{"id":63248,"name":"ballgown","description":"Bioconductor package \"ballgown\", devel version. Isoform-level differential expression analysis in R.","url":"https://github.com/alyssafrazee/ballgown","last_synced_at":"2025-09-08T12:55:23.650Z","repository":{"id":8097989,"uuid":"9512617","full_name":"alyssafrazee/ballgown","owner":"alyssafrazee","description":"Bioconductor package \"ballgown\", devel version. Isoform-level differential expression analysis in R.","archived":false,"fork":false,"pushed_at":"2021-08-30T01:32:50.000Z","size":16408,"stargazers_count":147,"open_issues_count":61,"forks_count":56,"subscribers_count":26,"default_branch":"master","last_synced_at":"2025-07-10T23:08:06.837Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"http://biorxiv.org/content/biorxiv/early/2014/09/05/003665.full.pdf","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/alyssafrazee.png","metadata":{"files":{"readme":"README.html","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2013-04-18T03:12:49.000Z","updated_at":"2025-05-05T17:09:37.000Z","dependencies_parsed_at":"2022-08-24T11:20:10.475Z","dependency_job_id":null,"html_url":"https://github.com/alyssafrazee/ballgown","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/alyssafrazee/ballgown","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/alyssafrazee%2Fballgown","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/alyssafrazee%2Fballgown/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/alyssafrazee%2Fballgown/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/alyssafrazee%2Fballgown/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/alyssafrazee","download_url":"https://codeload.github.com/alyssafrazee/ballgown/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/alyssafrazee%2Fballgown/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":274188910,"owners_count":25237853,"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":"2025-09-08T02:00:09.813Z","response_time":121,"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":"alyssafrazee","name":"Alyssa Frazee","uuid":"2006744","kind":"user","description":"","email":"","website":"alyssafrazee.com","location":"San Francisco","twitter":null,"company":null,"icon_url":"https://avatars.githubusercontent.com/u/2006744?u=40c24f1e76c37398a6c8bea3a4da443749122f7e\u0026v=4","repositories_count":30,"last_synced_at":"2023-05-10T23:05:11.690Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/alyssafrazee","funding_links":[],"total_stars":null,"followers":null,"following":null,"created_at":"2022-11-05T01:16:20.434Z","updated_at":"2023-05-10T23:05:11.694Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/alyssafrazee","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/alyssafrazee/repositories"},"packages":[],"commits":{"id":318931,"full_name":"alyssafrazee/ballgown","default_branch":"master","committers":[{"name":"Alyssa Frazee","email":"acfrazee@gmail.com","login":null,"count":613},{"name":"Alyssa Frazee","email":"alyssa.frazee@gmail.com","login":null,"count":289},{"name":"a.frazee","email":"a.frazee@bc3139a8-67e5-0310-9ffc-ced21a209358","login":null,"count":49},{"name":"Jack Fu","email":"jmfu@jhsph.edu","login":null,"count":20},{"name":"d.tenenbaum","email":"d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358","login":null,"count":13},{"name":"Dan Tenenbaum","email":"dtenenba@fhcrc.org","login":null,"count":11},{"name":"Nitesh Turaga","email":"nitesh.turaga@gmail.com","login":null,"count":10},{"name":"jtleek","email":"jtleek@gmail.com","login":null,"count":10},{"name":"Herve Pages","email":"hpages@fhcrc.org","login":null,"count":9},{"name":"hpages@fhcrc.org","email":"hpages@fhcrc.org@bc3139a8-67e5-0310-9ffc-ced21a209358","login":null,"count":7},{"name":"Andrew Jaffe","email":"andrew.jaffe@libd.org","login":null,"count":6},{"name":"Bioconductor Git-SVN Bridge","email":"bioc-sync@bioconductor.org","login":null,"count":5},{"name":"Alyssa Frazee","email":"alyssa@deck.tools","login":null,"count":3},{"name":"Hervé Pagès","email":"hpages@fredhutch.org","login":null,"count":3},{"name":"Alyssa Frazee","email":"afrazee@jhsph.edu","login":null,"count":2},{"name":"vobencha","email":"valerie.obenchain@roswellpark.org","login":null,"count":2},{"name":"vobencha","email":"vobencha@gmail.com","login":null,"count":2},{"name":"m.carlson","email":"m.carlson@bc3139a8-67e5-0310-9ffc-ced21a209358","login":null,"count":1},{"name":"lcolladotor","email":"lcollado@jhsph.edu","login":null,"count":1},{"name":"Marc