{"id":43737,"name":"scdownstream","description":"A single cell transcriptomics pipeline for QC, integration and making the data presentable","url":"https://github.com/nf-core/scdownstream","last_synced_at":"2025-09-05T09:58:32.758Z","repository":{"id":243796062,"uuid":"813470445","full_name":"nf-core/scdownstream","owner":"nf-core","description":"A single cell transcriptomics pipeline for QC, integration and making the data presentable","archived":false,"fork":false,"pushed_at":"2025-08-30T09:44:12.000Z","size":3574,"stargazers_count":70,"open_issues_count":45,"forks_count":38,"subscribers_count":185,"default_branch":"dev","last_synced_at":"2025-08-30T11:22:01.696Z","etag":null,"topics":["clustering","dimensionality-reduction","integration","nextflow","nf-core","pipeline","quality-control","scverse","single-cell","workflow"],"latest_commit_sha":null,"homepage":"https://nf-co.re/scdownstream","language":"Nextflow","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/nf-core.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,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2024-06-11T06:38:31.000Z","updated_at":"2025-08-28T08:22:07.000Z","dependencies_parsed_at":"2024-06-13T14:28:41.534Z","dependency_job_id":"2101f2ff-1b09-4ae9-8cd6-5bc19b4bedfc","html_url":"https://github.com/nf-core/scdownstream","commit_stats":null,"previous_names":["daisybio/scdownstream","nf-core/scdownstream"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/nf-core/scdownstream","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fscdownstream","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fscdownstream/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fscdownstream/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fscdownstream/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/nf-core","download_url":"https://codeload.github.com/nf-core/scdownstream/tar.gz/refs/heads/dev","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fscdownstream/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":273740851,"owners_count":25159434,"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":"nf-core","name":"nf-core","uuid":"35520196","kind":"organization","description":"A community effort to collect a curated set of analysis pipelines built using Nextflow.","email":"core@nf-co.re","website":"http://nf-co.re","location":null,"twitter":"nf_core","company":null,"icon_url":"https://avatars.githubusercontent.com/u/35520196?v=4","repositories_count":84,"last_synced_at":"2023-03-01T20:50:19.252Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/nf-core","funding_links":[],"total_stars":null,"followers":null,"following":null,"created_at":"2022-11-12T16:29:01.932Z","updated_at":"2023-03-01T20:50:19.281Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/nf-core","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/nf-core/repositories"},"packages":[],"commits":{"message":"Repository syncing started."},"issues_stats":{"full_name":"nf-core/scdownstream","html_url":"https://github.com/nf-core/scdownstream","last_synced_at":"2025-08-31T16:04:23.133Z","status":null,"issues_count":38,"pull_requests_count":46,"avg_time_to_close_issue":5333147.470588235,"avg_time_to_close_pull_request":1014523.9333333333,"issues_closed_count":17,"pull_requests_closed_count":30,"pull_request_authors_count":9,"issue_authors_count":17,"avg_comments_per_issue":0.7894736842105263,"avg_comments_per_pull_request":0.9347826086956522,"merged_pull_requests_count":26,"bot_issues_count":0,"bot_pull_requests_count":0,"past_year_issues_count":37,"past_year_pull_requests_count":46,"past_year_avg_time_to_close_issue":3828389.9375,"past_year_avg_time_to_close_pull_request":1014523.9333333333,"past_year_issues_closed_count":16,"past_year_pull_requests_closed_count":30,"past_year_pull_request