{"id":160844,"name":null,"description":"The tools that constitute a nontargeted LCMS metabolomics data processing pipeline, created and used by the Broad Institute Metabolomics Platform.","url":"https://github.com/broadinstitute/bmxp","last_synced_at":"2025-09-09T18:14:31.726Z","repository":{"id":60210221,"uuid":"468001801","full_name":"broadinstitute/bmxp","owner":"broadinstitute","description":"The tools that constitute a nontargeted LCMS metabolomics data processing pipeline, created and used by the Broad Institute Metabolomics Platform.","archived":false,"fork":false,"pushed_at":"2025-08-12T13:50:49.000Z","size":1629,"stargazers_count":13,"open_issues_count":0,"forks_count":0,"subscribers_count":4,"default_branch":"main","last_synced_at":"2025-09-05T04:39:01.068Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","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/broadinstitute.png","metadata":{"files":{"readme":"README.md","changelog":null,"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,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2022-03-09T16:14:51.000Z","updated_at":"2025-08-12T13:50:53.000Z","dependencies_parsed_at":"2024-02-09T19:41:37.151Z","dependency_job_id":"a11a786c-c754-4629-a586-02f96dc3fad2","html_url":"https://github.com/broadinstitute/bmxp","commit_stats":{"total_commits":9,"total_committers":4,"mean_commits":2.25,"dds":0.5555555555555556,"last_synced_commit":"a020b36df683f8ed80bc5ed950ecea95412e7961"},"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/broadinstitute/bmxp","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/broadinstitute%2Fbmxp","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/broadinstitute%2Fbmxp/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/broadinstitute%2Fbmxp/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/broadinstitute%2Fbmxp/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/broadinstitute","download_url":"https://codeload.github.com/broadinstitute/bmxp/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/broadinstitute%2Fbmxp/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":274340559,"owners_count":25267294,"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":"2025-09-09T02:00:10.223Z","response_time":80,"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":"broadinstitute","name":"Broad Institute","uuid":"393552","kind":"organization","description":"Broad Institute of MIT and Harvard","email":null,"website":"http://www.broadinstitute.org/","location":"Cambridge, MA","twitter":"broadinstitute","company":null,"icon_url":"https://avatars.githubusercontent.com/u/393552?v=4","repositories_count":1083,"last_synced_at":"2023-04-09T09:48:11.262Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/broadinstitute","funding_links":[],"total_stars":null,"followers":null,"following":null,"created_at":"2022-11-02T16:23:28.278Z","updated_at":"2023-04-09T09:48:11.836Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/broadinstitute","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/broadinstitute/repositories"},"packages":[{"id":5268883,"name":"bmxp","ecosystem":"pypi","description":"LCMS Processing tools used by the Metabolomics Platform at the Broad Institute.","homepage":null,"licenses":"MIT","normalized_licenses":["MIT"],"repository_url":"https://github.com/broadinstitute/bmxp","keywords_array":["LCMS","Alignment","Processing","Metabolomics","Clustering","Batch Correction","Drift Correction","QC","Filtering"],"namespace":null,"versions_count":51,"first_release_published_at":"2022-09-26T18:40:14.000Z","latest_release_published_at":"2025-07-25T15:31:38.000Z","latest_release_number":"0.3.15","last_synced_at":"2025-08-12T15:48:36.835Z","created_at":"2022-09-26T18:57:42.911Z","updated_at":"2025-08-13T02:08:14.302Z","registry_url":"https://pypi.org/project/bmxp/","install_command":"pip install bmxp --index-url https://pypi.org/simple","documentation_url":"https://bmxp.readthedocs.io/","metadata":{"funding":null,"documentation":null,"classifiers":["License :: OSI Approved :: MIT License","Programming Language :: Python :: 