{"id":61341,"name":"HiCExperiment","description":"Importing and manipulating Hi-C data in R","url":"https://github.com/js2264/hicexperiment","last_synced_at":"2025-09-08T12:29:27.006Z","repository":{"id":100715603,"uuid":"564703665","full_name":"js2264/HiCExperiment","owner":"js2264","description":"Importing and manipulating Hi-C data in R","archived":false,"fork":false,"pushed_at":"2023-10-04T18:40:22.000Z","size":2161,"stargazers_count":4,"open_issues_count":0,"forks_count":1,"subscribers_count":1,"default_branch":"devel","last_synced_at":"2023-11-20T15:30:21.524Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"http://js2264.github.io/HiCExperiment/","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/js2264.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,"roadmap":null,"authors":null}},"created_at":"2022-11-11T09:51:32.000Z","updated_at":"2024-01-10T14:50:06.070Z","dependencies_parsed_at":"2023-10-04T23:59:13.937Z","dependency_job_id":null,"html_url":"https://github.com/js2264/HiCExperiment","commit_stats":{"total_commits":142,"total_committers":3,"mean_commits":"47.333333333333336","dds":0.06338028169014087,"last_synced_commit":"3232261dcb98479040848c7b959bb339922c0dd7"},"previous_names":[],"tags_count":1,"template":null,"template_full_name":null,"purl":"pkg:github/js2264/HiCExperiment","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/js2264%2FHiCExperiment","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/js2264%2FHiCExperiment/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/js2264%2FHiCExperiment/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/js2264%2FHiCExperiment/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/js2264","download_url":"https://codeload.github.com/js2264/HiCExperiment/tar.gz/refs/heads/devel","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/js2264%2FHiCExperiment/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":274184900,"owners_count":25237276,"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":"js2264","name":"Jacques Serizay","uuid":"19528818","kind":"user","description":"","email":"","website":"js2264.github.io","location":"Paris, FR","twitter":null,"company":null,"icon_url":"https://avatars.githubusercontent.com/u/19528818?u=22e1ab33edbab83ab5f8d3cf4f9f446162c4911f\u0026v=4","repositories_count":12,"last_synced_at":"2023-03-11T20:11:05.717Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/js2264","funding_links":[],"total_stars":null,"followers":null,"following":null,"created_at":"2023-02-15T05:20:34.541Z","updated_at":"2023-03-11T20:11:05.718Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/js2264","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/js2264/repositories"},"packages":[{"id":8419626,"name":"HiCExperiment","ecosystem":"bioconductor","description":"Bioconductor class for interacting with Hi-C files in R","homepage":"https://github.com/js2264/HiCExperiment ","licenses":"MIT + file LICENSE","normalized_licenses":["MIT"],"repository_url":"https://github.com/js2264/HiCExperiment","keywords_array":["DNA3DStructure","DataImport","HiC","Software"],"namespace":null,"versions_count":5,"first_release_published_at":"2023-10-12T14:38:41.280Z","latest_release_published_at":"2025-05-07T07:49:27.485Z","latest_release_number":"1.8.0","last_synced_at":"2025-08-15T10:20:01.287Z","created_at":"2023-10-12T14:38:41.054Z","updated_at":"2025-08-15T10:20:01.288Z","registry_url":"https://bioconductor.org/packages/HiCExperiment","install_command":null,"documentation_url":"https://bioconductor.org/packages/release/bioc/vignettes/HiCExperiment/inst/doc/HiCExperiment.pdf","metadata":{},"repo_metadata":{"id":100715603,"uuid":"564703665","full_name":"js2264/HiCExperiment","owner":"js2264","description":"Importing and manipulating Hi-C data in R","archived":false,"fork":false,"pushed_at":"2023-10-04T18:40:22.000Z","size":2161,"stargazers_count":4,"open_issues_count":0,"forks_count":1,"subscribers_count":1,"default_branch":"devel","last_synced_at":"2023-11-20T15:30:21.524Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"http://js2264.github.io/HiCExperiment/","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/js2264.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,"roadmap":null,"authors":null}},"created_at":"2022-11-11T09:51:32.000Z","updated_at":"2024-01-10T14:50:06.070Z","dependencies_parsed_at":"2023-10-04T23:59:13.937Z","dependency_job_id":null,"html_url":"https://github.com/js2264/HiCExperiment","commit_stats":{"total_commits":142,"total_committers":3,"mean_commits":"47.333333333333336","dds":0.06338028169014087,"last_synced_commit":"3232261dcb98479040848c7b959bb339922c0dd7"},"previous_names":[],"tags_count":1,"template":null,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/js2264%2FHiCExperiment","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/js2264%2FHiCExperiment/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/js2264%2FHiCExperiment/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/js2264%2FHiCExperiment/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/js2264","download_url":"https://codeload.github.com/js2264/HiCExperiment/tar.gz/refs/heads/devel","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":219876486,"owners_count":16554762,"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":"js2264","name":"Jacques