_authors_count":9,"past_year_issue_authors_count":16,"past_year_avg_comments_per_issue":0.7297297297297297,"past_year_avg_comments_per_pull_request":0.9347826086956522,"past_year_bot_issues_count":0,"past_year_bot_pull_requests_count":0,"past_year_merged_pull_requests_count":26,"created_at":"2025-08-29T11:39:24.263Z","updated_at":"2025-09-03T06:21:25.645Z","repository_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fscdownstream","issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fscdownstream/issues","issue_labels_count":{"enhancement":44,"bug":30,"good first issue":6,"NBIS":5,"overview":2},"pull_request_labels_count":{"enhancement":5,"bug":1},"issue_author_associations_count":{"CONTRIBUTOR":45,"NONE":24,"COLLABORATOR":16},"pull_request_author_associations_count":{"CONTRIBUTOR":51,"COLLABORATOR":38,"NONE":13,"MEMBER":10},"issue_authors":{"nictru":50,"smoe":5,"LorenzoMerotto":3,"fbnrst":3,"paulinefx":2,"stevekm":2,"tyronechen":2,"KallyopeComp":2,"pakiessling":2,"KurayiChawatama":1,"milos7250":1,"alexhermida":1,"ryan2han":1,"alexblaessle":1,"fhausmann":1,"weishwu":1,"asabjorklund":1,"LeonHafner":1,"tbrittoborges":1,"alex-d13":1,"sitems":1,"wzheng0520":1,"marcus-tutert":1},"pull_request_authors":{"nictru":82,"nf-core-bot":10,"smoe":4,"fbnrst":3,"tbrittoborges":3,"KurayiChawatama":1,"fasterius":1,"paulinefx":1,"mgeaghan":1,"addityea":1,"stevekm":1,"LeonHafner":1,"nicoaira":1,"LN-rich":1,"CASTANYMIQUEL":1},"host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-05T00:00:10.444Z","repositories_count":10097364,"issues_count":31428117,"pull_requests_count":97242359,"authors_count":10701128,"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":{"enhancement":28,"bug":23,"good first issue":6,"NBIS":5},"past_year_pull_request_labels_count":{"enhancement":2,"bug":1},"past_year_issue_author_associations_count":{"NONE":23,"CONTRIBUTOR":18,"COLLABORATOR":16},"past_year_pull_request_author_associations_count":{"COLLABORATOR":38,"CONTRIBUTOR":14,"MEMBER":10,"NONE":10},"past_year_issue_authors":{"nictru":30,"LorenzoMerotto":3,"tyronechen":2,"stevekm":2,"KallyopeComp":2,"paulinefx":2,"pakiessling":2,"wzheng0520":1,"weishwu":1,"tbrittoborges":1,"sitems":1,"ryan2han":1,"milos7250":1,"marcus-tutert":1,"LeonHafner":1,"KurayiChawatama":1,"fhausmann":1,"asabjorklund":1,"alexhermida":1,"alex-d13":1,"alexblaessle":1},"past_year_pull_request_authors":{"nictru":50,"nf-core-bot":10,"tbrittoborges":3,"mgeaghan":1,"addityea":1,"LeonHafner":1,"LN-rich":1,"KurayiChawatama":1,"fasterius":1,"CASTANYMIQUEL":1,"stevekm":1,"paulinefx":1},"maintainers":[{"login":"nictru","count":54,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/nictru"},{"login":"nf-core-bot","count":10,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/nf-core-bot"}],"active_maintainers":[{"login":"nictru","count":54,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/nictru"},{"login":"nf-core-bot","count":10,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/nf-core-bot"}]},"events":{"total":{"CreateEvent":41,"CommitCommentEvent":1,"IssuesEvent":83,"WatchEvent":33,"DeleteEvent":44,"IssueCommentEvent":119,"PushEvent":242,"PullRequestReviewCommentEvent":32,"PullRequestReviewEvent":19,"PullRequestEvent":96,"ForkEvent":27},"last_year":{"CreateEvent":41,"CommitCommentEvent":1,"IssuesEvent":83,"WatchEvent":33,"DeleteEvent":44,"IssueCommentEvent":119,"PushEvent":242,"PullRequestReviewCommentEvent":32,"PullRequestReviewEvent":19,"PullRequestEvent":96,"ForkEvent":27}},"keywords":["clustering","dimensionality-reduction","integration","nextflow","nf-core","pipeline","quality-control","scverse","single-cell","workflow"],"dependencies":[{"ecosystem":"actions","filepath":".github/workflows/awsfulltest.yml","sha":null,"kind":"manifest","created_at":"2024-06-11T08:06:36.267Z","updated