3"],"normalized_name":"bmxp"},"repo_metadata":{"id":60210221,"uuid":"468001801","full_name":"broadinstitute/bmxp","owner":"broadinstitute","description":"The tools that constitute a nontargeted LCMS metabolomics data processing pipeline, created and used by the Broad Institute Metabolomics Platform.","archived":false,"fork":false,"pushed_at":"2025-08-12T13:50:49.000Z","size":1629,"stargazers_count":13,"open_issues_count":0,"forks_count":0,"subscribers_count":4,"default_branch":"main","last_synced_at":"2025-08-12T15:37:20.443Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","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/broadinstitute.png","metadata":{"files":{"readme":"README.md","changelog":null,"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":"2022-03-09T16:14:51.000Z","updated_at":"2025-08-12T13:50:53.000Z","dependencies_parsed_at":"2024-02-09T19:41:37.151Z","dependency_job_id":"a11a786c-c754-4629-a586-02f96dc3fad2","html_url":"https://github.com/broadinstitute/bmxp","commit_stats":{"total_commits":9,"total_committers":4,"mean_commits":2.25,"dds":0.5555555555555556,"last_synced_commit":"a020b36df683f8ed80bc5ed950ecea95412e7961"},"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/broadinstitute/bmxp","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/broadinstitute%2Fbmxp","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/broadinstitute%2Fbmxp/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/broadinstitute%2Fbmxp/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/broadinstitute%2Fbmxp/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/broadinstitute","download_url":"https://codeload.github.com/broadinstitute/bmxp/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/broadinstitute%2Fbmxp/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":270166108,"owners_count":24538445,"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":"2025-08-13T02:00:09.904Z","response_time":66,"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":"broadinstitute","name":"Broad Institute","uuid":"393552","kind":"organization","description":"Broad Institute of MIT and Harvard","email":null,"website":"http://www.broadinstitute.org/","location":"Cambridge, MA","twitter":"broadinstitute","company":null,"icon_url":"https://avatars.githubusercontent.com/u/393552?v=4","repositories_count":1083,"last_synced_at":"2023-04-09T09:48:11.262Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/broadinstitute","funding_links":[],"total_stars":null,"followers":null,"following":null,"created_at":"2022-11-02T16:23:28.278Z","updated_at":"2023-04-09T09:48:11.836Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/broadinstitute","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/broadinstitute/repositories"},"tags":[]},"repo_metadata_updated_at":"2025-08-13T02:08:14.301Z","dependent_packages_count":0,"downloads":193,"downloads_period":"last-month","dependent_repos_count":0,"rankings":{"downloads":13.020510242061341,"dependent_repos_count":30.61104109666564,"dependent_packages_count":6.633233862033089,"stargazers_count":28.202616726414746,"forks_count":30.49154493947922,"average":21.791789373330808},"purl":"pkg:pypi/bmxp","advisories":[],"docker_usage_url":"https://docker.ecosyste.ms/usage/pypi/bmxp","docker_dependents_count":null,"docker_downloads_count":null,"usage_url":"https://repos.ecosyste.ms/usage/pypi/bmxp","dependent_repositories_url":"https://repos.ecosyste.ms/api/v1/usage/pypi/bmxp/dependencies","status":null,"funding_links":[],"critical":null,"issue_metadata":{"last_synced_at":"2025-07-25T15:59:18.989Z","issues_count":0,"pull_requests_count":12,"avg_time_to_close_issue":null,"avg_time_to_close_pull_request":21230.083333333332,"issues_closed_count":0,"pull_requests_closed_count":12,"pull_request_authors_count":2,"issue_authors_count":0,"avg_comments_per_issue":null,"avg_comments_per_pull_request":0.0,"merged_pull_requests_count":12,"bot_issues_count":0,"bot_pull_requests_count":0,"past_year_issues_count":0,"past_year_pull_requests_count":8,"past_year_avg_time_to_close_issue":null,"past_year_avg_time_to_close_pull_request":357.875