{"id":59415,"name":"quantms","description":"Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.","url":"https://github.com/bigbio/quantms","last_synced_at":"2025-09-05T15:32:29.933Z","repository":{"id":37541507,"uuid":"421926463","full_name":"bigbio/quantms","owner":"bigbio","description":"Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.","archived":false,"fork":false,"pushed_at":"2025-08-14T07:16:41.000Z","size":26341,"stargazers_count":53,"open_issues_count":60,"forks_count":44,"subscribers_count":7,"default_branch":"master","last_synced_at":"2025-08-14T09:23:41.303Z","etag":null,"topics":["lfq","mass-spectrometry","proteogenomics","proteomics","tmt"],"latest_commit_sha":null,"homepage":"https://quantms.org","language":"Nextflow","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":"nf-core/quantms","license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/bigbio.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":".github/CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":"CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":"CITATIONS.md","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2021-10-27T18:13:00.000Z","updated_at":"2025-08-06T21:24:40.000Z","dependencies_parsed_at":"2023-02-01T06:16:02.294Z","dependency_job_id":"5f4748ca-f314-4a0e-8807-bb1fcf299433","html_url":"https://github.com/bigbio/quantms","commit_stats":null,"previous_names":[],"tags_count":4,"template":false,"template_full_name":null,"purl":"pkg:github/bigbio/quantms","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bigbio%2Fquantms","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bigbio%2Fquantms/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bigbio%2Fquantms/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bigbio%2Fquantms/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/bigbio","download_url":"https://codeload.github.com/bigbio/quantms/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bigbio%2Fquantms/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":273777080,"owners_count":25166250,"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":"bigbio","name":"BigBio Stack","uuid":"10880371","kind":"organization","description":"Provide big data solutions Bioinformatics","email":"proteomicsstack@gmail.com","website":"http://bigbio.xyz","location":"Cambridge, UK","twitter":null,"company":null,"icon_url":"https://avatars.githubusercontent.com/u/10880371?v=4","repositories_count":24,"last_synced_at":"2023-03-02T07:10:22.666Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/bigbio","funding_links":[],"total_stars":null,"followers":null,"following":null,"created_at":"2022-11-13T00:32:40.298Z","updated_at":"2023-03-02T07:10:22.706Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/bigbio","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/bigbio/repositories"},"packages":[],"commits":{"message":"Repository syncing started."},"issues_stats":{"full_name":"bigbio/quantms","html_url":"https://github.com/bigbio/quantms","last_synced_at":"2025-08-31T08:38:53.524Z","status":null,"issues_count":69,"pull_requests_count":58,"avg_time_to_close_issue":21279319.229166668,"avg_time_to_close_pull_request":227464.52380952382,"issues_closed_count":48,"pull_requests_closed_count":42,"pull_request_authors_count":8,"issue_authors_count":21,"avg_comments_per_issue":3.260869565217391,"avg_comments_per_pull_request":2.310344827586207,"merged_pull_requests_count":36,"bot_issues_count":0,"bot_pull_requests_count":0,"past_year_issues_count":55,"past_year_pull_requests_count":58,"past_year_avg_time_to_close_issue":4583967.117647059,"past_year_avg_time_to_close_pull_request":227464.52380952382,"past_year_issues_closed_count":34,"past_year_pull_requests_closed_count":42,"past_year_pull_request_authors_count":8,"past_year_issue_authors_count":19,"past_year_avg_comments_per_issue":3.1818181818181817,"past_year_avg_comments_per_pull_request":2.310344827586207,"past_year_bot_issues_count":0,"past_year_bot_pull_requests_count":0,"past_year_merged_pull_requests_count":36,"created_at":"2025-07-16T12:37:37.810Z","updated_at":"2025-09-03T06:58:34.014Z","repository_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/bigbio%2Fquantms","issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/bigbio%2Fquantms/issues","issue_labels_count":{"enhancement":57,"bug":53,"high-priority":9,"documentation":5,"dia