{"id":32111516,"url":"https://github.com/dessimozlab/omadb","last_synced_at":"2026-02-21T11:31:28.907Z","repository":{"id":106984291,"uuid":"159942332","full_name":"DessimozLab/OmaDB","owner":"DessimozLab","description":null,"archived":false,"fork":false,"pushed_at":"2024-04-18T06:09:45.000Z","size":446,"stargazers_count":2,"open_issues_count":0,"forks_count":2,"subscribers_count":4,"default_branch":"master","last_synced_at":"2026-02-05T11:18:13.019Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Jupyter Notebook","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/DessimozLab.png","metadata":{"files":{"readme":"README.md","changelog":"NEWS","contributing":null,"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,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2018-12-01T12:28:23.000Z","updated_at":"2024-07-23T08:38:28.000Z","dependencies_parsed_at":null,"dependency_job_id":"347f3e5e-28b0-4b24-877d-ddb357fee1d6","html_url":"https://github.com/DessimozLab/OmaDB","commit_stats":{"total_commits":148,"total_committers":8,"mean_commits":18.5,"dds":0.5540540540540541,"last_synced_commit":"77cbda3885faf39190007f89df92a36bcb45fde9"},"previous_names":[],"tags_count":3,"template":false,"template_full_name":null,"purl":"pkg:github/DessimozLab/OmaDB","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DessimozLab%2FOmaDB","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DessimozLab%2FOmaDB/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DessimozLab%2FOmaDB/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DessimozLab%2FOmaDB/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/DessimozLab","download_url":"https://codeload.github.com/DessimozLab/OmaDB/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DessimozLab%2FOmaDB/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29679802,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-21T11:29:27.227Z","status":"ssl_error","status_checked_at":"2026-02-21T11:29:20.292Z","response_time":107,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 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":[],"created_at":"2025-10-20T14:35:43.764Z","updated_at":"2026-02-21T11:31:28.896Z","avatar_url":"https://github.com/DessimozLab.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# OmaDB: R wrapper for the OMA REST API\n\nR package providing access to the data in the OMA browser, using the REST API. As such, it requires a stable internet connection to operate. We also provide a similar _wrapper for python (https://github.com/DessimozLab/pyOmaDB)_.\n\nAn notebook containing examples of how to use the package is available \u003ca href=\"https://github.com/DessimozLab/omadb/blob/master/manuscript_examples.ipynb\"\u003ehere\u003c/a\u003e.\n\n[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/DessimozLab/omadb/master?filepath=manuscript_examples.ipynb)\n\n## Citation\nIf you use our package in your work, please consider citing:\n\n_Kaleb K, Warwick Vesztrocy A, Altenhoff A and Dessimoz C. Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python. F1000Research 2019, 8:42\n(https://doi.org/10.12688/f1000research.17548.2)_\n\n## Installation\n\nThe package is available via Bioconductor (https://bioconductor.org) and can be installed as follows:\n\n```\nif (!requireNamespace(\"BiocManager\"))\n    install.packages(\"BiocManager\")\nBiocManager::install('OmaDB')\n\n#load the package\nlibrary(OmaDB)\n\n```\n\nNote that the v2.0 of the package requires R version \u003e= 3.6 and Bioconductor version \u003e=3.9. \n\nThe latest version of the OmaDB package can also be directly installed from the github repository as below:\n\n```\ninstall.packages('devtools')\nlibrary(devtools)\ninstall_github('dessimozlab/omadb')\n```\n\n\n## License\n\nOmaDB is free software: you can redistribute it and/or modify\nit under the terms of the GNU Lesser General Public License as published by\nthe Free Software Foundation, either version 3 of the License, or\n(at your option) any later version.\n\nOmaDB is distributed in the hope that it will be useful,\nbut WITHOUT ANY WARRANTY; without even the implied warranty of\nMERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\nGNU Lesser General Public License for more details.\nYou should have received a copy of the GNU Lesser General Public License\nalong with OmaDB.  If not, see \u003chttp://www.gnu.org/licenses/\u003e.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdessimozlab%2Fomadb","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdessimozlab%2Fomadb","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdessimozlab%2Fomadb/lists"}