{"id":61738,"name":"csdR","description":"Efficient CSD implementation in R","url":"https://github.com/almaaslab/csdr","last_synced_at":"2025-09-08T12:32:23.627Z","repository":{"id":41509242,"uuid":"310595034","full_name":"AlmaasLab/csdR","owner":"AlmaasLab","description":"Efficient CSD implementation in R","archived":false,"fork":false,"pushed_at":"2025-03-19T12:35:05.000Z","size":1829,"stargazers_count":7,"open_issues_count":0,"forks_count":1,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-03-19T13:35:11.075Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://almaaslab.github.io/csdR","language":"R","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/AlmaasLab.png","metadata":{"files":{"readme":"README.md","changelog":"NEWS.md","contributing":null,"funding":null,"license":"LICENSE.md","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":"2020-11-06T12:44:54.000Z","updated_at":"2025-03-19T12:27:18.000Z","dependencies_parsed_at":"2025-03-19T13:40:26.585Z","dependency_job_id":null,"html_url":"https://github.com/AlmaasLab/csdR","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/AlmaasLab/csdR","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AlmaasLab%2FcsdR","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AlmaasLab%2FcsdR/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AlmaasLab%2FcsdR/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AlmaasLab%2FcsdR/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/AlmaasLab","download_url":"https://codeload.github.com/AlmaasLab/csdR/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AlmaasLab%2FcsdR/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":274174106,"owners_count":25235202,"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":"AlmaasLab","name":"AlmaasLab","uuid":"62121167","kind":"organization","description":"Network Systems Biology","email":"eivind.almaas@ntnu.no","website":"http://www.ntnu.edu/almaaslab","location":"Trondheim, Norway","twitter":null,"company":null,"icon_url":"https://avatars.githubusercontent.com/u/62121167?v=4","repositories_count":4,"last_synced_at":"2023-03-05T21:04:09.648Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/AlmaasLab","funding_links":[],"total_stars":null,"followers":null,"following":null,"created_at":"2022-11-15T22:51:34.073Z","updated_at":"2023-03-05T21:04:09.672Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/AlmaasLab","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/AlmaasLab/repositories"},"packages":[{"id":8419138,"name":"csdR","ecosystem":"bioconductor","description":"Differential gene co-expression","homepage":"https://almaaslab.github.io/csdR https://github.com/AlmaasLab/csdR ","licenses":"GPL-3","normalized_licenses":["GPL-3.0"],"repository_url":"https://github.com/almaaslab/csdR","keywords_array":["DifferentialExpression","GeneExpression","GraphAndNetwork","Network","Software"],"namespace":null,"versions_count":5,"first_release_published_at":"2023-10-12T14:27:48.134Z","latest_release_published_at":"2025-04-28T16:20:13.086Z","latest_release_number":"1.14.0","last_synced_at":"2025-08-28T20:45:09.122Z","created_at":"2023-10-12T14:27:47.754Z","updated_at":"2025-08-28T20:45:09.123Z","registry_url":"https://bioconductor.org/packages/csdR","install_command":null,"documentation_url":"https://bioconductor.org/packages/release/bioc/vignettes/csdR/inst/doc/csdR.pdf","metadata":{},"repo_metadata":{"id":41509242,"uuid":"310595034","full_name":"AlmaasLab/csdR","owner":"AlmaasLab","description":"Efficient CSD implementation in R","archived":false,"fork":false,"pushed_at":"2022-11-24T13:26:52.000Z","size":1948,"stargazers_count":6,"open_issues_count":3,"forks_count":1,"subscribers_count":3,"default_branch":"main","last_synced_at":"2024-08-22T00:59:13.361Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://almaaslab.github.io/csdR","language":"R","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/AlmaasLab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.md","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2020-11-06T12:44:54.000Z","updated_at":"2024-08-22T00:59:13.362Z","dependencies_parsed_at":"2023-01-21T16:04:01.201Z","dependency_job_id":null,"html_url":"https://github.com/AlmaasLab/csdR","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AlmaasLab%2FcsdR","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AlmaasLab%2FcsdR/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AlmaasLab%2FcsdR/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AlmaasLab%2FcsdR/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/AlmaasLab","download_url":"https://codeload.github.com/AlmaasLab/csdR/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":219865573,"owners_count":16554160,"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","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_record":{"login":"AlmaasLab","name":"AlmaasLab","uuid":"62121167","kind":"organization","description":"Network