{"id":61856,"name":"tradeSeq","description":"TRAjectory-based Differential Expression analysis for SEQuencing data","url":"https://github.com/statomics/tradeseq","last_synced_at":"2025-09-08T12:34:07.089Z","repository":{"id":37733435,"uuid":"146580370","full_name":"statOmics/tradeSeq","owner":"statOmics","description":"TRAjectory-based Differential Expression analysis for SEQuencing data","archived":false,"fork":false,"pushed_at":"2025-06-17T14:45:51.000Z","size":64186,"stargazers_count":279,"open_issues_count":36,"forks_count":32,"subscribers_count":6,"default_branch":"master","last_synced_at":"2025-08-21T05:42:50.445Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"HTML","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/statOmics.png","metadata":{"files":{"readme":"README.md","changelog":"NEWS","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,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2018-08-29T09:56:04.000Z","updated_at":"2025-08-14T14:47:53.000Z","dependencies_parsed_at":"2023-02-17T22:31:07.173Z","dependency_job_id":"9124bf07-a01e-4d7d-b67e-a039226bd8b9","html_url":"https://github.com/statOmics/tradeSeq","commit_stats":{"total_commits":675,"total_committers":11,"mean_commits":61.36363636363637,"dds":0.6459259259259259,"last_synced_commit":"9ab4cdce4d98400ece2634ccdc3286a0daf702ea"},"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/statOmics/tradeSeq","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/statOmics%2FtradeSeq","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/statOmics%2FtradeSeq/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/statOmics%2FtradeSeq/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/statOmics%2FtradeSeq/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/statOmics","download_url":"https://codeload.github.com/statOmics/tradeSeq/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/statOmics%2FtradeSeq/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":"statOmics","name":"statOmics","uuid":"24431387","kind":"organization","description":"","email":null,"website":"https://statomics.github.io","location":null,"twitter":null,"company":null,"icon_url":"https://avatars.githubusercontent.com/u/24431387?v=4","repositories_count":33,"last_synced_at":"2023-03-05T17:57:23.860Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/statOmics","funding_links":[],"total_stars":null,"followers":null,"following":null,"created_at":"2022-11-15T20:23:11.124Z","updated_at":"2023-03-05T17:57:23.911Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/statOmics","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/statOmics/repositories"},"packages":[{"id":8420916,"name":"tradeSeq","ecosystem":"bioconductor","description":"trajectory-based differential expression analysis for sequencing data","homepage":"https://statomics.github.io/tradeSeq/index.html ","licenses":"MIT + file LICENSE","normalized_licenses":["MIT"],"repository_url":"https://github.com/statomics/tradeSeq","keywords_array":["Clustering","DifferentialExpression","GeneExpression","MultipleComparison","RNASeq","Regression","Sequencing","SingleCell","Software","TimeCourse","Transcriptomics","Visualization"],"namespace":null,"versions_count":5,"first_release_published_at":"2023-10-12T15:06:16.503Z","latest_release_published_at":"2025-05-23T07:33:26.650Z","latest_release_number":"1.22.0","last_synced_at":"2025-08-21T05:21:31.551Z","created_at":"2023-10-12T15:06:16.255Z","updated_at":"2025-08-21T06:08:22.795Z","registry_url":"https://bioconductor.org/packages/tradeSeq","install_command":null,"documentation_url":"https://bioconductor.org/packages/release/bioc/vignettes/tradeSeq/inst/doc/tradeSeq.pdf","metadata":{},"repo_metadata":{"id":37733435,"uuid":"146580370","full_name":"statOmics/tradeSeq","owner":"statOmics","description":"TRAjectory-based Differential Expression analysis for SEQuencing