{"id":73301,"name":"spatopic","description":"An R package for fast topic inference to identify tissue architecture in multiplexed images","url":"https://github.com/xiyupeng/spatopic","last_synced_at":"2025-09-08T16:00:51.732Z","repository":{"id":212188461,"uuid":"727882930","full_name":"xiyupeng/SpaTopic","owner":"xiyupeng","description":"An R package for fast topic inference to identify tissue architecture in multiplexed images","archived":false,"fork":false,"pushed_at":"2025-07-20T15:11:42.000Z","size":70424,"stargazers_count":11,"open_issues_count":0,"forks_count":2,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-08-24T19:01:37.525Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://xiyupeng.github.io/SpaTopic/","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/xiyupeng.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,"zenodo":null}},"created_at":"2023-12-05T19:15:43.000Z","updated_at":"2025-08-22T00:43:35.000Z","dependencies_parsed_at":null,"dependency_job_id":"3e75a889-5c14-4f93-9e2d-dc214c35a7f0","html_url":"https://github.com/xiyupeng/SpaTopic","commit_stats":null,"previous_names":["xiyupeng/spatopic"],"tags_count":3,"template":false,"template_full_name":null,"purl":"pkg:github/xiyupeng/SpaTopic","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/xiyupeng%2FSpaTopic","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/xiyupeng%2FSpaTopic/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/xiyupeng%2FSpaTopic/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/xiyupeng%2FSpaTopic/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/xiyupeng","download_url":"https://codeload.github.com/xiyupeng/SpaTopic/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/xiyupeng%2FSpaTopic/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":274210575,"owners_count":25241790,"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":"xiyupeng","name":"Xiyu","uuid":"23034624","kind":"user","description":"interested in bioinformatics and computational biology","email":"","website":"https://sites.google.com/view/xiyupeng/home","location":"New York","twitter":null,"company":"Memorial Sloan Kettering Cancer Center","icon_url":"https://avatars.githubusercontent.com/u/23034624?v=4","repositories_count":1,"last_synced_at":"2023-04-28T13:48:58.555Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/xiyupeng","funding_links":[],"total_stars":null,"followers":null,"following":null,"created_at":"2023-04-28T13:48:58.567Z","updated_at":"2023-04-28T13:48:58.567Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/xiyupeng","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/xiyupeng/repositories"},"packages":[{"id":8759575,"name":"SpaTopic","ecosystem":"cran","description":"Topic Inference to Identify Tissue Architecture in Multiplexed\nImages","homepage":"https://github.com/xiyupeng/SpaTopic","licenses":"GPL (≥ 3)","normalized_licenses":["CNRI-Python-GPL-Compatible"],"repository_url":"https://github.com/xiyupeng/SpaTopic","keywords_array":[],"namespace":null,"versions_count":3,"first_release_published_at":"2024-01-17T00:00:00.000Z","latest_release_published_at":"2025-03-03T00:00:00.000Z","latest_release_number":"1.2.0","last_synced_at":"2025-08-24T14:49:44.036Z","created_at":"2024-01-17T18:50:32.391Z","updated_at":"2025-08-24T23:07:42.851Z","registry_url":"https://cran.r-project.org/package=SpaTopic","install_command":null,"documentation_url":"http://cran.r-project.org/web/packages/SpaTopic/SpaTopic.pdf","metadata":{},"repo_metadata":{"id":212188461,"uuid":"727882930","full_name":"xiyupeng/SpaTopic","owner":"xiyupeng","description":"An R package for fast topic inference to identify tissue architecture in multiplexed images","archived":false,"fork":false,"pushed_at":"2025-07-20T15:11:42.000Z","size":70424,"stargazers_count":11,"open_issues_count":0,"forks_count":2,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-08-24T19:01:37.525Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://xiyupeng.github.io/SpaTopic/","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/xiyupeng.