{"id":20924,"name":"ksrates","description":"ksrates is a tool to position whole-genome duplications relative to speciation events using substitution-rate-adjusted mixed paralog-ortholog Ks distributions.","url":"https://github.com/vib-psb/ksrates","last_synced_at":"2025-09-05T00:45:44.935Z","repository":{"id":42985201,"uuid":"342957985","full_name":"VIB-PSB/ksrates","owner":"VIB-PSB","description":"ksrates is a tool to position whole-genome duplications relative to speciation events using substitution-rate-adjusted mixed paralog-ortholog Ks distributions.","archived":false,"fork":false,"pushed_at":"2025-08-08T13:10:53.000Z","size":47238,"stargazers_count":19,"open_issues_count":5,"forks_count":10,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-08-08T14:44:07.408Z","etag":null,"topics":["evolution","ks-distributions","substitution-rate","wgd","wgm","whole-genome-duplication"],"latest_commit_sha":null,"homepage":"https://ksrates.readthedocs.io","language":"Python","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/VIB-PSB.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2021-02-27T21:03:59.000Z","updated_at":"2025-08-08T13:10:58.000Z","dependencies_parsed_at":"2025-04-13T01:52:21.663Z","dependency_job_id":"0d157b16-a12a-45ac-bcde-d4cdfbb8b05c","html_url":"https://github.com/VIB-PSB/ksrates","commit_stats":null,"previous_names":[],"tags_count":11,"template":false,"template_full_name":null,"purl":"pkg:github/VIB-PSB/ksrates","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/VIB-PSB%2Fksrates","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/VIB-PSB%2Fksrates/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/VIB-PSB%2Fksrates/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/VIB-PSB%2Fksrates/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/VIB-PSB","download_url":"https://codeload.github.com/VIB-PSB/ksrates/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/VIB-PSB%2Fksrates/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":273695214,"owners_count":25151481,"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","status":"online","status_checked_at":"2025-09-04T02:00:08.968Z","response_time":61,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"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"}},"owner":{"login":"VIB-PSB","name":"VIB - PSB","uuid":"23654185","kind":"organization","description":"","email":null,"website":"http://www.psb.ugent.be/","location":"Technologiepark 71, 9052 Zwijnaarde, Belgium","twitter":null,"company":null,"icon_url":"https://avatars.githubusercontent.com/u/23654185?v=4","repositories_count":3,"last_synced_at":"2023-02-27T08:37:30.531Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/VIB-PSB","funding_links":[],"total_stars":null,"followers":null,"following":null,"created_at":"2023-02-27T08:37:30.531Z","updated_at":"2023-02-27T08:37:30.531Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/VIB-PSB","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/VIB-PSB/repositories"},"packages":[],"commits":{"message":"Repository syncing started."},"issues_stats":{"full_name":"VIB-PSB/ksrates","html_url":"https://github.com/VIB-PSB/ksrates","last_synced_at":null,"status":null,"issues_count":null,"pull_requests_count":null,"avg_time_to_close_issue":null,"avg_time_to_close_pull_request":null,"issues_closed_count":null,"pull_requests_closed_count":null,"pull_request_authors_count":null,"issue_authors_count":null,"avg_comments_per_issue":null,"avg_comments_per_pull_request":null,"merged_pull_requests_count":null,"bot_issues_count":null,"bot_pull_requests_count":null,"past_year_issues_count":null,"past_year_pull_requests_count":null,"past_year_avg_time_to_close_issue":null,"past_year_avg_time_to_close_pull_request":null,"past_year_issues_closed_count":null,"past_year_pull_requests_closed_count":null,"past_year_pull_request_authors_count":null,"past_year_issue_authors_count":null,"past_year_avg_comments_per