Systems Biology","email":"eivind.almaas@ntnu.no","website":"http://www.ntnu.edu/almaaslab","location":"Trondheim, Norway","twitter":null,"company":null,"icon_url":"https://avatars.githubusercontent.com/u/62121167?v=4","repositories_count":4,"last_synced_at":"2023-03-05T21:04:09.648Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/AlmaasLab","funding_links":[],"total_stars":null,"followers":null,"following":null,"created_at":"2022-11-15T22:51:34.073Z","updated_at":"2023-03-05T21:04:09.672Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/AlmaasLab","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/AlmaasLab/repositories"},"tags":[]},"repo_metadata_updated_at":"2024-09-21T23:20:05.679Z","dependent_packages_count":0,"downloads":6295,"downloads_period":"total","dependent_repos_count":0,"rankings":{"downloads":86.82505399568035,"dependent_repos_count":0.0,"dependent_packages_count":0.0,"stargazers_count":null,"forks_count":null,"docker_downloads_count":null,"average":28.941684665226784},"purl":"pkg:bioconductor/csdR","advisories":[],"docker_usage_url":"https://docker.ecosyste.ms/usage/bioconductor/csdR","docker_dependents_count":null,"docker_downloads_count":null,"usage_url":"https://repos.ecosyste.ms/usage/bioconductor/csdR","dependent_repositories_url":"https://repos.ecosyste.ms/api/v1/usage/bioconductor/csdR/dependencies","status":null,"funding_links":[],"critical":null,"issue_metadata":null,"versions_url":"https://packages.ecosyste.ms/api/v1/registries/bioconductor.org/packages/csdR/versions","version_numbers_url":"https://packages.ecosyste.ms/api/v1/registries/bioconductor.org/packages/csdR/version_numbers","dependent_packages_url":"https://packages.ecosyste.ms/api/v1/registries/bioconductor.org/packages/csdR/dependent_packages","related_packages_url":"https://packages.ecosyste.ms/api/v1/registries/bioconductor.org/packages/csdR/related_packages","maintainers":[{"uuid":"jakobpeder.pettersen@gmail.com","login":null,"name":"Jakob Peder Pettersen","email":"jakobpeder.pettersen@gmail.com","url":null,"packages_count":1,"html_url":null,"role":null,"created_at":"2023-11-20T10:41:04.734Z","updated_at":"2023-11-20T10:41:04.734Z","packages_url":"https://packages.ecosyste.ms/api/v1/registries/bioconductor.org/maintainers/jakobpeder.pettersen@gmail.com/packages"}],"registry":{"name":"bioconductor.org","url":"https://bioconductor.org","ecosystem":"bioconductor","default":true,"packages_count":2505,"maintainers_count":3164,"namespaces_count":0,"keywords_count":1086,"github":"Bioconductor","metadata":{"funded_packages_count":3},"icon_url":"https://github.com/Bioconductor.png","created_at":"2023-10-12T14:09:56.428Z","updated_at":"2025-09-08T06:51:28.460Z","packages_url":"https://packages.ecosyste.ms/api/v1/registries/bioconductor.org/packages","maintainers_url":"https://packages.ecosyste.ms/api/v1/registries/bioconductor.org/maintainers","namespaces_url":"https://packages.ecosyste.ms/api/v1/registries/bioconductor.org/namespaces"}}],"commits":{"id":1403155,"full_name":"almaaslab/csdR","default_branch":"main","committers":[{"name":"Jakob Peder Pettersen","email":"jakobpeder.pettersen@gmail.com","login":null,"count":34},{"name":"Nitesh Turaga","email":"nitesh.turaga@gmail.com","login":null,"count":4},{"name":"J Wokaty","email":"jennifer.wokaty@sph.cuny.edu","login":null,"count":2}],"total_commits":40,"total_committers":3,"total_bot_commits":0,"total_bot_committers":0,"mean_commits":13.333333333333334,"dds":0.15000000000000002,"past_year_committers":[{"name":"J Wokaty","email":"jennifer.wokaty@sph.cuny.edu","login":null,"count":2},{"name":"Jakob Peder