{"id":149131,"name":null,"description":"A framework for generating synthetic genomics data for the evaluation of  tumor-only somatic variant calling algorithms.","url":"https://github.com/biodataanalysisgroup/synth4bench","last_synced_at":"2025-09-09T15:08:54.288Z","repository":{"id":177522798,"uuid":"660202119","full_name":"BiodataAnalysisGroup/synth4bench","owner":"BiodataAnalysisGroup","description":"A framework for generating synthetic genomics data for the evaluation of  tumor-only somatic variant calling algorithms.","archived":false,"fork":true,"pushed_at":"2025-07-07T10:29:46.000Z","size":253411,"stargazers_count":4,"open_issues_count":0,"forks_count":1,"subscribers_count":0,"default_branch":"main","last_synced_at":"2025-07-07T11:33:39.510Z","etag":null,"topics":["benchmarking","bioinformatics","synthetic-dataset-generation","variant-calling"],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":"sfragkoul/synth4bench","license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/BiodataAnalysisGroup.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}},"created_at":"2023-06-29T13:24:43.000Z","updated_at":"2025-07-07T10:29:49.000Z","dependencies_parsed_at":"2023-10-11T20:57:53.949Z","dependency_job_id":null,"html_url":"https://github.com/BiodataAnalysisGroup/synth4bench","commit_stats":null,"previous_names":["biodataanalysisgroup/synth4bench"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/BiodataAnalysisGroup/synth4bench","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BiodataAnalysisGroup%2Fsynth4bench","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BiodataAnalysisGroup%2Fsynth4bench/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BiodataAnalysisGroup%2Fsynth4bench/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BiodataAnalysisGroup%2Fsynth4bench/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/BiodataAnalysisGroup","download_url":"https://codeload.github.com/BiodataAnalysisGroup/synth4bench/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BiodataAnalysisGroup%2Fsynth4bench/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":274316670,"owners_count":25262710,"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":"2025-09-09T02:00:10.223Z","response_time":80,"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":"BiodataAnalysisGroup","name":"Biodata Analysis Group","uuid":"9251685","kind":"organization","description":"","email":"fpsom@certh.gr","website":"https://biodataanalysisgroup.github.io/","location":null,"twitter":null,"company":null,"icon_url":"https://avatars.githubusercontent.com/u/9251685?v=4","repositories_count":17,"last_synced_at":"2023-03-01T02:45:41.301Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/BiodataAnalysisGroup","funding_links":[],"total_stars":null,"followers":null,"following":null,"created_at":"2022-11-12T02:39:16.975Z","updated_at":"2023-03-01T02:45:41.356Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/BiodataAnalysisGroup","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/BiodataAnalysisGroup/repositories"},"packages":[],"commits":{"message":"Repository syncing started."},"issues_stats":{"full_name":"BiodataAnalysisGroup/synth4bench","html_url":"https://github.com/BiodataAnalysisGroup/synth4bench","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":"2025-09-01T22:46:16.571Z","updated_at":"2025-09-02T19:47:02.066Z","repository_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/BiodataAnalysisGroup%2Fsynth4bench","issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/BiodataAnalysisGroup%2Fsynth4bench/issues","issue_labels_count":{},"pull_request_labels_count":{},"issue_author_associations_count":{"NONE":4},"pull_request_author_associations_count":{"NONE":19},"issue_authors":{"sfragkoul":4},"pull_request_authors":{"natanast":11,"sfragkoul":7,"npechl":1},"host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-09T00:00:11.778Z","repositories_count":10193878