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,"zenodo":null}},"created_at":"2023-12-05T19:15:43.000Z","updated_at":"2025-08-22T00:43:35.000Z","dependencies_parsed_at":null,"dependency_job_id":"3e75a889-5c14-4f93-9e2d-dc214c35a7f0","html_url":"https://github.com/xiyupeng/SpaTopic","commit_stats":null,"previous_names":["xiyupeng/spatopic"],"tags_count":3,"template":false,"template_full_name":null,"purl":"pkg:github/xiyupeng/SpaTopic","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/xiyupeng%2FSpaTopic","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/xiyupeng%2FSpaTopic/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/xiyupeng%2FSpaTopic/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/xiyupeng%2FSpaTopic/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/xiyupeng","download_url":"https://codeload.github.com/xiyupeng/SpaTopic/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/xiyupeng%2FSpaTopic/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":271970640,"owners_count":24851756,"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":"2025-08-24T02:00:11.135Z","response_time":111,"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":"xiyupeng","name":"Xiyu","uuid":"23034624","kind":"user","description":"interested in bioinformatics and computational biology","email":"","website":"https://sites.google.com/view/xiyupeng/home","location":"New York","twitter":null,"company":"Memorial Sloan Kettering Cancer Center","icon_url":"https://avatars.githubusercontent.com/u/23034624?v=4","repositories_count":1,"last_synced_at":"2023-04-28T13:48:58.555Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/xiyupeng","funding_links":[],"total_stars":null,"followers":null,"following":null,"created_at":"2023-04-28T13:48:58.567Z","updated_at":"2023-04-28T13:48:58.567Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/xiyupeng","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/xiyupeng/repositories"},"tags":[{"name":"v1.2.0","sha":"bb5738e0361e038507584f19a02cec788e39d647","kind":"commit","published_at":"2025-03-03T16:34:55.000Z","download_url":"https://codeload.github.com/xiyupeng/SpaTopic/tar.gz/v1.2.0","html_url":"https://github.com/xiyupeng/SpaTopic/releases/tag/v1.2.0","dependencies_parsed_at":null,"dependency_job_id":null,"purl":"pkg:github/xiyupeng/SpaTopic@v1.2.0","tag_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/xiyupeng%2FSpaTopic/tags/v1.2.0","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/xiyupeng%2FSpaTopic/tags/v1.2.0/manifests"},{"name":"v1.1.0","sha":"309c24d7df522a8b6534f06557753373d7554033","kind":"commit","published_at":"2024-04-22T23:23:51.000Z","download_url":"https://codeload.github.com/xiyupeng/SpaTopic/tar.gz/v1.1.0","html_url":"https://github.com/xiyupeng/SpaTopic/releases/tag/v1.1.0","dependencies_parsed_at":null,"dependency_job_id":null,"purl":"pkg:github/xiyupeng/SpaTopic@v1.1.0","tag_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/xiyupeng%2FSpaTopic/tags/v1.1.0","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/xiyupeng%2FSpaTopic/tags/v1.1.0/manifests"},{"name":"v1.0.1","sha":"2a9a1f6765293e9f4e4d8acf68fe218f1fe86d5d","kind":"commit","published_at":"2024-01-16T23:01:29.000Z","download_url":"https://codeload.github.com/xiyupeng/SpaTopic/tar.gz/v1.0.1","html_url":"https://github.com/xiyupeng/SpaTopic/releases/tag/v1.0.1","dependencies_parsed_at":null,"dependency_job_id":null,"purl":"pkg:github/xiyupeng/SpaTopic@v1.0.1","tag_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/xiyupeng%2FSpaTopic/tags/v1.0.1","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/xiyupeng%2FSpaTopic/tags/v1.0.1/manifests"}]},"repo_metadata_updated_at":"2025-08-24T23:07:42.851Z","dependent_packages_count":0,"downloads":179,"downloads_period":"last-month","dependent_repos_count":0,"rankings":{"downloads":84.87006991162116,"dependent_repos_count":36.38042474607572,"dependent_packages_count":28.391153321901246,"stargazers_count":null,"forks_count":null,"docker_downloads_count":null,"average":49.88054932653271},"purl":"pkg:cran/SpaTopic","advisories":[],"docker_usage_url":"https://docker.ecosyste.ms/usage/cran/SpaTopic","docker_dependents_count":null,"docker_downloads_count":null,"usage_url":"https://repos.ecosyste.ms/usage/cran/SpaTopic","dependent_repositories_url":"https://repos.ecosyste.ms/api/v1/usage/cran/SpaTopic/dependencies","status":null,"funding_links":[],"critical":null,"issue_metadata":null,"versions_url":"https://packages.ecosyste.ms/api/v1/registries/cran.r-project.org/packages/SpaTopic/versions","version_numbers_url":"https://packages.ecosyste.ms/api/v1/registries/cran.r-project.org/packages/SpaTopic/version_numbers","dependent_packages_url":"https://packages.ecosyste.ms/api/v1/registries/cran.r-project.org/packages/SpaTopic/dependent_packages","related_packages_url":"https://packages.ecosyste.ms/api/v1/registries/cran.r-project.org/packages/SpaTopic/related_packages","maintainers":[{"uuid":"pansypeng124@gmail.com","login":null,"name":"Xiyu