analysis":4,"low-priority":4,"stale-issue":3,"help wanted":2,"open-search":2,"good first issue":2,"release 1.3":2,"sage-support":2,"new-subworkflow":1,"question":1,"Bug fix":1},"pull_request_labels_count":{"Review effort 1/5":9,"Review effort 2/5":6,"bug":2,"release 1.3":2,"Review effort [1-5]: 2":2,"enhancement":2,"Review effort 3/5":1,"documentation":1,"new-subworkflow":1,"high-priority":1,"sage-support":1,"dia analysis":1,"Bug fix":1,"dependencies":1,"Review effort [1-5]: 3":1},"issue_author_associations_count":{"MEMBER":69,"NONE":37,"COLLABORATOR":14},"pull_request_author_associations_count":{"MEMBER":85,"COLLABORATOR":22,"NONE":11,"CONTRIBUTOR":1},"issue_authors":{"ypriverol":69,"jpfeuffer":7,"daichengxin":5,"MetteBoge":4,"wfondrie":3,"cecilia992":3,"hjn0415a":2,"enryH":2,"p20000000":2,"kai-lawsonmcdowall":2,"prvst":2,"MathiasJoensson":2,"mpage21":1,"jspaezp":1,"thanadol-git":1,"jackrogan":1,"nayanvs":1,"lazear":1,"hgbrian":1,"lcynwoods":1,"reem-abouward":1,"michaelsteidel86":1,"Ministreliya131":1,"NikoHensley":1,"martingarridorc":1,"PatrickvanZalm":1,"sooheon":1,"tillenglert":1,"EfraMP":1},"pull_request_authors":{"ypriverol":85,"daichengxin":19,"enryH":4,"wfondrie":3,"jspaezp":2,"kai-lawsonmcdowall":1,"jpfeuffer":1,"yueqixuan":1,"an-altosian":1,"fabianegli":1,"imeMFK01":1},"host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-05T00:00:10.444Z","repositories_count":10103789,"issues_count":31523126,"pull_requests_count":97734489,"authors_count":10703676,"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":{"bug":33,"enhancement":28,"high-priority":4,"dia analysis":1,"help wanted":1,"documentation":1,"question":1,"Bug fix":1,"good first issue":1},"past_year_pull_request_labels_count":{"Review effort 1/5":9,"Review effort 2/5":6,"Review effort [1-5]: 2":2,"enhancement":2,"Review effort 3/5":1,"dia analysis":1,"Bug fix":1,"dependencies":1,"Review effort [1-5]: 3":1},"past_year_issue_author_associations_count":{"MEMBER":33,"NONE":26,"COLLABORATOR":8},"past_year_pull_request_author_associations_count":{"MEMBER":61,"COLLABORATOR":8,"NONE":6,"CONTRIBUTOR":1},"past_year_issue_authors":{"ypriverol":33,"daichengxin":5,"MetteBoge":4,"cecilia992":3,"prvst":2,"p20000000":2,"MathiasJoensson":2,"kai-lawsonmcdowall":2,"hjn0415a":2,"enryH":2,"lcynwoods":1,"martingarridorc":1,"jpfeuffer":1,"EfraMP":1,"Ministreliya131":1,"nayanvs":1,"NikoHensley":1,"hgbrian":1,"reem-abouward":1,"thanadol-git":1},"past_year_pull_request_authors":{"ypriverol":61,"daichengxin":6,"enryH":4,"kai-lawsonmcdowall":1,"an-altosian":1,"fabianegli":1,"yueqixuan":1,"imeMFK01":1},"maintainers":[{"login":"ypriverol","count":154,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/ypriverol"},{"login":"daichengxin","count":24,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/daichengxin"},{"login":"jpfeuffer","count":8,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/jpfeuffer"},{"login":"enryH","count":3,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/enryH"},{"login":"thanadol-git","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/thanadol-git"}],"active_maintainers":[{"login":"ypriverol","count":94,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/ypriverol"},{"login":"daichengxin","count":11,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/daichengxin"},{"login":"enryH","count":3,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/enryH"},{"login":"thanadol-git","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/thanadol-git"},{"login":"jpfeuffer","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/jpfeuffer"}]},"events":{"total":{"CreateEvent":7,"ReleaseEvent":2,"IssuesEvent":112,"WatchEvent":20,"DeleteEvent":4,"MemberEvent":2,"IssueCommentEvent":576,"PushEvent":87,"PullRequestEvent":135,"PullRequestReviewEvent":185,"PullRequestReviewCommentEvent":112,"ForkEvent":9},"last_year":{"CreateEvent":7,"ReleaseEvent":2,"IssuesEvent":112,"WatchEvent":20,"DeleteEvent":4,"MemberEvent":2,"IssueCommentEvent":576,"PushEvent":87,"PullRequestEvent":135,"PullRequestReviewEvent":185,"PullRequestReviewCommentEvent":112,"ForkEvent":9}},"keywords":["lfq","mass-spectrometry","proteogenomics","proteomics","tmt"],"dependencies":[{"ecosystem":"actions","filepath":".github/workflows/awsfulltest.yml","sha":null,"kind":"manifest","created_at":"2023-02-01T06:16:01.026Z","updated_at":"2023-02-01T06:16:01.