_at":"2024-06-11T08:06:36.267Z","repository_link":"https://github.com/nf-core/scdownstream/blob/dev/.github/workflows/awsfulltest.yml","dependencies":[{"id":18537853277,"package_name":"seqeralabs/action-tower-launch","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":18537853911,"package_name":"actions/upload-artifact","ecosystem":"actions","requirements":"v4","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/awstest.yml","sha":null,"kind":"manifest","created_at":"2024-06-11T08:06:37.300Z","updated_at":"2024-06-11T08:06:37.300Z","repository_link":"https://github.com/nf-core/scdownstream/blob/dev/.github/workflows/awstest.yml","dependencies":[{"id":18537854563,"package_name":"seqeralabs/action-tower-launch","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":18537854564,"package_name":"actions/upload-artifact","ecosystem":"actions","requirements":"v4","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/branch.yml","sha":null,"kind":"manifest","created_at":"2024-06-11T08:06:37.681Z","updated_at":"2024-06-11T08:06:37.681Z","repository_link":"https://github.com/nf-core/scdownstream/blob/dev/.github/workflows/branch.yml","dependencies":[{"id":18537854628,"package_name":"mshick/add-pr-comment","ecosystem":"actions","requirements":"b8f338c590a895d50bcbfa6c5859251edc8952fc","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/ci.yml","sha":null,"kind":"manifest","created_at":"2024-06-11T08:06:38.119Z","updated_at":"2024-06-11T08:06:38.119Z","repository_link":"https://github.com/nf-core/scdownstream/blob/dev/.github/workflows/ci.yml","dependencies":[{"id":18537856372,"package_name":"actions/checkout","ecosystem":"actions","requirements":"0ad4b8fadaa221de15dcec353f45205ec38ea70b","direct":true,"kind":"composite","optional":false},{"id":18537856375,"package_name":"nf-core/setup-nextflow","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":18537857260,"package_name":"jlumbroso/free-disk-space","ecosystem":"actions","requirements":"54081f138730dfa15788a46383842cd2f914a1be","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/clean-up.yml","sha":null,"kind":"manifest","created_at":"2024-06-11T08:06:39.644Z","updated_at":"2024-06-11T08:06:39.644Z","repository_link":"https://github.com/nf-core/scdownstream/blob/dev/.github/workflows/clean-up.yml","dependencies":[{"id":18537857645,"package_name":"actions/stale","ecosystem":"actions","requirements":"28ca1036281a5e5922ead5184a1bbf96e5fc984e","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/download_pipeline.yml","sha":null,"kind":"manifest","created_at":"2024-06-11T08:06:40.224Z","updated_at":"2024-06-11T08:06:40.224Z","repository_link":"https://github.com/nf-core/scdownstream/blob/dev/.github/workflows/download_pipeline.yml","dependencies":[{"id":18537858935,"package_name":"nf-core/setup-nextflow","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":18537858936,"package_name":"jlumbroso/free-disk-space","ecosystem":"actions","requirements":"54081f138730dfa15788a46383842cd2f914a1be","direct":true,"kind":"composite","optional":false},{"id":18537858937,"package_name":"actions/setup-python","ecosystem":"actions","requirements":"82c7e631bb3cdc910f68e0081d67478d79c6982d","direct":true,"kind":"composite","optional":false},{"id":18537858938,"package_name":"eWaterCycle/setup-singularity","ecosystem":"actions","requirements":"931d4e31109e875b13309ae1d07c70ca8fbc8537","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/fix-linting.yml","sha":null,"kind":"manifest","created_at":"2024-06-11T08:06:41.192Z","updated_at":"2024-06-11T08:06:41.192Z","repository_link":"https://github.com/nf-core/scdownstream/blob/dev/.github/workflows/fix-linting.yml","dependencies":[{"id":18537861258,"package_name":"actions/checkout","ecosystem":"actions","requirements":"0ad4b8fadaa221de15dcec353f45