Peng","email":"pansypeng124@gmail.com","url":null,"packages_count":1,"html_url":null,"role":null,"created_at":"2024-01-17T19:16:47.866Z","updated_at":"2024-01-17T19:16:47.866Z","packages_url":"https://packages.ecosyste.ms/api/v1/registries/cran.r-project.org/maintainers/pansypeng124@gmail.com/packages"}],"registry":{"name":"cran.r-project.org","url":"https://cran.r-project.org","ecosystem":"cran","default":true,"packages_count":26181,"maintainers_count":14299,"namespaces_count":0,"keywords_count":8326,"github":"r-project-org","metadata":{"funded_packages_count":539},"icon_url":"https://github.com/r-project-org.png","created_at":"2022-04-06T16:32:25.637Z","updated_at":"2025-09-08T06:54:01.855Z","packages_url":"https://packages.ecosyste.ms/api/v1/registries/cran.r-project.org/packages","maintainers_url":"https://packages.ecosyste.ms/api/v1/registries/cran.r-project.org/maintainers","namespaces_url":"https://packages.ecosyste.ms/api/v1/registries/cran.r-project.org/namespaces"}}],"commits":{"message":"Repository syncing started."},"issues_stats":{"full_name":"xiyupeng/SpaTopic","html_url":"https://github.com/xiyupeng/SpaTopic","last_synced_at":"2025-09-08T08:00:40.532Z","status":null,"issues_count":5,"pull_requests_count":0,"avg_time_to_close_issue":7948936.333333333,"avg_time_to_close_pull_request":null,"issues_closed_count":3,"pull_requests_closed_count":0,"pull_request_authors_count":0,"issue_authors_count":3,"avg_comments_per_issue":0.0,"avg_comments_per_pull_request":null,"merged_pull_requests_count":0,"bot_issues_count":0,"bot_pull_requests_count":0,"past_year_issues_count":3,"past_year_pull_requests_count":0,"past_year_avg_time_to_close_issue":6223757.0,"past_year_avg_time_to_close_pull_request":null,"past_year_issues_closed_count":2,"past_year_pull_requests_closed_count":0,"past_year_pull_request_authors_count":0,"past_year_issue_authors_count":3,"past_year_avg_comments_per_issue":0.0,"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":"2025-08-29T22:37:41.892Z","updated_at":"2025-09-08T08:00:40.534Z","repository_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/xiyupeng%2FSpaTopic","issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/xiyupeng%2FSpaTopic/issues","issue_labels_count":{},"pull_request_labels_count":{},"issue_author_associations_count":{"OWNER":3,"NONE":2},"pull_request_author_associations_count":{},"issue_authors":{"xiyupeng":3,"wzhangwhu":1,"syparkmd":1},"pull_request_authors":{},"host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-08T00:00:17.013Z","repositories_count":10168397,"issues_count":32020286,"pull_requests_count":100254366,"authors_count":10730288,"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":2,"OWNER":1},"past_year_pull_request_author_associations_count":{},"past_year_issue_authors":{"syparkmd":1,"wzhangwhu":1,"xiyupeng":1},"past_year_pull_request_authors":{},"maintainers":[{"login":"xiyupeng","count":3,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/xiyupeng"}],"active_maintainers":[{"login":"xiyupeng","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/xiyupeng"}]},"events":{"total":{"CreateEvent":1,"ReleaseEvent":1,"IssuesEvent":5,"WatchEvent":6,"IssueCommentEvent":2,"PushEvent":27,"ForkEvent":2},"last_year":{"CreateEvent":1,"ReleaseEvent":1,"IssuesEvent":5,"WatchEvent":6,"IssueCommentEvent":2,"PushEvent":27,"ForkEvent":2}},"keywords":[],"dependencies":[],"score":null,"created_at":"2025-09-08T11:25:13.623Z","updated_at":"2025-10-07T08:26:37.855Z","avatar_url":"https://github.com/xiyupeng.png","language":"R","category":null,"sub_category":null,"monthly_downloads":179,"funding_links":[],"readme_doi_urls":["https://doi.org/10.1038/s41467-025-61821-y","https://doi.org/10.1101/2024.10.08.617293"],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":[],"project_url":"https://science.ecosyste.ms/api/v1/projects/73301","html_url":"https://science.ecosyste.ms/projects/73301"}