{"id":19682263,"url":"https://github.com/kanduric/simairr","last_synced_at":"2026-02-13T14:08:01.500Z","repository":{"id":101574580,"uuid":"475609581","full_name":"KanduriC/simAIRR","owner":"KanduriC","description":"A tool for simulation of antigen-experienced adaptive immune receptor repertoire (AIRR) datasets for benchmarking of machine learning (ML) methods.","archived":false,"fork":false,"pushed_at":"2025-01-20T06:00:50.000Z","size":4118,"stargazers_count":0,"open_issues_count":0,"forks_count":1,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-04-30T07:23:24.423Z","etag":null,"topics":["adaptive-immune-receptor-repertoires","airr","benchmarking","machine-learning","ml","simulation"],"latest_commit_sha":null,"homepage":"https://kanduric.github.io/simAIRR/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"agpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/KanduriC.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":"2022-03-29T20:29:33.000Z","updated_at":"2025-01-20T06:00:52.000Z","dependencies_parsed_at":null,"dependency_job_id":"f84b25b1-1018-49bf-8d83-1a26f2731217","html_url":"https://github.com/KanduriC/simAIRR","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/KanduriC/simAIRR","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KanduriC%2FsimAIRR","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KanduriC%2FsimAIRR/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KanduriC%2FsimAIRR/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KanduriC%2FsimAIRR/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/KanduriC","download_url":"https://codeload.github.com/KanduriC/simAIRR/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KanduriC%2FsimAIRR/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29409598,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-13T06:24:03.484Z","status":"ssl_error","status_checked_at":"2026-02-13T06:23:12.830Z","response_time":78,"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":["adaptive-immune-receptor-repertoires","airr","benchmarking","machine-learning","ml","simulation"],"created_at":"2024-11-11T18:10:06.555Z","updated_at":"2026-02-13T14:08:01.483Z","avatar_url":"https://github.com/KanduriC.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# simAIRR\n\n![unit_tests](https://github.com/KanduriC/simAIRR/actions/workflows/run_unit_tests.yml/badge.svg)\n![docker](https://github.com/KanduriC/simAIRR/actions/workflows/push_docker.yml/badge.svg)\n\nsimAIRR provides a simulation approach to generate synthetic AIRR datasets that are suitable for benchmarking machine learning (ML) methods, where undesirable access to ground truth signals in training datasets for ML methods is mitigated. Unlike state-of-the-art approaches, simAIRR constructs antigen-experienced-like baseline repertoires and introduces signals by following the empirical relationship between generation probability and sharing pattern of public sequences calibrated from real-world experimental datasets.\n\nGetting started\n---------------\n\nTo get started:\n\n- For installation instructions and tutorials, see [documentation](https://kanduric.github.io/simAIRR/): https://kanduric.github.io/simAIRR/\n- Consult the [tutorials](https://kanduric.github.io/simAIRR/tutorials.html) for detailed examples of different workflows\n- Read a brief overview of simAIRR's simulation approach under [simulation approach](https://kanduric.github.io/simAIRR/overview.html)\n- Consult the descriptions of valid [parameter configurations](https://kanduric.github.io/simAIRR/configuration.html)\n\nInstallation\n============\n\nInstall using pip\n------------------\n\n``` \n$ pip install simAIRR \n```\n\nManual installation using git\n------------------------------\n\n``` \n$ pip install git+https://github.com/KanduriC/simAIRR.git\n```\n\nUse simAIRR through Docker\n--------------------------\n\n```\n$ docker run -it -v $(pwd):/wd --name my_container kanduric/simairr:latest sim_airr --help\n```","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkanduric%2Fsimairr","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fkanduric%2Fsimairr","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkanduric%2Fsimairr/lists"}