205ec38ea70b","direct":true,"kind":"composite","optional":false},{"id":18537861259,"package_name":"peter-evans/create-or-update-comment","ecosystem":"actions","requirements":"71345be0265236311c031f5c7866368bd1eff043","direct":true,"kind":"composite","optional":false},{"id":18537861260,"package_name":"actions/setup-python","ecosystem":"actions","requirements":"82c7e631bb3cdc910f68e0081d67478d79c6982d","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/linting.yml","sha":null,"kind":"manifest","created_at":"2024-06-11T08:06:41.522Z","updated_at":"2024-06-11T08:06:41.522Z","repository_link":"https://github.com/nf-core/scdownstream/blob/dev/.github/workflows/linting.yml","dependencies":[{"id":18537861574,"package_name":"actions/checkout","ecosystem":"actions","requirements":"0ad4b8fadaa221de15dcec353f45205ec38ea70b","direct":true,"kind":"composite","optional":false},{"id":18537861575,"package_name":"actions/setup-python","ecosystem":"actions","requirements":"82c7e631bb3cdc910f68e0081d67478d79c6982d","direct":true,"kind":"composite","optional":false},{"id":18537863012,"package_name":"nf-core/setup-nextflow","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":18537863013,"package_name":"actions/upload-artifact","ecosystem":"actions","requirements":"65462800fd760344b1a7b4382951275a0abb4808","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/linting_comment.yml","sha":null,"kind":"manifest","created_at":"2024-06-11T08:06:43.630Z","updated_at":"2024-06-11T08:06:43.630Z","repository_link":"https://github.com/nf-core/scdownstream/blob/dev/.github/workflows/linting_comment.yml","dependencies":[{"id":18537863232,"package_name":"dawidd6/action-download-artifact","ecosystem":"actions","requirements":"09f2f74827fd3a8607589e5ad7f9398816f540fe","direct":true,"kind":"composite","optional":false},{"id":18537863233,"package_name":"marocchino/sticky-pull-request-comment","ecosystem":"actions","requirements":"331f8f5b4215f0445d3c07b4967662a32a2d3e31","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/release-announcements.yml","sha":null,"kind":"manifest","created_at":"2024-06-11T08:06:43.963Z","updated_at":"2024-06-11T08:06:43.963Z","repository_link":"https://github.com/nf-core/scdownstream/blob/dev/.github/workflows/release-announcements.yml","dependencies":[{"id":18537867705,"package_name":"rzr/fediverse-action","ecosystem":"actions","requirements":"master","direct":true,"kind":"composite","optional":false},{"id":18537869146,"package_name":"actions/setup-python","ecosystem":"actions","requirements":"82c7e631bb3cdc910f68e0081d67478d79c6982d","direct":true,"kind":"composite","optional":false},{"id":18537869147,"package_name":"zentered/bluesky-post-action","ecosystem":"actions","requirements":"80dbe0a7697de18c15ad22f4619919ceb5ccf597","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"cpan","filepath":"modules/nf-core/multiqc/meta.yml","sha":null,"kind":"manifest","created_at":"2024-06-11T08:07:03.058Z","updated_at":"2024-06-11T08:07:03.058Z","repository_link":"https://github.com/nf-core/scdownstream/blob/dev/modules/nf-core/multiqc/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"subworkflows/nf-core/utils_nextflow_pipeline/meta.yml","sha":null,"kind":"manifest","created_at":"2024-06-11T08:07:03.157Z","updated_at":"2024-06-11T08:07:03.157Z","repository_link":"https://github.com/nf-core/scdownstream/blob/dev/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"subworkflows/nf-core/utils_nfcore_pipeline/meta.yml","sha":null,"kind":"manifest","created_at":"2024-06-11T08:07:03.385Z","updated_at":"2024-06-11T08:07:03.385Z","repository_link":"https://github.com/nf-core/scdownstream/blob/dev/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml","sha":null,"kind":"manifest","created_at":"2024-06-11T08:07:03.460Z","updated_at":"2024-06-11T08:07:03.460Z","repository_link":"https://github.com/nf-core/scdownstream/blob/dev/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml","dependencies":[]},{"ecosystem":"conda","filepath":"modules/local/adata/extend/environment.yml","sha":null,"kind":"manifest","created_at":"2024-06-13T14:28:21.152Z","updated_at":"2024-06-13T14:28:21.152Z","repository_link":"https://github.com/nf-core/scdownstream/blob/dev/modules/local/adata/extend/environment.yml","dependencies":[{"id":18588063086,"package_name":"anndata","ecosystem":"conda","requirements":"0.10.7.