{"id":61865,"name":"SpotClean","description":"R package for decontaminating the spot swapping effect and recovering true expression in spatial transcriptomics data","url":"https://github.com/zijianni/spotclean","last_synced_at":"2025-09-08T12:34:09.543Z","repository":{"id":42034375,"uuid":"357988505","full_name":"zijianni/SpotClean","owner":"zijianni","description":"R package for decontaminating the spot swapping effect and recovering true expression in spatial transcriptomics data","archived":false,"fork":false,"pushed_at":"2024-06-08T17:59:39.000Z","size":4206,"stargazers_count":32,"open_issues_count":11,"forks_count":10,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-08-28T15:21:54.737Z","etag":null,"topics":["rna-seq","spatial-transcriptomics"],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/zijianni.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"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}},"created_at":"2021-04-14T17:30:04.000Z","updated_at":"2025-06-02T20:37:53.000Z","dependencies_parsed_at":"2024-06-08T18:58:55.606Z","dependency_job_id":"c4c7d8b8-7939-4a4c-8cea-163dc7b226b1","html_url":"https://github.com/zijianni/SpotClean","commit_stats":{"total_commits":104,"total_committers":5,"mean_commits":20.8,"dds":"0.45192307692307687","last_synced_commit":"14d1596de2e10b45af14d88ba63af4771afebf5e"},"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/zijianni/SpotClean","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zijianni%2FSpotClean","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zijianni%2FSpotClean/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zijianni%2FSpotClean/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zijianni%2FSpotClean/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/zijianni","download_url":"https://codeload.github.com/zijianni/SpotClean/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zijianni%2FSpotClean/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":274174267,"owners_count":25235203,"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":"zijianni","name":"Zijian Ni","uuid":"47869792","kind":"user","description":"Applied Scientist @ Amazon Prime ML","email":"","website":null,"location":"Seattle, WA","twitter":null,"company":"Amazon","icon_url":"https://avatars.githubusercontent.com/u/47869792?u=288a8995163703ece1e830a8e29b19353d114eb7\u0026v=4","repositories_count":2,"last_synced_at":"2023-10-12T21:17:22.756Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/zijianni","funding_links":[],"total_stars":null,"followers":null,"following":null,"created_at":"2023-10-12T21:17:22.764Z","updated_at":"2023-10-12T21:17:22.764Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/zijianni","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/zijianni/repositories"},"packages":[{"id":8420794,"name":"SpotClean","ecosystem":"bioconductor","description":"SpotClean adjusts for spot swapping in spatial transcriptomics data","homepage":"https://github.com/zijianni/SpotClean ","licenses":"GPL-3","normalized_licenses":["GPL-3.0"],"repository_url":"https://github.com/zijianni/SpotClean","keywords_array":["DataImport","GeneExpression","Preprocessing","RNASeq","Sequencing","SingleCell","Software","Spatial","Transcriptomics"],"namespace":null,"versions_count":7,"first_release_published_at":"2023-10-12T15:02:44.405Z","latest_release_published_at":"2025-04-21T08:17:49.355Z","latest_release_number":"1.10.0","last_synced_at":"2025-08-28T09:05:26.378Z","created_at":"2023-10-12T15:02:44.105Z","updated_at":"2025-08-28T10:09:52.091Z","registry_url":"https://bioconductor.org/packages/SpotClean","install_command":null,"documentation_url":"https://bioconductor.org/packages/release/bioc/vignettes/SpotClean/inst/doc/SpotClean.pdf","metadata":{},"repo_metadata":{"id":42034375,"uuid":"357988505","full_name":"zijianni/SpotClean","owner":"zijianni","description":"R package for decontaminating the spot swapping effect and recovering true expression in spatial transcriptomics data","archived":false,"fork":false,"pushed_at":"2024-06-08T17:59:39.000Z","size":4206,"stargazers_count":32,"open_issues_count":11,"forks_count":10,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-07-28T08:49:57.607Z","etag":null,"topics":["rna-seq","spatial-transcriptomics"],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/zijianni.