026Z","repository_link":"https://github.com/bigbio/quantms/blob/master/.github/workflows/awsfulltest.yml","dependencies":[{"id":7291629537,"package_name":"nf-core/tower-action","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":7291629538,"package_name":"actions/upload-artifact","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/awstest.yml","sha":null,"kind":"manifest","created_at":"2023-02-01T06:16:01.218Z","updated_at":"2023-02-01T06:16:01.218Z","repository_link":"https://github.com/bigbio/quantms/blob/master/.github/workflows/awstest.yml","dependencies":[{"id":7291629609,"package_name":"nf-core/tower-action","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":7291629610,"package_name":"actions/upload-artifact","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/branch.yml","sha":null,"kind":"manifest","created_at":"2023-02-01T06:16:01.329Z","updated_at":"2023-02-01T06:16:01.329Z","repository_link":"https://github.com/bigbio/quantms/blob/master/.github/workflows/branch.yml","dependencies":[{"id":7291630261,"package_name":"mshick/add-pr-comment","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/ci.yml","sha":null,"kind":"manifest","created_at":"2023-02-01T06:16:01.440Z","updated_at":"2023-02-01T06:16:01.440Z","repository_link":"https://github.com/bigbio/quantms/blob/master/.github/workflows/ci.yml","dependencies":[{"id":7291630543,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":7291630544,"package_name":"nf-core/setup-nextflow","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":7291630545,"package_name":"conda-incubator/setup-miniconda","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":7291630546,"package_name":"actions/upload-artifact","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/fix-linting.yml","sha":null,"kind":"manifest","created_at":"2023-02-01T06:16:01.608Z","updated_at":"2023-02-01T06:16:01.608Z","repository_link":"https://github.com/bigbio/quantms/blob/master/.github/workflows/fix-linting.yml","dependencies":[{"id":7291630575,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":7291630576,"package_name":"actions/setup-node","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/linting.yml","sha":null,"kind":"manifest","created_at":"2023-02-01T06:16:01.665Z","updated_at":"2023-02-01T06:16:01.665Z","repository_link":"https://github.com/bigbio/quantms/blob/master/.github/workflows/linting.yml","dependencies":[{"id":7291630621,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":7291630623,"package_name":"actions/setup-node","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":7291630625,"package_name":"psf/black","ecosystem":"actions","requirements":"stable","direct":true,"kind":"composite","optional":false},{"id":7291630627,"package_name":"mshick/add-pr-comment","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":7291630628,"package_name":"nf-core/setup-nextflow","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":7291630630,"package_name":"actions/setup-python","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":7291630632,"package_name":"actions/upload-artifact","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/linting_comment.yml","sha":null,"kind":"manifest","created_at":"2023-02-01T06:16:01.748Z","updated_at":"2023-02-01T06:16:01.748Z","repository_link":"https://github.com/bigbio/quantms/blob/master/.github/workflows/linting_comment.yml","dependencies":[{"id":7291630754,"package_name":"dawidd6/action-download-artifact","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":7291630755,"package_name":"marocchino/sticky-pull-request-comment","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false}]}],"score":null,"created_at":"2025-09-04T15:51:36.055Z","updated_at":"2025-10-07T08:23:21.790Z","avatar_url":"https://github.com/bigbio.png","language":"Nextflow","category":null,"sub_category":null,"monthly_downloads":0,"funding_links":[],"readme_doi_urls":["https://doi.org/10.5281/zenodo.15573386","https://doi.org/10.1038/s41592-024-02343-1","https://dx.doi.org/10.1038/s41587-020-0439-x"],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":[],"project_url":"https://science.ecosyste.ms/api/v1/projects/59415","html_url":"https://science.ecosyste.ms/projects/59415","bibtex_url":"https://science.ecosyste.ms/projects/59415/export.bibtex","apalike_url":"https://science.ecosyste.ms/projects/59415/export.apalike"}