,"past_year_issues_closed_count":0,"past_year_pull_requests_closed_count":8,"past_year_pull_request_authors_count":2,"past_year_issue_authors_count":0,"past_year_avg_comments_per_issue":null,"past_year_avg_comments_per_pull_request":0.0,"past_year_bot_issues_count":0,"past_year_bot_pull_requests_count":0,"past_year_merged_pull_requests_count":8,"issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/broadinstitute%2Fbmxp/issues","maintainers":[{"login":"danhitchcock","count":11,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/danhitchcock"},{"login":"jkrejci7","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/jkrejci7"}],"active_maintainers":[{"login":"danhitchcock","count":3,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/danhitchcock"},{"login":"jkrejci7","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/jkrejci7"}]},"versions_url":"https://packages.ecosyste.ms/api/v1/registries/pypi.org/packages/bmxp/versions","version_numbers_url":"https://packages.ecosyste.ms/api/v1/registries/pypi.org/packages/bmxp/version_numbers","dependent_packages_url":"https://packages.ecosyste.ms/api/v1/registries/pypi.org/packages/bmxp/dependent_packages","related_packages_url":"https://packages.ecosyste.ms/api/v1/registries/pypi.org/packages/bmxp/related_packages","maintainers":[{"uuid":"danhitchcock","login":"danhitchcock","name":null,"email":null,"url":null,"packages_count":4,"html_url":"https://pypi.org/user/danhitchcock/","role":null,"created_at":"2022-12-10T20:52:02.917Z","updated_at":"2022-12-10T20:52:02.917Z","packages_url":"https://packages.ecosyste.ms/api/v1/registries/pypi.org/maintainers/danhitchcock/packages"},{"uuid":"jkrejci","login":"jkrejci","name":null,"email":null,"url":null,"packages_count":2,"html_url":"https://pypi.org/user/jkrejci/","role":null,"created_at":"2022-12-10T20:52:02.931Z","updated_at":"2022-12-10T20:52:02.931Z","packages_url":"https://packages.ecosyste.ms/api/v1/registries/pypi.org/maintainers/jkrejci/packages"},{"uuid":"chloesturgeon","login":"chloesturgeon","name":null,"email":null,"url":null,"packages_count":1,"html_url":"https://pypi.org/user/chloesturgeon/","role":"Maintainer","created_at":"2025-04-05T22:51:22.952Z","updated_at":"2025-04-05T22:51:22.952Z","packages_url":"https://packages.ecosyste.ms/api/v1/registries/pypi.org/maintainers/chloesturgeon/packages"}],"registry":{"name":"pypi.org","url":"https://pypi.org","ecosystem":"pypi","default":true,"packages_count":726649,"maintainers_count":308881,"namespaces_count":0,"keywords_count":238369,"github":"pypi","metadata":{"funded_packages_count":50594},"icon_url":"https://github.com/pypi.png","created_at":"2022-04-04T15:19:23.364Z","updated_at":"2025-09-09T06:31:19.922Z","packages_url":"https://packages.ecosyste.ms/api/v1/registries/pypi.org/packages","maintainers_url":"https://packages.ecosyste.ms/api/v1/registries/pypi.org/maintainers","namespaces_url":"https://packages.ecosyste.ms/api/v1/registries/pypi.org/namespaces"}}],"commits":{"id":690019,"full_name":"broadinstitute/bmxp","default_branch":"main","committers":[{"name":"jkrejci7","email":"55155636+jkrejci7@users.noreply.github.com","count":4},{"name":"Daniel Hitchcock","email":"daniel.s.hitchcock@gmail.com","count":3},{"name":"Daniel Hitchcock","email":"dhitch@broadinstitute.org","count":1},{"name":"Daniel Hitchcock","email":"45922986+danhitchcock@users.noreply.github.com","count":1}],"total_commits":9,"total_committers":4,"total_bot_commits":0,"total_bot_committers":0,"mean_commits":2.25,"dds":0.5555555555555556,"past_year_committers":null,"past_year_total_commits":null,"past_year_total_committers":null,"past_year_total_bot_commits":null,"past_year_total_bot_committers":null,"past_year_mean_commits":null,"past_year_dds":null,"last_synced_at":"2023-03-20T10:13:27.387Z","last_synced_commit":"a020b36df683f8ed80bc5ed950ecea95412e7961","created_at":"2023-03-09T11:21:03.231Z","updated_at":"2023-09-19T17:39:25.847Z","commits_url":"https://commits.ecosyste.ms/api/v1/hosts/GitHub/repositories/broadinstitute%2Fbmxp/commits","host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-08-07T00:00:15