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"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}},"created_at":"2021-04-14T17:30:04.000Z","updated_at":"2025-06-02T20:37:53.000Z","dependencies_parsed_at":"2024-06-08T18:58:55.606Z","dependency_job_id":"c4c7d8b8-7939-4a4c-8cea-163dc7b226b1","html_url":"https://github.com/zijianni/SpotClean","commit_stats":{"total_commits":104,"total_committers":5,"mean_commits":20.8,"dds":"0.45192307692307687","last_synced_commit":"14d1596de2e10b45af14d88ba63af4771afebf5e"},"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/zijianni/SpotClean","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zijianni%2FSpotClean","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zijianni%2FSpotClean/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zijianni%2FSpotClean/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zijianni%2FSpotClean/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/zijianni","download_url":"https://codeload.github.com/zijianni/SpotClean/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zijianni%2FSpotClean/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":272481561,"owners_count":24941757,"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":"2025-08-28T02:00:10.768Z","response_time":74,"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":"zijianni","name":"Zijian Ni","uuid":"47869792","kind":"user","description":"Applied Scientist @ Amazon Prime ML","email":"","website":null,"location":"Seattle, WA","twitter":null,"company":"Amazon","icon_url":"https://avatars.githubusercontent.com/u/47869792?u=288a8995163703ece1e830a8e29b19353d114eb7\u0026v=4","repositories_count":2,"last_synced_at":"2023-10-12T21:17:22.756Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/zijianni","funding_links":[],"total_stars":null,"followers":null,"following":null,"created_at":"2023-10-12T21:17:22.764Z","updated_at":"2023-10-12T21:17:22.764Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/zijianni","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/zijianni/repositories"},"tags":[{"name":"NComm","sha":"6f006556bd5332926c4e0540fc0d85db80281c6c","kind":"commit","published_at":"2022-04-16T18:28:49.000Z","download_url":"https://codeload.github.com/zijianni/SpotClean/tar.gz/NComm","html_url":"https://github.com/zijianni/SpotClean/releases/tag/NComm","dependencies_parsed_at":null,"dependency_job_id":null,"purl":"pkg:github/zijianni/SpotClean@NComm","tag_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zijianni%2FSpotClean/tags/NComm","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zijianni%2FSpotClean/tags/NComm/manifests"}]},"repo_metadata_updated_at":"2025-08-28T10:09:52.091Z","dependent_packages_count":0,"downloads":7824,"downloads_period":"total","dependent_repos_count":0,"rankings":{"downloads":89.86547085201794,"dependent_repos_count":0.0,"dependent_packages_count":0.0,"stargazers_count":12.595419847328243,"forks_count":8.396946564885496,"docker_downloads_count":null,"average":22.171567452846336},"purl":"pkg:bioconductor/SpotClean","advisories":[],"docker_usage_url":"https://docker.ecosyste.ms/usage/bioconductor/SpotClean","docker_dependents_count":null,"docker_downloads_count":null,"usage_url":"https://repos.ecosyste.ms/usage/bioconductor/SpotClean","dependent_repositories_url":"https://repos.ecosyste.ms/api/v1/usage/bioconductor/SpotClean/dependencies","status":null,"funding_links":[],"critical":null,"issue_metadata":null,"versions_url":"https://packages.ecosyste.ms/api/v1/registries/bioconductor.org/packages/SpotClean/versions","version_numbers_url":"https://packages.ecosyste.ms/api/v1/registries/bioconductor.org/packages/SpotClean/version_numbers","dependent_packages_url":"https://packages.ecosyste.ms/api/v1/registries/bioconductor.org/packages/SpotClean/dependent_packages","related_packages_url":"https://packages.ecosyste.ms/api/v1/registries/bioconductor.org/packages/SpotClean/related_packages","maintainers":[{"uuid":"zni25@wisc.edu","login":null,"name":"Zijian Ni","email":"zni25@wisc.edu","url":null,"packages_count":2,"html_url":null,"role":null,"created_at":"2023-11-04T04:29:20.646Z","updated_at":"2023-11-04T04:29:20.646Z","packages_url":"https://packages.ecosyste.ms/api/v1/registries/bioconductor.org/maintainers/zni25@wisc.edu/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":1403488,"full_name":"zijianni/SpotClean","default_branch":"master","committers":[{"name":"Zijian Ni","email":"412182180@qq.com","login":null,"count":57},{"name":"Zijian Ni","email":"zni25@wisc.edu","login":null,"count":43},{"name":"J Wokaty","email":"jennifer.wokaty@sph.cuny.edu","login":null,"count":2},{"name":"Hannah A Pliner","email":"hpliner@gmail.com","login":null,"count":1},{"name":"Zijian Ni","email":"47869792+zijianni","login":"zijianni","count":1}],"total_commits":104,"total_committers":5,"total_bot_commits":0,"total_bot_committers":0,"mean_commits":20.8,"dds":0.45192307692307687,"past_year_committers":[{"name":"Zijian Ni","email":"412182180@qq.com","login":null,"count":3},{"name":"J