{"id":66636,"name":"SpectralTAD","description":"TAD Calling using spectral clustering in R","url":"https://github.com/dozmorovlab/spectraltad","last_synced_at":"2025-09-08T13:42:26.088Z","repository":{"id":133391950,"uuid":"169597214","full_name":"dozmorovlab/SpectralTAD","owner":"dozmorovlab","description":"TAD Calling using spectral clustering in R","archived":false,"fork":false,"pushed_at":"2023-08-29T14:04:21.000Z","size":1610,"stargazers_count":11,"open_issues_count":2,"forks_count":3,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-08-19T00:01:34.673Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://dozmorovlab.github.io/SpectralTAD/","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/dozmorovlab.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":"2019-02-07T15:51:08.000Z","updated_at":"2025-07-29T13:58:32.000Z","dependencies_parsed_at":null,"dependency_job_id":"283a3717-44ee-49f9-8adb-f8ee282a894d","html_url":"https://github.com/dozmorovlab/SpectralTAD","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/dozmorovlab/SpectralTAD","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dozmorovlab%2FSpectralTAD","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dozmorovlab%2FSpectralTAD/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dozmorovlab%2FSpectralTAD/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dozmorovlab%2FSpectralTAD/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/dozmorovlab","download_url":"https://codeload.github.com/dozmorovlab/SpectralTAD/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dozmorovlab%2FSpectralTAD/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":274195190,"owners_count":25239146,"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":"dozmorovlab","name":"Dozmorov Lab","uuid":"26965156","kind":"organization","description":"Genomics, bionformatics, computational biology, 3D genome, Hi-C","email":null,"website":"https://dozmorovlab.github.io/","location":null,"twitter":"mikhaildozmorov","company":null,"icon_url":"https://avatars.githubusercontent.com/u/26965156?v=4","repositories_count":5,"last_synced_at":"2023-03-10T04:01:17.269Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/dozmorovlab","funding_links":[],"total_stars":null,"followers":null,"following":null,"created_at":"2022-11-19T22:02:50.598Z","updated_at":"2023-03-10T04:01:17.276Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/dozmorovlab","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/dozmorovlab/repositories"},"packages":[{"id":8420777,"name":"SpectralTAD","ecosystem":"bioconductor","description":"SpectralTAD: Hierarchical TAD detection using spectral clustering","homepage":"https://github.com/dozmorovlab/SpectralTAD ","licenses":"MIT + file LICENSE","normalized_licenses":["MIT"],"repository_url":"https://github.com/dozmorovlab/SpectralTAD","keywords_array":["Clustering","FeatureExtraction","HiC","Sequencing","Software"],"namespace":null,"versions_count":5,"first_release_published_at":"2023-10-12T15:02:14.238Z","latest_release_published_at":"2025-05-13T02:19:09.382Z","latest_release_number":"1.24.0","last_synced_at":"2025-08-18T23:45:55.879Z","created_at":"2023-10-12T15:02:13.911Z","updated_at":"2025-08-19T00:11:51.479Z","registry_url":"https://bioconductor.org/packages/SpectralTAD","install_command":null,"documentation_url":"https://bioconductor.org/packages/release/bioc/vignettes/SpectralTAD/inst/doc/SpectralTAD.pdf","metadata":{},"repo_metadata":{"id":133391950,"uuid":"169597214","full_name":"dozmorovlab/SpectralTAD","owner":"dozmorovlab","description":"TAD Calling using spectral clustering in R","archived":false,"fork":false,"pushed_at":"2023-08-29T14:04:21.000Z","size":1610,"stargazers_count":10,"open_issues_count":2,"forks_count":3,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-06-14T14:03:01.001Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://dozmorovlab.github.io/SpectralTAD/","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/dozmorovlab.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":"2019-02-07T15:51:08.000Z","updated_at":"2025-05-31T23:05:55.000Z","dependencies_parsed_at":null,"dependency_job_id":"283a3717-44ee-49f9-8adb-f8ee282a894d","html_url":"https://github.com/dozmorovlab/SpectralTAD","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/dozmorovlab/SpectralTAD","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dozmorovlab%2FSpectralTAD","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dozmorovlab%2FSpectralTAD/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dozmorovlab%2FSpectralTAD/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dozmorovlab%2FSpectralTAD/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/dozmorovlab","download_url":"https://codeload.github.com/dozmorovlab/SpectralTAD/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dozmorovlab%2FSpectralTAD/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":271077942,"owners_count":24695466,"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":"2025-08-18T02:00:08.743Z","response_time":89,"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_record":{"login":"dozmorovlab","name":"Dozmorov Lab","uuid":"26965156","kind":"organization","description":"Genomics, bionformatics, computational biology, 3D