{"id":32294,"name":"cell-seek","description":"One single-cell pipeline to rule them all, one pipeline to find them, one pipeline to unify them all, and with the data bind them.","url":"https://github.com/openomics/cell-seek","last_synced_at":"2025-09-05T05:24:11.353Z","repository":{"id":181875182,"uuid":"627101519","full_name":"OpenOmics/cell-seek","owner":"OpenOmics","description":"One single-cell pipeline to rule them all, one pipeline to find them, one pipeline to unify them all, and with the data bind them.","archived":false,"fork":false,"pushed_at":"2025-07-22T15:00:12.000Z","size":738,"stargazers_count":1,"open_issues_count":0,"forks_count":1,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-07-22T15:39:08.650Z","etag":null,"topics":["10xgenomics","single-cell-atac-seq","single-cell-cite-seq","single-cell-omics","single-cell-rna-seq","single-cell-vdj"],"latest_commit_sha":null,"homepage":"https://openomics.github.io/cell-seek/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/OpenOmics.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2023-04-12T19:36:24.000Z","updated_at":"2025-07-22T13:52:23.000Z","dependencies_parsed_at":"2023-07-17T23:35:46.813Z","dependency_job_id":"619b850c-c9cf-4fcc-8e7e-5274227d6978","html_url":"https://github.com/OpenOmics/cell-seek","commit_stats":null,"previous_names":["openomics/cell-seek"],"tags_count":9,"template":false,"template_full_name":"OpenOmics/baseline","purl":"pkg:github/OpenOmics/cell-seek","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/OpenOmics%2Fcell-seek","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/OpenOmics%2Fcell-seek/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/OpenOmics%2Fcell-seek/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/OpenOmics%2Fcell-seek/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/OpenOmics","download_url":"https://codeload.github.com/OpenOmics/cell-seek/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/OpenOmics%2Fcell-seek/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":273713955,"owners_count":25154703,"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":"2025-09-05T02:00:09.113Z","response_time":402,"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":"OpenOmics","name":"OpenOmics","uuid":"97639341","kind":"organization","description":"Open Bioinformatics Research","email":null,"website":null,"location":"United States of America","twitter":null,"company":null,"icon_url":"https://avatars.githubusercontent.com/u/97639341?v=4","repositories_count":9,"last_synced_at":"2023-03-06T03:38:04.692Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/OpenOmics","funding_links":[],"total_stars":null,"followers":null,"following":null,"created_at":"2022-11-16T04:01:51.158Z","updated_at":"2023-03-06T03:38:04.726Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/OpenOmics","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/OpenOmics/repositories"},"packages":[],"commits":{"message":"Repository syncing started."},"issues_stats":{"full_name":"OpenOmics/cell-seek","html_url":"https://github.com/OpenOmics/cell-seek","last_synced_at":"2025-08-31T09:42:41.126Z","status":null,"issues_count":1,"pull_requests_count":4,"avg_time_to_close_issue":null,"avg_time_to_close_pull_request":303573.0,"issues_closed_count":0,"pull_requests_closed_count":4,"pull_request_authors_count":2,"issue_authors_count":1,"avg_comments_per_issue":0.0,"avg_comments_per_pull_request":1.0,"merged_pull_requests_count":4,"bot_issues_count":0,"bot_pull_requests_count":0,"past_year_issues_count":1,"past_year_pull_requests_count":4,"past_year_avg_time_to_close_issue":null,"past_year_avg_time_to_close_pull_request":303573.0,"past_year_issues_closed_count":0,"past_year_pull_requests_closed_count":4,"past_year_pull_request_authors_count":2,"past_year_issue_authors_count":1,"past_year_avg_comments_per_issue":0.0,"past_year_avg_comments_per_pull_request":1.0,"past_year_bot_issues_count":0,"past_year_bot_pull_requests_count":0,"past_year_merged_pull_requests_count":4,"created_at":"2025-08-30T11:16:47.954Z","updated_at":"2025-09-01T10