{"id":44257460,"url":"https://github.com/compomics/oui-discovery","last_synced_at":"2026-02-10T16:35:41.427Z","repository":{"id":301377888,"uuid":"1009048096","full_name":"CompOmics/oui-discovery","owner":"CompOmics","description":"Collaboration between CompOmics \u0026 OpenProt group","archived":false,"fork":false,"pushed_at":"2025-12-19T18:50:30.000Z","size":231036,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":0,"default_branch":"main","last_synced_at":"2025-12-22T08:02:16.591Z","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":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/CompOmics.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,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2025-06-26T13:48:09.000Z","updated_at":"2025-12-19T18:50:36.000Z","dependencies_parsed_at":"2025-10-16T03:10:15.500Z","dependency_job_id":"93c44a3f-f387-485f-bd16-ce7ee1de87df","html_url":"https://github.com/CompOmics/oui-discovery","commit_stats":null,"previous_names":["compomics/oui-discovery"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/CompOmics/oui-discovery","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CompOmics%2Foui-discovery","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CompOmics%2Foui-discovery/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CompOmics%2Foui-discovery/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CompOmics%2Foui-discovery/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/CompOmics","download_url":"https://codeload.github.com/CompOmics/oui-discovery/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CompOmics%2Foui-discovery/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29307916,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-10T16:09:25.305Z","status":"ssl_error","status_checked_at":"2026-02-10T16:08:52.170Z","response_time":65,"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":[],"created_at":"2026-02-10T16:35:39.924Z","updated_at":"2026-02-10T16:35:41.419Z","avatar_url":"https://github.com/CompOmics.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"This repository contains code for publication [DOI].\n\nInput data is on Zenodo: 10.5281/zenodo.18023698\n\nTo reproduce the entrapment analysis: https://github.com/Labo-MAB/Ionbot_FDP/tree/tpp-fragpipe-ranks-groupwalk\n\nTPP and FragPipe parameters (oui-discovery-vv): tpp_run/ \u0026 fragpipe_run/\n\nFigures in .svg: publication-data/Final-figures/\n\nPanels for figures 1-5 \u0026 8-10: oui-discovery-vv-plot/\n\n### To reproduce figures\n\n**f1** oui-discovery-vv/: plot-0-fdp.ipynb\n\n**f2-3** oui-discovery-vv/: explore-1-tpp-1-preprocess.ipynb → do-0-protein-inference-tpp-fragpipe.ipynb \u0026 explore-1-tpp-2-stats.ipynb; explore-1-ionbot-1-preprocess.ipynb → explore-1-ionbot-closed-2-stats.ipynb; compare-2-tpp-ionbot-closed.ipynb\n\n**f4-5** oui-discovery-vv/: explore-1-fragpipe-1-preprocess.ipynb → do-0-protein-inference-tpp-fragpipe.ipynb \u0026 explore-1-fragpipe-2-stats.ipynb; explore-1-ionbot-1-preprocess.ipynb → explore-1-ionbot-open-2-stats.ipynb; compare-2-fragpipe-ionbot-open.ipynb\n\n**f6**: Comparison-4-new-Sankey-global.ipynb \u0026 Comparison-5-ionbot-features-tr-combo-global.ipynb\n\n**f7**: Comparison-6b-open-vs-closed-search-global.ipynb\n\n**f8** oui-discovery-vv/: explore-1-ionbot-1-preprocess.ipynb → explore-1-ionbot-open-2-stats.ipynb\n\n**f9**  oui-discovery-vv/: explore-1-ionbot-1-preprocess.ipynb → explore-1-ionbot-open-2-stats.ipynb \u0026 explore-1-ionbot-closed-2-stats.ipynb → compare-2-ionbot-closed-open.ipynb\n\n**f10** oui-discovery-vv/: explore-1-ionbot-1-preprocess.ipynb → explore-1-ionbot-open-2-stats.ipynb → explore-3-ionbot-open-noncanon-hpp.ipynb \u0026 explore-3-ionbot-open-noncanon-spectra.ipynb\n\n**fs1-2** oui-discovery-vv/: plot-0-fdr-vs-ranks.ipynb\n\n**fs3**: see f2-5\n\n**fs4**: see f10\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcompomics%2Foui-discovery","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcompomics%2Foui-discovery","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcompomics%2Foui-discovery/lists"}