,"issues_count":32254962,"pull_requests_count":101822519,"authors_count":10740620,"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":3},"past_year_pull_request_author_associations_count":{"NONE":16},"past_year_issue_authors":{"sfragkoul":3},"past_year_pull_request_authors":{"natanast":11,"sfragkoul":5},"maintainers":[],"active_maintainers":[]},"events":{"total":{"IssuesEvent":6,"DeleteEvent":2,"IssueCommentEvent":1,"PushEvent":78,"PullRequestEvent":27,"ForkEvent":1,"CreateEvent":1},"last_year":{"IssuesEvent":6,"DeleteEvent":2,"IssueCommentEvent":1,"PushEvent":78,"PullRequestEvent":27,"ForkEvent":1,"CreateEvent":1}},"keywords":["benchmarking","bioinformatics","synthetic-dataset-generation","variant-calling"],"dependencies":[{"ecosystem":"pypi","filepath":"environment.yml","sha":null,"kind":"manifest","created_at":"2023-10-11T20:57:53.935Z","updated_at":"2023-10-11T20:57:53.935Z","repository_link":"https://github.com/BiodataAnalysisGroup/synth4bench/blob/main/environment.yml","dependencies":[{"id":14157808018,"package_name":"biopython","ecosystem":"pypi","requirements":"==1.80","direct":true,"kind":"runtime","optional":false},{"id":14157808019,"package_name":"contourpy","ecosystem":"pypi","requirements":"==1.0.6","direct":true,"kind":"runtime","optional":false},{"id":14157808020,"package_name":"cycler","ecosystem":"pypi","requirements":"==0.11.0","direct":true,"kind":"runtime","optional":false},{"id":14157808021,"package_name":"fonttools","ecosystem":"pypi","requirements":"==4.38.0","direct":true,"kind":"runtime","optional":false},{"id":14157808022,"package_name":"kiwisolver","ecosystem":"pypi","requirements":"==1.4.4","direct":true,"kind":"runtime","optional":false},{"id":14157808023,"package_name":"matplotlib","ecosystem":"pypi","requirements":"==3.6.2","direct":true,"kind":"runtime","optional":false},{"id":14157808024,"package_name":"matplotlib-venn","ecosystem":"pypi","requirements":"==0.11.7","direct":true,"kind":"runtime","optional":false},{"id":14157808025,"package_name":"numpy","ecosystem":"pypi","requirements":"==1.24.0","direct":true,"kind":"runtime","optional":false},{"id":14157808026,"package_name":"packaging","ecosystem":"pypi","requirements":"==22.0","direct":true,"kind":"runtime","optional":false},{"id":14157808027,"package_name":"pandas","ecosystem":"pypi","requirements":"==1.5.2","direct":true,"kind":"runtime","optional":false},{"id":14157808028,"package_name":"pillow","ecosystem":"pypi","requirements":"==9.3.0","direct":true,"kind":"runtime","optional":false},{"id":14157808029,"package_name":"pyparsing","ecosystem":"pypi","requirements":"==3.0.9","direct":true,"kind":"runtime","optional":false},{"id":14157808030,"package_name":"pysam","ecosystem":"pypi","requirements":"==0.19.1","direct":true,"kind":"runtime","optional":false},{"id":14157808031,"package_name":"python-dateutil","ecosystem":"pypi","requirements":"==2.8.2","direct":true,"kind":"runtime","optional":false},{"id":14157808032,"package_name":"pytz","ecosystem":"pypi","requirements":"==2022.7","direct":true,"kind":"runtime","optional":false},{"id":14157808033,"package_name":"scipy","ecosystem":"pypi","requirements":"==1.9.3","direct":true,"kind":"runtime","optional":false},{"id":14157808034,"package_name":"six","ecosystem":"pypi","requirements":"==1.16.0","direct":true,"kind":"runtime","optional":false}]}],"score":null,"created_at":"2025-09-09T00:26:34.638Z","updated_at":"2025-10-07T08:37:16.290Z","avatar_url":"https://github.com/BiodataAnalysisGroup.png","language":"R","category":null,"sub_category":null,"monthly_downloads":0,"funding_links":[],"readme_doi_urls":["https://doi.org/10.7490/f1000research.1119793.1","https://doi.org/10.5281/zenodo.8432060","https://doi.org/10.7490/f1000research.1119575.1"],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":[],"project_url":"https://science.ecosyste.ms/api/v1/projects/149131","html_url":"https://science.ecosyste.ms/projects/149131"}