:52:03.072Z","repository_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/OpenOmics%2Fcell-seek","issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/OpenOmics%2Fcell-seek/issues","issue_labels_count":{},"pull_request_labels_count":{},"issue_author_associations_count":{"COLLABORATOR":1},"pull_request_author_associations_count":{"COLLABORATOR":7},"issue_authors":{"rroutsong":1},"pull_request_authors":{"chenv3":4,"rroutsong":3},"host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-05T00:00:10.444Z","repositories_count":10086255,"issues_count":31275313,"pull_requests_count":96382867,"authors_count":10695584,"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":{"COLLABORATOR":1},"past_year_pull_request_author_associations_count":{"COLLABORATOR":4},"past_year_issue_authors":{"rroutsong":1},"past_year_pull_request_authors":{"rroutsong":3,"chenv3":1},"maintainers":[{"login":"chenv3","count":4,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/chenv3"},{"login":"rroutsong","count":4,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/rroutsong"}],"active_maintainers":[{"login":"rroutsong","count":4,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/rroutsong"},{"login":"chenv3","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/chenv3"}]},"events":{"total":{"CreateEvent":10,"CommitCommentEvent":1,"IssuesEvent":1,"ReleaseEvent":2,"DeleteEvent":4,"IssueCommentEvent":5,"MemberEvent":1,"PushEvent":38,"PullRequestReviewEvent":2,"PullRequestEvent":8},"last_year":{"CreateEvent":10,"CommitCommentEvent":1,"IssuesEvent":1,"ReleaseEvent":2,"DeleteEvent":4,"IssueCommentEvent":5,"MemberEvent":1,"PushEvent":38,"PullRequestReviewEvent":2,"PullRequestEvent":8}},"keywords":["10xgenomics","single-cell-atac-seq","single-cell-cite-seq","single-cell-omics","single-cell-rna-seq","single-cell-vdj"],"dependencies":[{"ecosystem":"actions","filepath":".github/workflows/docs.yml","sha":null,"kind":"manifest","created_at":"2023-07-17T23:35:45.117Z","updated_at":"2023-07-17T23:35:45.117Z","repository_link":"https://github.com/OpenOmics/cell-seek/blob/main/.github/workflows/docs.yml","dependencies":[{"id":11625778939,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":11625778940,"package_name":"actions/setup-python","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/main.yaml","sha":null,"kind":"manifest","created_at":"2023-07-17T23:35:45.321Z","updated_at":"2023-07-17T23:35:45.321Z","repository_link":"https://github.com/OpenOmics/cell-seek/blob/main/.github/workflows/main.yaml","dependencies":[{"id":11625780207,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":11625780208,"package_name":"docker://snakemake/snakemake","ecosystem":"actions","requirements":"v5.24.2","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"pypi","filepath":"docs/requirements.txt","sha":null,"kind":"manifest","created_at":"2023-07-17T23:35:46.485Z","updated_at":"2023-07-17T23:35:46.485Z","repository_link":"https://github.com/OpenOmics/cell-seek/blob/main/docs/requirements.txt","dependencies":[{"id":11625780972,"package_name":"babel","ecosystem":"pypi","requirements":"\u003e=2.9.1","direct":true,"kind":"runtime","optional":false},{"id":11625780973,"package_name":"click","ecosystem":"pypi","requirements":"==7.1.2","direct":true,"kind":"runtime","optional":false},{"id":11625780974,"package_name":"future","ecosystem":"pypi","requirements":"==0.18.2","direct":true,"kind":"runtime","optional":false},{"id":11625780975,"package_name":"gitdb","ecosystem":"pypi","requirements":"==4.0.5","direct":true,"kind":"runtime","optional":false},{"id":11625780976,"package_name":"GitPython","ecosystem":"pypi","requirements":"==3.1.7","direct":true,"kind":"runtime","optional":false},{"id":11625780978,"package_name":"htmlmin","ecosystem":"pypi","requirements":"==0.1.12","direct":true,"kind":"runtime","optional":false},{"id":11625780980,"package_name":"importlib-metadata","ecosystem":"pypi","requirements":"\u003e=3.10","direct":true,"kind":"runtime","optional":false},{"id":11625780981,"package_name":"Jinja2","ecosystem":"pypi","requirements":"==2.11.3","direct":