genome, Hi-C","email":null,"website":"https://dozmorovlab.github.io/","location":null,"twitter":"mikhaildozmorov","company":null,"icon_url":"https://avatars.githubusercontent.com/u/26965156?v=4","repositories_count":5,"last_synced_at":"2023-03-10T04:01:17.269Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/dozmorovlab","funding_links":[],"total_stars":null,"followers":null,"following":null,"created_at":"2022-11-19T22:02:50.598Z","updated_at":"2023-03-10T04:01:17.276Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/dozmorovlab","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/dozmorovlab/repositories"},"tags":[]},"repo_metadata_updated_at":"2025-08-19T00:11:51.478Z","dependent_packages_count":1,"downloads":12197,"downloads_period":"total","dependent_repos_count":0,"rankings":{"downloads":66.72645739910314,"dependent_repos_count":0.0,"dependent_packages_count":19.86547085201794,"stargazers_count":14.885496183206106,"forks_count":14.440433212996389,"docker_downloads_count":null,"average":23.183571529464714},"purl":"pkg:bioconductor/SpectralTAD","advisories":[],"docker_usage_url":"https://docker.ecosyste.ms/usage/bioconductor/SpectralTAD","docker_dependents_count":null,"docker_downloads_count":null,"usage_url":"https://repos.ecosyste.ms/usage/bioconductor/SpectralTAD","dependent_repositories_url":"https://repos.ecosyste.ms/api/v1/usage/bioconductor/SpectralTAD/dependencies","status":null,"funding_links":[],"critical":null,"issue_metadata":null,"versions_url":"https://packages.ecosyste.ms/api/v1/registries/bioconductor.org/packages/SpectralTAD/versions","version_numbers_url":"https://packages.ecosyste.ms/api/v1/registries/bioconductor.org/packages/SpectralTAD/version_numbers","dependent_packages_url":"https://packages.ecosyste.ms/api/v1/registries/bioconductor.org/packages/SpectralTAD/dependent_packages","related_packages_url":"https://packages.ecosyste.ms/api/v1/registries/bioconductor.org/packages/SpectralTAD/related_packages","maintainers":[{"uuid":"mikhail.dozmorov@gmail.com","login":null,"name":"Mikhail Dozmorov","email":"mikhail.dozmorov@gmail.com","url":null,"packages_count":5,"html_url":null,"role":null,"created_at":"2023-11-25T14:30:15.603Z","updated_at":"2023-11-25T14:30:15.603Z","packages_url":"https://packages.ecosyste.ms/api/v1/registries/bioconductor.org/maintainers/mikhail.dozmorov@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":1403485,"full_name":"dozmorovlab/SpectralTAD","default_branch":"master","committers":[{"name":"cresswellkg","email":"cresswellkg@vcu.edu","login":null,"count":102},{"name":"Mikhail Dozmorov","email":"mikhail.dozmorov@gmail.com","login":null,"count":39},{"name":"Nitesh Turaga","email":"nitesh.turaga@gmail.com","login":null,"count":14},{"name":"jstansfield0","email":"stansfieldjc@vcu.edu","login":null,"count":3},{"name":"J Wokaty","email":"jennifer.wokaty@sph.cuny.edu","login":null,"count":2},{"name":"anastasiya-pendragon","email":"102726974+anastasiya-pendragon","login":"anastasiya-pendragon","count":1},{"name":"J Wokaty","email":"jwokaty","login":"jwokaty","count":1},{"name":"Steve Pederson","email":"steveped","login":"steveped","count":1}],"total_commits":163,"total_committers":8,"total_bot_commits":0,"total_bot_committers":0,"mean_commits":20.375,"dds":0.3742331288343558,"past_year_committers":[{"name":"Mikhail Dozmorov","email":"mikhail.dozmorov@gmail.com","login":null,"count":8},{"name":"J Wokaty","email":"jennifer.wokaty@sph.cuny.edu","login":null,"count":2},{"name":"J Wokaty","email":"jwokaty","login":"jwokaty","count":1},{"name":"anastasiya-pendragon","email":"102726974+anastasiya-pendragon","login":"anastasiya-pendragon","count":1}],"past_year_total_commits":12,"past_year_total_committers":4,"past_year_total_bot_commits":0,"past_year_total_bot_committers":0,"past_year_mean_commits":3.0,"past_year_dds":0.33333333333333337,"last_synced_at":"2023-10-25T13:17:17.928Z","last_synced_commit":"3516632dcda11302ee8e5a58762ad234a1d582e5","created_at":"2023-10-25T13:16:13.179Z","updated_at":"2023-10-25T13:17:17.928Z","commits_url":"https://commits.ecosyste.ms/api/v1/hosts/GitHub/repositories/dozmorovlab%2FSpectralTAD/commits","host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-08T00:00:16.827Z","repositories_count":5483952,"commits_count":854322234,"contributors_count":31144137,"owners_count":908840,"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":"dozmorovlab/SpectralTAD","html_url":"https://github.com/dozmorovlab/SpectralTAD","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":"2025-08-30T19:34:20.141Z","updated_at":"2025-09-02T01:36:57.600Z","repository_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/dozmorovlab%2FSpectralTAD","issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/dozmorovlab%2FSpectralTAD/issues","issue_labels_count":{},"pull_request_labels_count":{},"issue_author_associations_count":{"NONE":3},"pull_request_author_associations_count":{},"issue_authors":{"gorliver":1,"QiliShi":1,"Naveen-Ahuja":1},"pull_request_authors":{},"host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-08T00:00:17.013Z","repositories_count":10166699,"issues_count":32013288,"pull_requests_count":100268859,"authors_count":10729412,"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":1},"past_year_pull_request_author_associations_count":{},"past_year_issue_authors":{"QiliShi":1},"past_year_pull_request_authors":{},"maintainers":[],"active_maintainers":[]},"events":{"total":{"IssuesEvent":2,"WatchEvent":1,"IssueCommentEvent":5},"last_year":{"IssuesEvent":2,"WatchEvent":1,"IssueCommentEvent":5}},"keywords":[],"dependencies":[],"score":14.05350015929011,"created_at":"2025-09-08T11:18:43.510Z","updated_at":"2025-10-07T08:25:13.154Z","avatar_url":"https://github.com/dozmorovlab.png","language":"R","category":null,"sub_category":null,"monthly_downloads":0,"funding_links":[],"readme_doi_urls":["https://doi.org/10.1186/s12859-020-03652-w"],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":["bioconductor-package","grna-sequence","immune-repertoire","gene","transcriptomics","ontology","sequencing","genomics","proteomics","recount3"],"project_url":"https://science.ecosyste.ms/api/v1/projects/66636","html_url":"https://science.ecosyste.ms/projects/66636"}