.324Z","repositories_count":5397169,"commits_count":847295188,"contributors_count":30859853,"owners_count":903338,"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":"broadinstitute/bmxp","html_url":"https://github.com/broadinstitute/bmxp","last_synced_at":"2025-08-31T13:33:42.350Z","status":null,"issues_count":0,"pull_requests_count":11,"avg_time_to_close_issue":null,"avg_time_to_close_pull_request":23076.727272727272,"issues_closed_count":0,"pull_requests_closed_count":11,"pull_request_authors_count":2,"issue_authors_count":0,"avg_comments_per_issue":null,"avg_comments_per_pull_request":0.0,"merged_pull_requests_count":11,"bot_issues_count":0,"bot_pull_requests_count":0,"past_year_issues_count":0,"past_year_pull_requests_count":4,"past_year_avg_time_to_close_issue":null,"past_year_avg_time_to_close_pull_request":213.5,"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":0,"past_year_avg_comments_per_issue":null,"past_year_avg_comments_per_pull_request":0.0,"past_year_bot_issues_count":0,"past_year_bot_pull_requests_count":0,"past_year_merged_pull_requests_count":4,"created_at":"2023-05-15T04:58:12.754Z","updated_at":"2025-09-03T02:26:17.149Z","repository_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/broadinstitute%2Fbmxp","issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/broadinstitute%2Fbmxp/issues","issue_labels_count":{},"pull_request_labels_count":{},"issue_author_associations_count":{},"pull_request_author_associations_count":{"COLLABORATOR":22},"issue_authors":{},"pull_request_authors":{"danhitchcock":20,"jkrejci7":2},"host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-06T00:00:15.144Z","repositories_count":10119197,"issues_count":31685955,"pull_requests_count":98654270,"authors_count":10709553,"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":{},"past_year_pull_request_author_associations_count":{"COLLABORATOR":6},"past_year_issue_authors":{},"past_year_pull_request_authors":{"danhitchcock":4,"jkrejci7":2},"maintainers":[{"login":"danhitchcock","count":20,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/danhitchcock"},{"login":"jkrejci7","count":2,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/jkrejci7"}],"active_maintainers":[{"login":"danhitchcock","count":4,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/danhitchcock"},{"login":"jkrejci7","count":2,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/jkrejci7"}]},"events":{"total":{"WatchEvent":9,"DeleteEvent":2,"MemberEvent":1,"PushEvent":14,"PullRequestEvent":6,"CreateEvent":3},"last_year":{"WatchEvent":9,"DeleteEvent":2,"MemberEvent":1,"PushEvent":14,"PullRequestEvent":6,"CreateEvent":3}},"keywords":[],"dependencies":[{"ecosystem":"pypi","filepath":"requirements.txt","sha":null,"kind":"manifest","created_at":"2022-09-26T19:13:57.700Z","updated_at":"2022-09-26T19:13:57.700Z","repository_link":"https://github.com/broadinstitute/bmxp/blob/main/requirements.txt","dependencies":[{"id":6147177702,"package_name":"networkx","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":6147177703,"package_name":"pandas","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":6147177704,"package_name":"scipy","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":6147177705,"package_name":"statsmodels","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":6147177706,"package_name":"matplotlib","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"pypi","filepath":"setup.py","sha":null,"kind":"manifest","created_at":"2024-02-09T19:41:37.039Z","updated_at":"2024-02-09T19:41:37.039Z","repository_link":"https://github.com/broadinstitute/bmxp/blob/main/setup.py","dependencies":[]}],"score":9.229358377811945,"created_at":"2025-09-09T00:56:38.970Z","updated_at":"2025-10-07T08:38:28.285Z","avatar_url":"https://github.com/broadinstitute.png","language":"Python","category":null,"sub_category":null,"monthly_downloads":193,"funding_links":[],"readme_doi_urls":[],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":[],"project_url":"https://science.ecosyste.ms/api/v1/projects/160844","html_url":"https://science.ecosyste.ms/projects/160844"}