data","archived":false,"fork":false,"pushed_at":"2025-06-17T14:45:51.000Z","size":64186,"stargazers_count":270,"open_issues_count":40,"forks_count":31,"subscribers_count":6,"default_branch":"master","last_synced_at":"2025-07-20T06:34:02.337Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"HTML","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/statOmics.png","metadata":{"files":{"readme":"README.md","changelog":"NEWS","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,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2018-08-29T09:56:04.000Z","updated_at":"2025-07-18T19:14:46.000Z","dependencies_parsed_at":"2023-02-17T22:31:07.173Z","dependency_job_id":"9124bf07-a01e-4d7d-b67e-a039226bd8b9","html_url":"https://github.com/statOmics/tradeSeq","commit_stats":{"total_commits":675,"total_committers":11,"mean_commits":61.36363636363637,"dds":0.6459259259259259,"last_synced_commit":"9ab4cdce4d98400ece2634ccdc3286a0daf702ea"},"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/statOmics/tradeSeq","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/statOmics%2FtradeSeq","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/statOmics%2FtradeSeq/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/statOmics%2FtradeSeq/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/statOmics%2FtradeSeq/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/statOmics","download_url":"https://codeload.github.com/statOmics/tradeSeq/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/statOmics%2FtradeSeq/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":271430634,"owners_count":24758332,"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":"2025-08-21T02:00:08.990Z","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":"statOmics","name":"statOmics","uuid":"24431387","kind":"organization","description":"","email":null,"website":"https://statomics.github.io","location":null,"twitter":null,"company":null,"icon_url":"https://avatars.githubusercontent.com/u/24431387?v=4","repositories_count":33,"last_synced_at":"2023-03-05T17:57:23.860Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/statOmics","funding_links":[],"total_stars":null,"followers":null,"following":null,"created_at":"2022-11-15T20:23:11.124Z","updated_at":"2023-03-05T17:57:23.911Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/statOmics","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/statOmics/repositories"},"tags":[{"name":"v0.99.46","sha":"55e6267f1e9527940927f7fdd544dc6339e2acae","kind":"commit","published_at":"2019-08-27T13:30:26.000Z","download_url":"https://codeload.github.com/statOmics/tradeSeq/tar.gz/v0.99.46","html_url":"https://github.com/statOmics/tradeSeq/releases/tag/v0.99.46","dependencies_parsed_at":null,"dependency_job_id":null,"purl":"pkg:github/statOmics/tradeSeq@v0.99.46","tag_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/statOmics%2FtradeSeq/tags/v0.99.46","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/statOmics%2FtradeSeq/tags/v0.99.46/manifests"}]},"repo_metadata_updated_at":"2025-08-21T06:08:22.795Z","dependent_packages_count":0,"downloads":46588,"downloads_period":"total","dependent_repos_count":0,"rankings":{"downloads":31.659192825112108,"dependent_repos_count":0.0,"dependent_packages_count":0.0,"stargazers_count":0.672645739910314,"forks_count":1.748878923766816,"docker_downloads_count":null,"average":6.816143497757848},"purl":"pkg:bioconductor/tradeSeq","advisories":[],"docker_usage_url":"https://docker.ecosyste.ms/usage/bioconductor/tradeSeq","docker_dependents_count":null,"docker_downloads_count":null,"usage_url":"https://repos.ecosyste.ms/usage/bioconductor/tradeSeq","dependent_repositories_url":"https://repos.ecosyste.ms/api/v1/usage/bioconductor/tradeSeq/dependencies","status":null,"funding_links":[],"critical":null,"issue_metadata":{"last_synced_at":"2025-07-20T06:04:59.941Z","issues_count":97,"pull_requests_count":3,"avg_time_to_close_issue":7272395.303030303,"avg_time_to_close_pull_request":3385135.3333333335,"issues_closed_count":66,"pull