{"id":66952,"name":"HiCcompare","description":"Joint normalization of two Hi-C matrices, visualization and detection of differential chromatin interactions. See multiHiCcompare for the analysis of multiple Hi-C matrices","url":"https://github.com/dozmorovlab/hiccompare","last_synced_at":"2025-09-08T13:47:16.705Z","repository":{"id":133391853,"uuid":"95918953","full_name":"dozmorovlab/HiCcompare","owner":"dozmorovlab","description":"Joint normalization of two Hi-C matrices, visualization and detection of differential chromatin interactions. See multiHiCcompare for the analysis of multiple Hi-C matrices","archived":false,"fork":false,"pushed_at":"2023-06-04T01:46:52.000Z","size":86860,"stargazers_count":15,"open_issues_count":1,"forks_count":3,"subscribers_count":3,"default_branch":"master","last_synced_at":"2024-04-26T14:05:35.329Z","etag":null,"topics":["difference-detection","hi-c","hic","normalization","visualization"],"latest_commit_sha":null,"homepage":"https://dozmorovlab.github.io/HiCcompare/","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":"2017-06-30T19:44:45.000Z","updated_at":"2024-03-12T09:51:13.000Z","dependencies_parsed_at":"2023-06-13T08:30:46.005Z","dependency_job_id":null,"html_url":"https://github.com/dozmorovlab/HiCcompare","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/dozmorovlab/HiCcompare","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dozmorovlab%2FHiCcompare","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dozmorovlab%2FHiCcompare/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dozmorovlab%2FHiCcompare/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dozmorovlab%2FHiCcompare/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/dozmorovlab","download_url":"https://codeload.github.com/dozmorovlab/HiCcompare/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dozmorovlab%2FHiCcompare/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":274195572,"owners_count":25239147,"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":8419623,"name":"HiCcompare","ecosystem":"bioconductor","description":"HiCcompare: Joint normalization and comparative analysis of multiple Hi-C datasets","homepage":"https://github.com/dozmorovlab/HiCcompare ","licenses":"MIT + file LICENSE","normalized_licenses":["MIT"],"repository_url":"https://github.com/dozmorovlab/HiCcompare","keywords_array":["HiC","Normalization","Sequencing","Software"],"namespace":null,"versions_count":5,"first_release_published_at":"2023-10-12T14:38:36.830Z","latest_release_published_at":"2025-04-21T04:01:39.785Z","latest_release_number":"1.30.0","last_synced_at":"2025-08-28T21:00:29.200Z","created_at":"2023-10-12T14:38:35.474Z","updated_at":"2025-08-28T21:00:29.200Z","registry_url":"https://bioconductor.org/packages/HiCcompare","install_command":null,"documentation_url":"https://bioconductor.org/packages/release/bioc/vignettes/HiCcompare/inst/doc/HiCcompare.pdf","metadata":{},"repo_metadata":{"id":133391853,"uuid":"95918953","full_name":"dozmorovlab/HiCcompare","owner":"dozmorovlab","description":"Joint normalization of two Hi-C matrices, visualization and detection of differential chromatin interactions. See multiHiCcompare for the analysis of multiple Hi-C matrices","archived":false,"fork":false,"pushed_at":"2023-06-04T01:46:52.000Z","size":86860,"stargazers_count":15,"open_issues_count":1,"forks_count":3,"subscribers_count":3,"default_branch":"master","last_synced_at":"2024-04-26T14:05:35.329Z","etag":null,"topics":["difference-detection","hi-c","hic","normalization","visualization"],"latest_commit_sha":null,"homepage":"https://dozmorovlab.github.io/HiCcompare/","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":"2017-06-30T19:44:45.000Z","updated_at":"2024-03-12T09:51:13.000Z","dependencies_parsed_at":"2023-06-13T08:30:46.005Z","dependency_job_id":null,"html_url":"https://github.com/dozmorovlab/HiCcompare","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/dozmorovlab%2FHiCcompare","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dozmorovlab%2FHiCcompare/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dozmorovlab%2FHiCcompare/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dozmorovlab%2FHiCcompare/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/dozmorovlab","download_url":"https://codeload.github.com/dozmorovlab/HiCcompare/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":219869867,"owners_count":16555205,"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":"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":"2024-10-04T09:06:36.185Z","dependent_packages_count":3,"downloads":28409,"downloads_period":"total","dependent_repos_count":0,"rankings":{"downloads":44.81641468682505,"dependent_repos_count":0.0,"dependent_packages_count":0.0,"stargazers_count":null,"forks_count":null,"docker_downloads_count":null,"average":14.93880489560835},"purl":"pkg:bioconductor/HiCcompare","advisories":[],"docker_usage_url":"https://docker.ecosyste.ms/usage/bioconductor/HiCcompare","docker_dependents_count":null,"docker_downloads_count":null,"usage_url":"https://repos.ecosyste.ms/usage/bioconductor/HiCcompare","dependent_repositories_url":"https://repos.ecosyste.ms/api/v1/usage/bioconductor/HiCcompare/dependencies","status":null,"funding_links":[],"critical":null,"issue_metadata":null,"versions_url":"https://packages.ecosyste.ms/api/v1/registries/bioconductor.org/packages/HiCcompare/versions","version_numbers_url":"https://packages.ecosyste.ms/api/v1/registries/bioconductor.org/packages/HiCcompare/version_numbers","dependent_packages_url":"https://packages.ecosyste.ms/api/v1/registries/bioconductor.org/packages/HiCcompare/dependent_packages","related_packages_url":"https://packages.ecosyste.ms/api/v1/registries/bioconductor.org/packages/HiCcompare/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":"2023-11-25T14:03:58.609Z","updated_at":"2023-11-25T14:03:58.609Z","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":1402964,"full_name":"dozmorovlab/HiCcompare","default_branch":"master","committers":[{"name":"jstansfield0","email":"stansfieldjc@vcu.edu","login":null,"count":151},{"name":"Nitesh Turaga","email":"nitesh.turaga@gmail.com","login":null,"count":14},{"name":"Mikhail Dozmorov","email":"mikhail.dozmorov@gmail.com","login":null,"count":12},{"name":"Hervé Pagès","email":"hpages@fredhutch.org","login":null,"count":3},{"name":"J Wokaty","email":"jennifer.wokaty@sph.cuny.