_in_Differential_Gene_Expression_Studies_with_Short_Oligonucleotide_Arrays/file/9fcfd4fbe8b3e5387a.pdf) Leo Lahti, Laura L. Elo, Tero Aittokallio, and Samuel Kaski. _IEEE/ACM Transactions on Computational Biology and Bioinformatics_ 8(1):217-25, 2011. \n\n * [Robust Probabilistic Analysis (RPA)](http://bioconductor.org/packages/release/bioc/html/RPA.html). Bioconductor package. Leo Lahti, 2013. URL: http://bioconductor.org/packages/release/bioc/html/RPA.html \n\n\nRPA has also been used in the context of phylogenetic microarrays, see\nfor instance:\n\n  * [Tipping elements in the human intestinal ecosystem](http://www.nature.com/ncomms/2014/140708/ncomms5344/full/ncomms5344.html)\n\n\n\n\n\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmicrobiome%2Frpa","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmicrobiome%2Frpa","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmicrobiome%2Frpa/lists"}