_requests_closed_count":3,"pull_request_authors_count":3,"issue_authors_count":74,"avg_comments_per_issue":2.7216494845360826,"avg_comments_per_pull_request":0.6666666666666666,"merged_pull_requests_count":3,"bot_issues_count":0,"bot_pull_requests_count":0,"past_year_issues_count":11,"past_year_pull_requests_count":1,"past_year_avg_time_to_close_issue":12716135.0,"past_year_avg_time_to_close_pull_request":7505362.0,"past_year_issues_closed_count":1,"past_year_pull_requests_closed_count":1,"past_year_pull_request_authors_count":1,"past_year_issue_authors_count":9,"past_year_avg_comments_per_issue":1.1818181818181819,"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":1,"issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/statomics%2FtradeSeq/issues","maintainers":[{"login":"jgilis","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/jgilis"}],"active_maintainers":[]},"versions_url":"https://packages.ecosyste.ms/api/v1/registries/bioconductor.org/packages/tradeSeq/versions","version_numbers_url":"https://packages.ecosyste.ms/api/v1/registries/bioconductor.org/packages/tradeSeq/version_numbers","dependent_packages_url":"https://packages.ecosyste.ms/api/v1/registries/bioconductor.org/packages/tradeSeq/dependent_packages","related_packages_url":"https://packages.ecosyste.ms/api/v1/registries/bioconductor.org/packages/tradeSeq/related_packages","maintainers":[{"uuid":"hector.rouxdebezieux@berkeley.edu","login":null,"name":"Hector Roux de Bezieux","email":"hector.rouxdebezieux@berkeley.edu","url":null,"packages_count":3,"html_url":null,"role":null,"created_at":"2023-11-25T14:03:50.905Z","updated_at":"2023-11-25T14:03:50.905Z","packages_url":"https://packages.ecosyste.ms/api/v1/registries/bioconductor.org/maintainers/hector.rouxdebezieux@berkeley.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":1403545,"full_name":"statomics/tradeSeq","default_branch":"master","committers":[{"name":"Hector","email":"hector.rouxdebezieux@berkeley.edu","login":null,"count":239},{"name":"koenvandenberge","email":"koen.vandenberge@ugent.be","login":null,"count":222},{"name":"koenvandenberge","email":"koen.vdberge@gmail.com","login":null,"count":172},{"name":"Koen Van den Berge","email":"KVande14@its.jnj.com","login":null,"count":14},{"name":"Nitesh Turaga","email":"nitesh.turaga@gmail.com","login":null,"count":12},{"name":"Kelly Street","email":"kstreet@root-pcs-MacBook-Air.local","login":null,"count":5},{"name":"Koen Van den Berge","email":"koenvandenberge@w135h002.wireless.ugent.be","login":null,"count":4},{"name":"statOmics","email":"lieven.clement@ugent.be","login":null,"count":3},{"name":"J Wokaty","email":"jennifer.wokaty@sph.cuny.edu","login":null,"count":2},{"name":"szcf-weiya","email":"szcfweiya@gmail.com","login":null,"count":1},{"name":"Angela Ling","email":"angela@Angelas-MacBook-Pro-2.local","login":null,"count":1}],"total_commits":675,"total_committers":11,"total_bot_commits":0,"total_bot_committers":0,"mean_commits":61.36363636363637,"dds":0.6459259259259259,"past_year_committers":[{"name":"Koen Van den Berge","email":"KVande14@its.jnj.com","login":null,"count":10},{"name":"J Wokaty","email":"jennifer.wokaty@sph.cuny.edu","login":null,"count":2},{"name":"Hector","email":"hector.rouxdebezieux@berkeley.edu","login":null,"count":1},{"name":"szcf-weiya","email":"szcfweiya@gmail.com","login":null,"count":1}],"past_year_total_commits":14,"past_year_total_committers":4,"past_year_total_bot_commits":0,"past_year_total_bot_committers":0,"past_year_mean_commits":3.5,"past_year_dds":0.2857142857142857,"last_synced_at":"2023-10-25T13:17:48.790Z","last_synced_commit":"9ab4cdce4d98400ece2634ccdc3286a0daf702ea","created_at":"2023-10-25T13:16:16.249Z","updated_at":"2023-10-25T13:17:48.791Z","commits_url":"https://commits.ecosyste.ms/api/v1/hosts/GitHub/repositories/statomics%2FtradeSeq/commits","host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-08T00:00:16.827Z","repositories_count":5481818,"commits_count":853721292,"contributors_count":31101221,"owners_count":907366,"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":"statomics/tradeSeq","html_url":"https://github.com/statomics/tradeSeq","last_synced_at":"2025-08-31T16:55:25.552Z","status":null,"issues_count":97,"pull_requests_count":4,"avg_time_to_close_issue":7622664.955223881,"avg_time_to_close_pull_request":3385135.3333333335,"issues_closed_count":67,"pull_requests_closed_count":3,"pull_request_authors_count":3,"issue_authors_count":74,"avg_comments_per_issue":2.711340206185567,"avg_comments_per_pull_request":0.5,"merged_pull_requests_count":3,"bot_issues_count":0,"bot_pull_requests_count":0,"past_year_issues_count":7,"past_year_pull_requests_count":2,"past_year_avg_time_to_close_issue":12716135.0,"past_year_avg_time_to_close_pull_request":7505362.0,"past_year_issues_closed_count":1,"past_year_pull_requests_closed_count":1,"past_year_pull_request_authors_count":1,"past_year_issue_authors_count":7,"past_year_avg_comments_per_issue":1.0,"past_year_avg_comments_per_pull_request":0.5,"past_year_bot_issues_count":0,"past_year_bot_pull_requests_count":0,"past_year_merged_pull_requests_count":1,"created_at":"2025-05-24T00:26:12.122Z","updated_at":"2025-09-02T13:04:56.535Z","repository_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/statomics%2FtradeSeq","issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/statomics%2FtradeSeq/issues","issue_labels_count":{"enhancement":1,"bug":1},"pull_request_labels_count":{},"issue_author_associations_count":{"NONE":99,"MEMBER":1},"pull_request_author_associations_count":{"NONE":2,"CONTRIBUTOR":2},"issue_authors":{"pchiang5":5,"FADHLyemen":4,"Sophia409":3,"beazors":3,"nickhir":3,"lihong911002":2,"flde":2,"AndreaYCT":2,"JesseRop":2,"Dazcam":2,"fluentin44":2,"carbycrab":2,"gabrielnegreira":2,"yashuap":2,"83years":1,"wangmhan":1,"ZHIDIHUAYUAN":1,"marcus-tutert":1,"kaibtan":1,"ATpoint":1,"AnjaliC4":1,"EH0234":1,"JRPortman":1,"graddi":1,"sam-israel":1,"synatkeamsk":1,"Abeer-hes":1,"haerin0106":1,"jiangzh-coder":1,"JensFGG":1,"zhangol":1,"No2Ross":1,"lengfei5":1,"nouhaylaeraysy":1,"klai001":1,"ishars00":1,"choiismath":1,"ccasar":1,"KemperNiklas":1,"JuanXie19":1,"e-manduchi":1,"tbrunetti":1,"Haikelnb":1,"grimwoo":1,"nouhay":1,"Matthew1309":1,"zji90":1,"eblchen":1,"kweir6":1,"apekshasingh":1,"Siteng999":1,"SONGDONGYUAN1994":1,"pavsol":1,"jgilis":1,"crist156":1,"kmh005":1,"DustinSokolowski":1,"hiuchi":1,"irenerh":1,"Sidy2015":1,"A-legac45":1,"Tommy0398":1,"Yanst86":1,"dfermin":1,"Sa753":1,"dcruz5h":1,"Biglinboy":1,"cohenp05":1,"SeverinMe0":1,"chungsai":1,"jjia1":1,"Alexis-Varin":1,"Jaimelan":1,"ylxing001":1,"jblich870":1,"rayajallad":1,"Evenlyeven":1,"yxiao832":1},"pull_request_authors":{"Alexis-Varin":2,"szcf-weiya":1,"carbycrab":1},"host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-06T00:00:15.144Z","repositories_count":10120850,"issues_count":31689152,"pull_requests_count":98733958,"authors_count":10710360,"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":{"NONE":1,"CONTRIBUTOR":1},"past_year_issue_authors":{"beazors":1,"gabrielnegreira":1,"ishars00":1,"marcus-tutert":1,"rayajallad":1,"Yanst86":1,"yxiao832":1},"past_year_pull_request_authors":{"Alexis-Varin":2},"maintainers":[{"login":"jgilis","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/jgilis"}],"active_maintainers":[]},"events":{"total":{"IssuesEvent":7,"WatchEvent":32,"IssueCommentEvent":13,"PushEvent":9,"PullRequestEvent":1,"ForkEvent":5},"last_year":{"IssuesEvent":7,"WatchEvent":32,"IssueCommentEvent":13,"PushEvent":9,"PullRequestEvent":1,"ForkEvent":5}},"keywords":[],"dependencies":[{"ecosystem":"cran","filepath":"DESCRIPTION","sha":null,"kind":"manifest","created_at":"2022-07-15T21:48:17.467Z","updated_at":"2022-07-15T21:48:17.467Z","repository_link":"https://github.com/statOmics/tradeSeq/blob/master/DESCRIPTION","dependencies":[{"id":226041196,"package_name":"R","ecosystem":"cran","requirements":"\u003e= 