Serizay","uuid":"19528818","kind":"user","description":"","email":"","website":"js2264.github.io","location":"Paris, FR","twitter":null,"company":null,"icon_url":"https://avatars.githubusercontent.com/u/19528818?u=22e1ab33edbab83ab5f8d3cf4f9f446162c4911f\u0026v=4","repositories_count":12,"last_synced_at":"2023-03-11T20:11:05.717Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/js2264","funding_links":[],"total_stars":null,"followers":null,"following":null,"created_at":"2023-02-15T05:20:34.541Z","updated_at":"2023-03-11T20:11:05.718Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/js2264","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/js2264/repositories"},"tags":[{"name":"0.99.9","sha":"67256361ddf73a04cf3dbb6ac4507e0ed1343713","kind":"commit","published_at":"2023-02-13T07:32:39.000Z","download_url":"https://codeload.github.com/js2264/HiCExperiment/tar.gz/0.99.9","html_url":"https://github.com/js2264/HiCExperiment/releases/tag/0.99.9","dependencies_parsed_at":null,"dependency_job_id":null,"tag_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/js2264%2FHiCExperiment/tags/0.99.9","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/js2264%2FHiCExperiment/tags/0.99.9/manifests"}]},"repo_metadata_updated_at":"2024-09-28T20:17:58.508Z","dependent_packages_count":2,"downloads":8584,"downloads_period":"total","dependent_repos_count":0,"rankings":{"downloads":95.15608180839612,"dependent_repos_count":0.0,"dependent_packages_count":0.0,"stargazers_count":null,"forks_count":null,"docker_downloads_count":null,"average":31.71869393613204},"purl":"pkg:bioconductor/HiCExperiment","advisories":[],"docker_usage_url":"https://docker.ecosyste.ms/usage/bioconductor/HiCExperiment","docker_dependents_count":null,"docker_downloads_count":null,"usage_url":"https://repos.ecosyste.ms/usage/bioconductor/HiCExperiment","dependent_repositories_url":"https://repos.ecosyste.ms/api/v1/usage/bioconductor/HiCExperiment/dependencies","status":null,"funding_links":[],"critical":null,"issue_metadata":null,"versions_url":"https://packages.ecosyste.ms/api/v1/registries/bioconductor.org/packages/HiCExperiment/versions","version_numbers_url":"https://packages.ecosyste.ms/api/v1/registries/bioconductor.org/packages/HiCExperiment/version_numbers","dependent_packages_url":"https://packages.ecosyste.ms/api/v1/registries/bioconductor.org/packages/HiCExperiment/dependent_packages","related_packages_url":"https://packages.ecosyste.ms/api/v1/registries/bioconductor.org/packages/HiCExperiment/related_packages","maintainers":[{"uuid":"jacquesserizay@gmail.com","login":null,"name":"Jacques Serizay","email":"jacquesserizay@gmail.com","url":null,"packages_count":8,"html_url":null,"role":null,"created_at":"2023-11-20T15:30:18.840Z","updated_at":"2023-11-20T15:30:18.840Z","packages_url":"https://packages.ecosyste.ms/api/v1/registries/bioconductor.org/maintainers/jacquesserizay@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":1403166,"full_name":"js2264/HiCExperiment","default_branch":"devel","committers":[{"name":"js2264","email":"jacquesserizay@gmail.com","login":null,"count":133},{"name":"cmdoret","email":"cyril.mattheydoret@gmail.com","login":null,"count":7},{"name":"J Wokaty","email":"jwokaty","login":"jwokaty","count":2}],"total_commits":142,"total_committers":3,"total_bot_commits":0,"total_bot_committers":0,"mean_commits":47.333333333333336,"dds":0.06338028169014087,"past_year_committers":[{"name":"js2264","email":"jacquesserizay@gmail.com","login":null,"count":133},{"name":"cmdoret","email":"cyril.mattheydoret@gmail.com","login":null,"count":7},{"name":"J Wokaty","email":"jwokaty","login":"jwokaty","count":2}],"past_year_total_commits":142,"past_year_total_committers":3,"past_year_total_bot_commits":0,"past_year_total_bot_committers":0,"past_year_mean_commits":47.333333333333336,"past_year_dds":0.06338028169014087,"last_synced_at":"2023-10-25T13:15:44.315Z","last_synced_commit":"3232261dcb98479040848c7b959bb339922c0dd7","created_at":"2023-10-25T13:15:41.688Z","updated_at":"2023-10-25T13:15:44.316Z","commits_url":"https://commits.ecosyste.ms/api/v1/hosts/GitHub/repositories/js2264%2FHiCExperiment/commits","host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-06T00:00:13.651Z","repositories_count":5480019,"commits_count":853389126,"contributors_count":31098155,"owners_count":906558,"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":"js2264/HiCExperiment","html_url":"https://github.com/js2264/HiCExperiment","last_synced_at":"2025-08-31T17:13:29.171Z","status":null,"issues_count":2,"pull_requests_count":0,"avg_time_to_close_issue":992.0,"avg_time_to_close_pull_request":null,"issues_closed_count":1,"pull_requests_closed_count":0,"pull_request_authors_count":0,"issue_authors_count":2,"avg_comments_per_issue":0.5,"avg_comments_per_pull_request":null,"merged_pull_requests_count":0,"bot_issues_count":0,"bot_pull_requests_count":0,"past_year_issues_count":2,"past_year_pull_requests_count":0,"past_year_avg_time_to_close_issue":992.0,"past_year_avg_time_to_close_pull_request":null,"past_year_issues_closed_count":1,"past_year_pull_requests_closed_count":0,"past_year_pull_request