Wokaty","email":"jennifer.wokaty@sph.cuny.edu","login":null,"count":2}],"past_year_total_commits":5,"past_year_total_committers":2,"past_year_total_bot_commits":0,"past_year_total_bot_committers":0,"past_year_mean_commits":2.5,"past_year_dds":0.4,"last_synced_at":"2023-10-25T13:17:19.160Z","last_synced_commit":"14d1596de2e10b45af14d88ba63af4771afebf5e","created_at":"2023-10-25T13:16:13.310Z","updated_at":"2023-10-25T13:17:19.162Z","commits_url":"https://commits.ecosyste.ms/api/v1/hosts/GitHub/repositories/zijianni%2FSpotClean/commits","host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-07T00:00:09.744Z","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":"zijianni/SpotClean","html_url":"https://github.com/zijianni/SpotClean","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":"2025-08-29T17:01:31.700Z","updated_at":"2025-09-03T05:54:11.645Z","repository_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/zijianni%2FSpotClean","issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/zijianni%2FSpotClean/issues","issue_labels_count":{},"pull_request_labels_count":{},"issue_author_associations_count":{"NONE":11},"pull_request_author_associations_count":{},"issue_authors":{"aowenson-imm":1,"forrwill":1,"Urology-weiyu":1,"nicholashowell":1,"ab-gd1":1,"Icenin":1,"KarolineHoller":1,"Zockimonster":1,"ahwanpandey":1,"JoyOtten":1,"oyxf":1},"pull_request_authors":{},"host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-08T00:00:17.013Z","repositories_count":10164853,"issues_count":31989996,"pull_requests_count":100212161,"authors_count":10728603,"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":7},"past_year_pull_request_author_associations_count":{},"past_year_issue_authors":{"ab-gd1":1,"ahwanpandey":1,"forrwill":1,"Icenin":1,"JoyOtten":1,"nicholashowell":1,"Zockimonster":1},"past_year_pull_request_authors":{},"maintainers":[],"active_maintainers":[]},"events":{"total":{"IssuesEvent":5,"WatchEvent":10,"IssueCommentEvent":2},"last_year":{"IssuesEvent":5,"WatchEvent":10,"IssueCommentEvent":2}},"keywords":["rna-seq","spatial-transcriptomics"],"dependencies":[{"ecosystem":"cran","filepath":"DESCRIPTION","sha":null,"kind":"manifest","created_at":"2022-09-21T19:40:29.992Z","updated_at":"2022-09-21T19:40:29.992Z","repository_link":"https://github.com/zijianni/SpotClean/blob/master/DESCRIPTION","dependencies":[{"id":5768898365,"package_name":"R","ecosystem":"cran","requirements":"\u003e= 4.2.0","direct":true,"kind":"depends","optional":false},{"id":5768898366,"package_name":"stats","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":5768898367,"package_name":"methods","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":5768898368,"package_name":"utils","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":5768898369,"package_name":"dplyr","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":5768898370,"package_name":"S4Vectors","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":5768898371,"package_name":"SummarizedExperiment","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":5768898372,"package_name":"SpatialExperiment","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":5768898373,"package_name":"Matrix","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":5768898374,"package_name":"rhdf5","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":5768898375,"package_name":"ggplot2","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":5768898376,"package_name":"grid","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":5768898377,"package_name":"readbitmap","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":5768898378,"package_name":"rjson","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":5768898379,"package_name":"tibble","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":5768898380,"package_name":"viridis","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":5768898381,"package_name":"grDevices","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":5768898382,"package_name":"RColorBrewer","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":5768898383,"package_name":"Seurat","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":5768898384,"package_name":"rlang","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":5768898385,"package_name":"testthat","ecosystem":"cran","requirements":"\u003e= 2.1.0","direct":true,"kind":"suggests","optional":false},{"id":5768898386,"package_name":"knitr","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":5768898387,"package_name":"BiocStyle","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":5768898388,"package_name":"rmarkdown","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":5768898389,"package_name":"R.utils","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":5768898390,"package_name":"spelling","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false}]}],"score":14.335717043536018,"created_at":"2025-09-08T10:46:55.219Z","updated_at":"2025-10-07T08:24:13.066Z","avatar_url":"https://github.com/zijianni.png","language":"R","category":null,"sub_category":null,"monthly_downloads":0,"funding_links":[],"readme_doi_urls":["https://doi.org/10.1038/s41467-022-30587-y"],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":[],"project_url":"https://science.ecosyste.ms/api/v1/projects/61865","html_url":"https://science.ecosyste.ms/projects/61865"}