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":"J Wokaty","email":"jwokaty","login":"jwokaty","count":2},{"name":"Hervé Pagès","email":"hpages.on.github@gmail.com","login":null,"count":1},{"name":"cresswellkg","email":"cresswellkg@vcu.edu","login":null,"count":1},{"name":"LiNk-NY","email":"mramos09@gmail.com","login":null,"count":1},{"name":"Martin Morgan","email":"mtmorgan@fhcrc.org","login":null,"count":1}],"total_commits":192,"total_committers":12,"total_bot_commits":0,"total_bot_committers":0,"mean_commits":16.0,"dds":0.21354166666666663,"past_year_committers":[{"name":"Mikhail Dozmorov","email":"mikhail.dozmorov@gmail.com","login":null,"count":4},{"name":"J Wokaty","email":"jennifer.wokaty@sph.cuny.edu","login":null,"count":2},{"name":"J Wokaty","email":"jwokaty","login":"jwokaty","count":2}],"past_year_total_commits":8,"past_year_total_committers":3,"past_year_total_bot_commits":0,"past_year_total_bot_committers":0,"past_year_mean_commits":2.6666666666666665,"past_year_dds":0.5,"last_synced_at":"2023-10-25T13:04:32.505Z","last_synced_commit":"310a927372e836fdd0438452e4790d4d2a611c1b","created_at":"2023-10-25T13:04:16.292Z","updated_at":"2023-10-25T13:04:32.506Z","commits_url":"https://commits.ecosyste.ms/api/v1/hosts/GitHub/repositories/dozmorovlab%2FHiCcompare/commits","host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-08T00:00:16.827Z","repositories_count":5484000,"commits_count":854343132,"contributors_count":31144857,"owners_count":908866,"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/HiCcompare","html_url":"https://github.com/dozmorovlab/HiCcompare","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":"2025-09-01T01:28:07.174Z","updated_at":"2025-09-02T09:19:53.019Z","repository_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/dozmorovlab%2FHiCcompare","issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/dozmorovlab%2FHiCcompare/issues","issue_labels_count":{},"pull_request_labels_count":{},"issue_author_associations_count":{"NONE":2},"pull_request_author_associations_count":{},"issue_authors":{"xs254":1,"ashishjain1988":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":{"xs254":1},"past_year_pull_request_authors":{},"maintainers":[],"active_maintainers":[]},"events":{"total":{"WatchEvent":4,"IssueCommentEvent":4},"last_year":{"WatchEvent":4,"IssueCommentEvent":4}},"keywords":["difference-detection","hi-c","hic","normalization","visualization"],"dependencies":[{"ecosystem":"cran","filepath":"DESCRIPTION","sha":null,"kind":"manifest","created_at":"2023-06-13T08:30:45.954Z","updated_at":"2023-06-13T08:30:45.954Z","repository_link":"https://github.com/dozmorovlab/HiCcompare/blob/master/DESCRIPTION","dependencies":[{"id":10640517181,"package_name":"R","ecosystem":"cran","requirements":"\u003e= 3.4.0","direct":true,"kind":"depends","optional":false},{"id":10640517182,"package_name":"dplyr","ecosystem":"cran","requirements":"*","direct":true,"kind":"depends","optional":false},{"id":10640517183,"package_name":"data.table","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":10640517184,"package_name":"ggplot2","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":10640517185,"package_name":"gridExtra","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":10640517186,"package_name":"mgcv","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":10640517187,"package_name":"stats","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":10640517188,"package_name":"InteractionSet","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":10640517189,"package_name":"GenomicRanges","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":10640517192,"package_name":"IRanges","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":10640517193,"package_name":"S4Vectors","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":10640517194,"package_name":"BiocParallel","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":10640517195,"package_name":"KernSmooth","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":10640517196,"package_name":"methods","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":10640517197,"package_name":"utils","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":10640517198,"package_name":"graphics","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":10640517199,"package_name":"pheatmap","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":10640517200,"package_name":"gtools","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":10640517201,"package_name":"rhdf5","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":10640517202,"package_name":"knitr","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":10640517203,"package_name":"rmarkdown","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":10640517204,"package_name":"testthat","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":10640517205,"package_name":"multiHiCcompare","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false}]}],"score":15.512097437921993,"created_at":"2025-09-08T11:18:44.978Z","updated_at":"2025-10-07T08:25:17.651Z","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/s12859-018-2288-x","https://doi.org/10.1101/147850","https://doi.org/10.1002/cpbi.76"],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":["bioconductor-package","gene","genomics","transcriptomics","proteomics","rna-seq","tumor-heterogeneity","tumor-mutational-burden","tumor-purity","core-package"],"project_url":"https://science.ecosyste.ms/api/v1/projects/66952","html_url":"https://science.ecosyste.ms/projects/66952"}