Pettersen","email":"jakobpeder.pettersen@gmail.com","login":null,"count":2}],"past_year_total_commits":4,"past_year_total_committers":2,"past_year_total_bot_commits":0,"past_year_total_bot_committers":0,"past_year_mean_commits":2.0,"past_year_dds":0.5,"last_synced_at":"2023-10-25T13:15:44.107Z","last_synced_commit":"6fc4bf9a9c54cb20998732c2d7470b2ce47eddbf","created_at":"2023-10-25T13:15:40.473Z","updated_at":"2023-10-25T13:15:44.107Z","commits_url":"https://commits.ecosyste.ms/api/v1/hosts/GitHub/repositories/almaaslab%2FcsdR/commits","host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-08T00:00:16.827Z","repositories_count":5481641,"commits_count":853635064,"contributors_count":31099484,"owners_count":907162,"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":"AlmaasLab/csdR","html_url":"https://github.com/AlmaasLab/csdR","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":"2025-08-30T20:59:16.270Z","updated_at":"2025-08-30T20:59:16.270Z","repository_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/AlmaasLab%2FcsdR","issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/AlmaasLab%2FcsdR/issues","issue_labels_count":{},"pull_request_labels_count":{},"issue_author_associations_count":{"NONE":3},"pull_request_author_associations_count":{},"issue_authors":{"mdmanurung":1,"GettyScience":1,"iorilondon":1},"pull_request_authors":{},"host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-08T00:00:17.013Z","repositories_count":10164087,"issues_count":31988492,"pull_requests_count":100218704,"authors_count":10728235,"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":{"IssuesEvent":3,"WatchEvent":1,"PushEvent":8},"last_year":{"IssuesEvent":3,"WatchEvent":1,"PushEvent":8}},"keywords":[],"dependencies":[{"ecosystem":"cran","filepath":"DESCRIPTION","sha":null,"kind":"manifest","created_at":"2022-09-21T11:14:01.044Z","updated_at":"2022-09-21T11:14:01.044Z","repository_link":"https://github.com/AlmaasLab/csdR/blob/main/DESCRIPTION","dependencies":[{"id":5723390080,"package_name":"R","ecosystem":"cran","requirements":"\u003e= 4.1.0","direct":true,"kind":"depends","optional":false},{"id":5723390081,"package_name":"WGCNA","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":5723390082,"package_name":"glue","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":5723390083,"package_name":"RhpcBLASctl","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":5723390084,"package_name":"matrixStats","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":5723390085,"package_name":"Rcpp","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":5723390086,"package_name":"rmarkdown","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":5723390087,"package_name":"knitr","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":5723390088,"package_name":"testthat","ecosystem":"cran","requirements":"\u003e= 3.0.0","direct":true,"kind":"suggests","optional":false},{"id":5723390089,"package_name":"BiocStyle","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":5723390090,"package_name":"magrittr","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":5723390091,"package_name":"igraph","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":5723390092,"package_name":"dplyr","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/pkgdown.yaml","sha":null,"kind":"manifest","created_at":"2023-01-21T16:04:01.181Z","updated_at":"2023-01-21T16:04:01.181Z","repository_link":"https://github.com/AlmaasLab/csdR/blob/main/.github/workflows/pkgdown.yaml","dependencies":[{"id":7080601621,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":7080601622,"package_name":"r-lib/actions/setup-r","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":7080601623,"package_name":"r-lib/actions/setup-pandoc","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":7080601624,"package_name":"actions/cache","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false}]}],"score":11.792192227820662,"created_at":"2025-09-08T10:46:26.682Z","updated_at":"2025-10-07T08:24:10.698Z","avatar_url":"https://github.com/AlmaasLab.png","language":"R","category":null,"sub_category":null,"monthly_downloads":0,"funding_links":[],"readme_doi_urls":["https://doi.org/10.1186/s12859-022-04605-1"],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":["bioconductor-package","gene","genomics","sequencing","ontology","grna-sequence","proteomics"],"project_url":"https://science.ecosyste.ms/api/v1/projects/61738","html_url":"https://science.ecosyste.ms/projects/61738"}