Carlson","email":"mcarlson@fhcrc.org","login":null,"count":1},{"name":"LiNk-NY","email":"mramos09@gmail.com","login":null,"count":1},{"name":"Kayla-Morrell","email":"kayla.morrell@roswellpark.org","login":null,"count":1},{"name":"student-t","email":"WongMingYin@gmail.com","login":null,"count":1}],"total_commits":1060,"total_committers":23,"total_bot_commits":0,"total_bot_committers":0,"mean_commits":46.08695652173913,"dds":0.42169811320754713,"past_year_committers":[],"past_year_total_commits":0,"past_year_total_committers":0,"past_year_total_bot_commits":0,"past_year_total_bot_committers":0,"past_year_mean_commits":0.0,"past_year_dds":0.0,"last_synced_at":"2023-10-25T13:02:57.614Z","last_synced_commit":"0d2092fb816a17abf2796061153ac6f489d80bb7","created_at":"2023-03-08T17:07:05.828Z","updated_at":"2023-10-25T13:02:57.615Z","commits_url":"https://commits.ecosyste.ms/api/v1/hosts/GitHub/repositories/alyssafrazee%2Fballgown/commits","host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-08T00:00:16.827Z","repositories_count":5483322,"commits_count":854270774,"contributors_count":31138750,"owners_count":908526,"icon_url":"https://github.com/github.png","host_url":"https://commits.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://commits.ecosyste.ms/api/v1/hosts/GitHub/repositories"}},"issues_stats":{"full_name":"alyssafrazee/ballgown","html_url":"https://github.com/alyssafrazee/ballgown","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":"2025-09-01T04:59:34.205Z","updated_at":"2025-09-01T04:59:34.205Z","repository_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/alyssafrazee%2Fballgown","issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/alyssafrazee%2Fballgown/issues","issue_labels_count":{},"pull_request_labels_count":{},"issue_author_associations_count":{},"pull_request_author_associations_count":{},"issue_authors":{},"pull_request_authors":{},"host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-08T00:00:17.013Z","repositories_count":10165784,"issues_count":31999265,"pull_requests_count":100269215,"authors_count":10729006,"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":{},"past_year_pull_request_author_associations_count":{},"past_year_issue_authors":{},"past_year_pull_request_authors":{},"maintainers":[],"active_maintainers":[]},"events":{"total":{"WatchEvent":6,"IssueCommentEvent":1},"last_year":{"WatchEvent":6,"IssueCommentEvent":1}},"keywords":[],"dependencies":[{"ecosystem":"cran","filepath":"DESCRIPTION","sha":null,"kind":"manifest","created_at":"2022-08-24T11:20:10.279Z","updated_at":"2022-08-24T11:20:10.279Z","repository_link":"https://github.com/alyssafrazee/ballgown/blob/master/DESCRIPTION","dependencies":[{"id":2490405577,"package_name":"R","ecosystem":"cran","requirements":"\u003e= 3.1.1","direct":true,"kind":"depends","optional":false},{"id":2490405578,"package_name":"methods","ecosystem":"cran","requirements":"*","direct":true,"kind":"depends","optional":false},{"id":2490405579,"package_name":"GenomicRanges","ecosystem":"cran","requirements":"\u003e= 1.17.25","direct":true,"kind":"imports","optional":false},{"id":2490405580,"package_name":"IRanges","ecosystem":"cran","requirements":"\u003e= 1.99.22","direct":true,"kind":"imports","optional":false},{"id":2490405581,"package_name":"S4Vectors","ecosystem":"cran","requirements":"\u003e= 0.9.39","direct":true,"kind":"imports","optional":false},{"id":2490405582,"package_name":"RColorBrewer","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":2490405583,"package_name":"splines","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":2490405584,"package_name":"sva","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":2490405585,"package_name":"limma","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":2490405586,"package_name":"rtracklayer","ecosystem":"cran","requirements":"\u003e= 1.29.25","direct":true,"kind":"imports","optional":false},{"id":2490405587,"package_name":"Biobase","ecosystem":"cran","requirements":"\u003e= 2.25.0","direct":true,"kind":"imports","optional":false},{"id":2490405588,"package_name":"GenomeInfoDb","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":2490405589,"package_name":"testthat","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":2490405590,"package_name":"knitr","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":2490405591,"package_name":"markdown","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false}]}],"score":8.473032295630468,"created_at":"2025-09-08T11:18:28.942Z","updated_at":"2025-10-07T08:24:31.546Z","avatar_url":"https://github.com/alyssafrazee.png","language":"R","category":null,"sub_category":null,"monthly_downloads":0,"funding_links":[],"readme_doi_urls":["http://dx.doi.org/10.1038/nbt.1621","http://dx.doi.org/10.1371/journal.pcbi.1003118","http://dx.doi.org/10.1073/pnas.1530509100","http://dx.doi.org/10.1186/gb-2014-15-2-r29","http://dx.doi.org/10.1186/gb-2010-11-10-r106","http://dx.doi.org/10.1101/gr.133744.111","http://dx.doi.org/10.1093/bioinformatics/btp616"],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":["bioconductor-package","genomics","bioconductor","gene","proteomics","rnaseq","derfinder","bioinformatics","mass-spectrometry","annotation-agnostic"],"project_url":"https://science.ecosyste.ms/api/v1/projects/63248","html_url":"https://science.ecosyste.ms/projects/63248"}