true,"kind":"runtime","optional":false},{"id":11625780982,"package_name":"joblib","ecosystem":"pypi","requirements":"==0.16.0","direct":true,"kind":"runtime","optional":false},{"id":11625780983,"package_name":"jsmin","ecosystem":"pypi","requirements":"==3.0.0","direct":true,"kind":"runtime","optional":false},{"id":11625780984,"package_name":"livereload","ecosystem":"pypi","requirements":"==2.6.1","direct":true,"kind":"runtime","optional":false},{"id":11625780985,"package_name":"lunr","ecosystem":"pypi","requirements":"==0.5.8","direct":true,"kind":"runtime","optional":false},{"id":11625780986,"package_name":"Markdown","ecosystem":"pypi","requirements":"==3.2.2","direct":true,"kind":"runtime","optional":false},{"id":11625780987,"package_name":"MarkupSafe","ecosystem":"pypi","requirements":"==1.1.1","direct":true,"kind":"runtime","optional":false},{"id":11625780988,"package_name":"mkdocs","ecosystem":"pypi","requirements":"\u003e=1.3.0","direct":true,"kind":"runtime","optional":false},{"id":11625780989,"package_name":"mkdocs-awesome-pages-plugin","ecosystem":"pypi","requirements":"==2.2.1","direct":true,"kind":"runtime","optional":false},{"id":11625781001,"package_name":"mkdocs-git-revision-date-localized-plugin","ecosystem":"pypi","requirements":"==0.7","direct":true,"kind":"runtime","optional":false},{"id":11625781002,"package_name":"mkdocs-material","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":11625781003,"package_name":"mkdocs-material-extensions","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":11625781004,"package_name":"mkdocs-minify-plugin","ecosystem":"pypi","requirements":"==0.3.0","direct":true,"kind":"runtime","optional":false},{"id":11625781005,"package_name":"mkdocs-redirects","ecosystem":"pypi","requirements":"==1.0.1","direct":true,"kind":"runtime","optional":false},{"id":11625781006,"package_name":"nltk","ecosystem":"pypi","requirements":"\u003e=3.6.6","direct":true,"kind":"runtime","optional":false},{"id":11625781007,"package_name":"pygments","ecosystem":"pypi","requirements":"\u003e=2.12","direct":true,"kind":"runtime","optional":false},{"id":11625781008,"package_name":"pymdown-extensions","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":11625781009,"package_name":"pytz","ecosystem":"pypi","requirements":"==2020.1","direct":true,"kind":"runtime","optional":false},{"id":11625781010,"package_name":"PyYAML","ecosystem":"pypi","requirements":"\u003e=5.4","direct":true,"kind":"runtime","optional":false},{"id":11625781011,"package_name":"regex","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":11625781012,"package_name":"six","ecosystem":"pypi","requirements":"==1.15.0","direct":true,"kind":"runtime","optional":false},{"id":11625781013,"package_name":"smmap","ecosystem":"pypi","requirements":"==3.0.4","direct":true,"kind":"runtime","optional":false},{"id":11625781014,"package_name":"tornado","ecosystem":"pypi","requirements":"==6.0.4","direct":true,"kind":"runtime","optional":false},{"id":11625781015,"package_name":"tqdm","ecosystem":"pypi","requirements":"==4.48.2","direct":true,"kind":"runtime","optional":false},{"id":11625781016,"package_name":"zipp","ecosystem":"pypi","requirements":"==3.1.0","direct":true,"kind":"runtime","optional":false},{"id":11625781017,"package_name":"mkdocs-git-revision-date-plugin","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":11625781018,"package_name":"mike","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false}]}],"score":null,"created_at":"2025-09-04T15:51:05.368Z","updated_at":"2025-10-07T08:13:42.645Z","avatar_url":"https://github.com/OpenOmics.png","language":"Python","category":null,"sub_category":null,"monthly_downloads":0,"funding_links":[],"readme_doi_urls":["https://doi.org/10.5281/zenodo.10181524"],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":[],"project_url":"https://science.ecosyste.ms/api/v1/projects/32294","html_url":"https://science.ecosyste.ms/projects/32294","bibtex_url":"https://science.ecosyste.ms/projects/32294/export.bibtex","apalike_url":"https://science.ecosyste.ms/projects/32294/export.apalike"}