_issue":null,"past_year_avg_comments_per_pull_request":null,"past_year_bot_issues_count":null,"past_year_bot_pull_requests_count":null,"past_year_merged_pull_requests_count":null,"created_at":"2025-08-29T13:01:02.765Z","updated_at":"2025-09-02T17:06:38.251Z","repository_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/VIB-PSB%2Fksrates","issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/VIB-PSB%2Fksrates/issues","issue_labels_count":{},"pull_request_labels_count":{},"issue_author_associations_count":{"NONE":7},"pull_request_author_associations_count":{"COLLABORATOR":9},"issue_authors":{"sjfleck":2,"abcbot123":2,"tamsen":1,"zhouxp9709":1,"majssssa":1},"pull_request_authors":{"Cecilia-Sensalari":9},"host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-05T00:00:10.444Z","repositories_count":10082304,"issues_count":31220387,"pull_requests_count":96069062,"authors_count":10694175,"icon_url":"https://github.com/github.png","host_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories","owners_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/owners","authors_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors"},"past_year_issue_labels_count":{},"past_year_pull_request_labels_count":{},"past_year_issue_author_associations_count":{"NONE":2},"past_year_pull_request_author_associations_count":{"COLLABORATOR":6},"past_year_issue_authors":{"sjfleck":2},"past_year_pull_request_authors":{"Cecilia-Sensalari":6},"maintainers":[{"login":"Cecilia-Sensalari","count":9,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/Cecilia-Sensalari"}],"active_maintainers":[{"login":"Cecilia-Sensalari","count":6,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/Cecilia-Sensalari"}]},"events":{"total":{"CreateEvent":9,"ReleaseEvent":6,"IssuesEvent":3,"WatchEvent":5,"DeleteEvent":4,"IssueCommentEvent":14,"PushEvent":61,"PullRequestReviewEvent":4,"PullRequestEvent":9,"ForkEvent":1},"last_year":{"CreateEvent":9,"ReleaseEvent":6,"IssuesEvent":3,"WatchEvent":5,"DeleteEvent":4,"IssueCommentEvent":14,"PushEvent":61,"PullRequestReviewEvent":4,"PullRequestEvent":9,"ForkEvent":1}},"keywords":["evolution","ks-distributions","substitution-rate","wgd","wgm","whole-genome-duplication"],"dependencies":[{"ecosystem":"pypi","filepath":"requirements.txt","sha":null,"kind":"manifest","created_at":"2022-09-24T10:10:34.324Z","updated_at":"2022-09-24T10:10:34.324Z","repository_link":"https://github.com/VIB-PSB/ksrates/blob/master/requirements.txt","dependencies":[{"id":6028155158,"package_name":"click","ecosystem":"pypi","requirements":"==8.0.1","direct":true,"kind":"runtime","optional":false},{"id":6028155159,"package_name":"numpy","ecosystem":"pypi","requirements":"==1.21.2","direct":true,"kind":"runtime","optional":false},{"id":6028155160,"package_name":"scipy","ecosystem":"pypi","requirements":"==1.7.1","direct":true,"kind":"runtime","optional":false},{"id":6028155161,"package_name":"seaborn","ecosystem":"pypi","requirements":"==0.11.2","direct":true,"kind":"runtime","optional":false},{"id":6028155162,"package_name":"matplotlib","ecosystem":"pypi","requirements":"==3.4.3","direct":true,"kind":"runtime","optional":false},{"id":6028155163,"package_name":"configparser","ecosystem":"pypi","requirements":"==5.0.2","direct":true,"kind":"runtime","optional":false},{"id":6028155164,"package_name":"ete3","ecosystem":"pypi","requirements":"==3.1.2","direct":true,"kind":"runtime","optional":false},{"id":6028155165,"package_name":"pandas","ecosystem":"pypi","requirements":"==1.3.2","direct":true,"kind":"runtime","optional":false},{"id":6028155166,"package_name":"scikit-learn","ecosystem":"pypi","requirements":"==0.24.2","direct":true,"kind":"runtime","optional":false},{"id":6028155167,"package_name":"PyQt5","ecosystem":"pypi","requirements":"==5.15.2","direct":true,"kind":"runtime","optional":false},{"id":6028155168,"package_name":"biopython","ecosystem":"pypi","requirements":"==1.79","direct":true