_authors_count":0,"past_year_issue_authors_count":2,"past_year_avg_comments_per_issue":0.5,"past_year_avg_comments_per_pull_request":null,"past_year_bot_issues_count":0,"past_year_bot_pull_requests_count":0,"past_year_merged_pull_requests_count":0,"created_at":"2025-08-30T16:10:35.649Z","updated_at":"2025-09-02T20:27:11.851Z","repository_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/js2264%2FHiCExperiment","issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/js2264%2FHiCExperiment/issues","issue_labels_count":{},"pull_request_labels_count":{},"issue_author_associations_count":{"NONE":8},"pull_request_author_associations_count":{},"issue_authors":{"ClownJay":1,"GiveHeartToU":1,"hackkr":1,"LucasMcNU":1,"Codezy99":1,"ratheraarif":1,"wangmhan":1,"xiasijian":1},"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":{"NONE":3},"past_year_pull_request_author_associations_count":{},"past_year_issue_authors":{"ClownJay":1,"GiveHeartToU":1,"xiasijian":1},"past_year_pull_request_authors":{},"maintainers":[],"active_maintainers":[]},"events":{"total":{"IssuesEvent":5,"IssueCommentEvent":14,"PushEvent":7,"ForkEvent":1},"last_year":{"IssuesEvent":5,"IssueCommentEvent":14,"PushEvent":7,"ForkEvent":1}},"keywords":[],"dependencies":[{"ecosystem":"actions","filepath":".github/workflows/rworkflows.yml","sha":null,"kind":"manifest","created_at":"2023-10-04T23:59:13.702Z","updated_at":"2023-10-04T23:59:13.702Z","repository_link":"https://github.com/js2264/HiCExperiment/blob/devel/.github/workflows/rworkflows.yml","dependencies":[{"id":14113833583,"package_name":"neurogenomics/rworkflows","ecosystem":"actions","requirements":"master","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"cran","filepath":"DESCRIPTION","sha":null,"kind":"manifest","created_at":"2023-10-04T23:59:13.725Z","updated_at":"2023-10-04T23:59:13.725Z","repository_link":"https://github.com/js2264/HiCExperiment/blob/devel/DESCRIPTION","dependencies":[{"id":14113833584,"package_name":"R","ecosystem":"cran","requirements":"\u003e= 4.2","direct":true,"kind":"depends","optional":false},{"id":14113833585,"package_name":"InteractionSet","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":14113833586,"package_name":"strawr","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":14113833589,"package_name":"GenomeInfoDb","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":14113833590,"package_name":"GenomicRanges","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":14113833591,"package_name":"IRanges","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":14113833592,"package_name":"S4Vectors","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":14113833593,"package_name":"BiocGenerics","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":14113833594,"package_name":"BiocIO","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":14113833595,"package_name":"BiocParallel","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":14113833596,"package_name":"methods","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":14113833597,"package_name":"rhdf5","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":14113833598,"package_name":"Matrix","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":14113833599,"package_name":"vroom","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":14113833600,"package_name":"dplyr","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":14113833601,"package_name":"stats","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":14113833602,"package_name":"HiContacts","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":14113833603,"package_name":"HiContactsData","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":14113833604,"package_name":"BiocFileCache","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":14113833605,"package_name":"rtracklayer","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":14113833606,"package_name":"testthat","ecosystem":"cran","requirements":"\u003e= 3.0.0","direct":true,"kind":"suggests","optional":false},{"id":14113833607,"package_name":"BiocStyle","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":14113833608,"package_name":"knitr","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":14113833609,"package_name":"rmarkdown","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false}]},{"ecosystem":"docker","filepath":"Dockerfile","sha":null,"kind":"manifest","created_at":"2023-10-04T23:59:13.923Z","updated_at":"2023-10-04T23:59:13.923Z","repository_link":"https://github.com/js2264/HiCExperiment/blob/devel/Dockerfile","dependencies":[{"id":14113833610,"package_name":"bioconductor/bioconductor_docker","ecosystem":"docker","requirements":"RELEASE_3_17","direct":true,"kind":"build","optional":false}]}],"score":11.542911360460485,"created_at":"2025-09-08T10:44:39.464Z","updated_at":"2025-10-07T08:24:02.409Z","avatar_url":"https://github.com/js2264.png","language":"R","category":null,"sub_category":null,"monthly_downloads":0,"funding_links":[],"readme_doi_urls":["https://doi.org/10.1038/s41467-024-44761-x"],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":[],"project_url":"https://science.ecosyste.ms/api/v1/projects/61341","html_url":"https://science.ecosyste.ms/projects/61341"}