3.6","direct":true,"kind":"depends","optional":false},{"id":226041197,"package_name":"mgcv","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":226041198,"package_name":"edgeR","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":226041199,"package_name":"SingleCellExperiment","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":226041200,"package_name":"SummarizedExperiment","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":226041201,"package_name":"slingshot","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":226041202,"package_name":"magrittr","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":226041203,"package_name":"RColorBrewer","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":226041204,"package_name":"BiocParallel","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":226041205,"package_name":"Biobase","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":226041206,"package_name":"pbapply","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":226041207,"package_name":"igraph","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":226041208,"package_name":"ggplot2","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":226041209,"package_name":"princurve","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":226041210,"package_name":"methods","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":226041211,"package_name":"S4Vectors","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":226041212,"package_name":"tibble","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":226041213,"package_name":"Matrix","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":226041214,"package_name":"TrajectoryUtils","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":226041215,"package_name":"viridis","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":226041216,"package_name":"matrixStats","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":226041217,"package_name":"MASS","ecosystem":"cran","requirements":"*","direct":true,"kind":"imports","optional":false},{"id":226041218,"package_name":"knitr","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":226041219,"package_name":"rmarkdown","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":226041220,"package_name":"testthat","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":226041221,"package_name":"covr","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false},{"id":226041222,"package_name":"clusterExperiment","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/RCmdCheck.yaml","sha":null,"kind":"manifest","created_at":"2023-02-17T22:31:07.011Z","updated_at":"2023-02-17T22:31:07.011Z","repository_link":"https://github.com/statOmics/tradeSeq/blob/master/.github/workflows/RCmdCheck.yaml","dependencies":[{"id":7747723923,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":7747723924,"package_name":"r-lib/actions/setup-r","ecosystem":"actions","requirements":"master","direct":true,"kind":"composite","optional":false},{"id":7747723925,"package_name":"r-lib/actions/setup-pandoc","ecosystem":"actions","requirements":"master","direct":true,"kind":"composite","optional":false},{"id":7747723926,"package_name":"actions/cache","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":7747723927,"package_name":"actions/upload-artifact","ecosystem":"actions","requirements":"master","direct":true,"kind":"composite","optional":false}]}],"score":18.899587652371054,"created_at":"2025-09-08T10:46:55.181Z","updated_at":"2025-10-07T08:24:12.894Z","avatar_url":"https://github.com/statOmics.png","language":"HTML","category":null,"sub_category":null,"monthly_downloads":0,"funding_links":[],"readme_doi_urls":[],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":["bioconductor-package","gene","genomics","sequencing","ontology","grna-sequence","immune-repertoire","proteomics"],"project_url":"https://science.ecosyste.ms/api/v1/projects/61856","html_url":"https://science.ecosyste.ms/projects/61856"}