,"kind":"runtime","optional":false},{"id":6028155169,"package_name":"coloredlogs","ecosystem":"pypi","requirements":"==15.0.1","direct":true,"kind":"runtime","optional":false},{"id":6028155170,"package_name":"fastcluster","ecosystem":"pypi","requirements":"==1.1.25","direct":true,"kind":"runtime","optional":false},{"id":6028155171,"package_name":"plumbum","ecosystem":"pypi","requirements":"==1.7.0","direct":true,"kind":"runtime","optional":false},{"id":6028155172,"package_name":"progressbar2","ecosystem":"pypi","requirements":"==3.53.1","direct":true,"kind":"runtime","optional":false},{"id":6028155173,"package_name":"joblib","ecosystem":"pypi","requirements":"==0.11","direct":true,"kind":"runtime","optional":false},{"id":6028155174,"package_name":"bokeh","ecosystem":"pypi","requirements":"==1.4.0","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"pypi","filepath":"setup.py","sha":null,"kind":"manifest","created_at":"2022-09-24T10:10:34.382Z","updated_at":"2022-09-24T10:10:34.382Z","repository_link":"https://github.com/VIB-PSB/ksrates/blob/master/setup.py","dependencies":[{"id":6028155873,"package_name":"required","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/push_container.yml","sha":null,"kind":"manifest","created_at":"2023-02-10T14:45:12.899Z","updated_at":"2023-02-10T14:45:12.899Z","repository_link":"https://github.com/VIB-PSB/ksrates/blob/master/.github/workflows/push_container.yml","dependencies":[{"id":7531533966,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":7531533967,"package_name":"docker/metadata-action","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":7531533968,"package_name":"docker/login-action","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":7531533969,"package_name":"docker/setup-qemu-action","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":7531533970,"package_name":"docker/setup-buildx-action","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":7531533971,"package_name":"docker/build-push-action","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/test_pipeline.yml","sha":null,"kind":"manifest","created_at":"2023-02-10T14:45:12.965Z","updated_at":"2023-02-10T14:45:12.965Z","repository_link":"https://github.com/VIB-PSB/ksrates/blob/master/.github/workflows/test_pipeline.yml","dependencies":[{"id":7531534278,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"docker","filepath":"Dockerfile","sha":null,"kind":"manifest","created_at":"2023-02-10T14:45:13.121Z","updated_at":"2023-02-10T14:45:13.121Z","repository_link":"https://github.com/VIB-PSB/ksrates/blob/master/Dockerfile","dependencies":[{"id":7531534329,"package_name":"vibpsb/i-adhore","ecosystem":"docker","requirements":"latest","direct":true,"kind":"build","optional":false}]},{"ecosystem":"pypi","filepath":"doc/source/requirements.txt","sha":null,"kind":"manifest","created_at":"2024-06-27T17:08:10.321Z","updated_at":"2024-06-27T17:08:10.321Z","repository_link":"https://github.com/VIB-PSB/ksrates/blob/master/doc/source/requirements.txt","dependencies":[{"id":18856334911,"package_name":"sphinx","ecosystem":"pypi","requirements":"==7.2.6","direct":true,"kind":"runtime","optional":false},{"id":18856334912,"package_name":"sphinx_rtd_theme","ecosystem":"pypi","requirements":"==2.0.0","direct":true,"kind":"runtime","optional":false}]}],"score":null,"created_at":"2025-09-04T15:50:52.370Z","updated_at":"2025-10-07T08:10:11.974Z","avatar_url":"https://github.com/VIB-PSB.png","language":"Python","category":null,"sub_category":null,"monthly_downloads":0,"funding_links":[],"readme_doi_urls":["https://doi.org/10.1093/bioinformatics/btab602"],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":[],"project_url":"https://science.ecosyste.ms/api/v1/projects/20924","html_url":"https://science.ecosyste.ms/projects/20924","bibtex_url":"https://science.ecosyste.ms/projects/20924/export.bibtex","apalike_url":"https://science.ecosyste.ms/projects/20924/export.apalike"}