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/local/adata/merge/environment.yml","sha":null,"kind":"manifest","created_at":"2024-06-13T14:28:21.590Z","updated_at":"2024-06-13T14:28:21.590Z","repository_link":"https://github.com/nf-core/scdownstream/blob/dev/modules/local/adata/merge/environment.yml","dependencies":[{"id":18588063143,"package_name":"scanpy","ecosystem":"conda","requirements":"1.10.1.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/local/adata/readrds/environment.yml","sha":null,"kind":"manifest","created_at":"2024-06-13T14:28:21.937Z","updated_at":"2024-06-13T14:28:21.937Z","repository_link":"https://github.com/nf-core/scdownstream/blob/dev/modules/local/adata/readrds/environment.yml","dependencies":[{"id":18588063148,"package_name":"anndata","ecosystem":"conda","requirements":"0.10.7.*","direct":true,"kind":"runtime","optional":false},{"id":18588063149,"package_name":"anndata2ri","ecosystem":"conda","requirements":"1.3.1.*","direct":true,"kind":"runtime","optional":false},{"id":18588063330,"package_name":"r-seurat","ecosystem":"conda","requirements":"5.0.3.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/local/adata/tords/environment.yml","sha":null,"kind":"manifest","created_at":"2024-06-13T14:28:24.942Z","updated_at":"2024-06-13T14:28:24.942Z","repository_link":"https://github.com/nf-core/scdownstream/blob/dev/modules/local/adata/tords/environment.yml","dependencies":[{"id":18588065761,"package_name":"anndata","ecosystem":"conda","requirements":"0.10.7.*","direct":true,"kind":"runtime","optional":false},{"id":18588065762,"package_name":"anndata2ri","ecosystem":"conda","requirements":"1.3.1.*","direct":true,"kind":"runtime","optional":false},{"id":18588065763,"package_name":"r-seurat","ecosystem":"conda","requirements":"5.0.3.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/local/adata/unify/environment.yml","sha":null,"kind":"manifest","created_at":"2024-06-13T14:28:25.092Z","updated_at":"2024-06-13T14:28:25.092Z","repository_link":"https://github.com/nf-core/scdownstream/blob/dev/modules/local/adata/unify/environment.yml","dependencies":[{"id":18588065764,"package_name":"scanpy","ecosystem":"conda","requirements":"1.10.1.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/local/adata/upsetgenes/environment.yml","sha":null,"kind":"manifest","created_at":"2024-06-13T14:28:25.291Z","updated_at":"2024-06-13T14:28:25.291Z","repository_link":"https://github.com/nf-core/scdownstream/blob/dev/modules/local/adata/upsetgenes/environment.yml","dependencies":[{"id":18588065769,"package_name":"scanpy","ecosystem":"conda","requirements":"1.10.1.*","direct":true,"kind":"runtime","optional":false},{"id":18588065770,"package_name":"upsetplot","ecosystem":"conda","requirements":"0.9.0.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/local/celda/decontx/environment.yml","sha":null,"kind":"manifest","created_at":"2024-06-13T14:28:25.382Z","updated_at":"2024-06-13T14:28:25.382Z","repository_link":"https://github.com/nf-core/scdownstream/blob/dev/modules/local/celda/decontx/environment.yml","dependencies":[{"id":18588065771,"package_name":"anndata","ecosystem":"conda","requirements":"0.10.7.*","direct":true,"kind":"runtime","optional":false},{"id":18588065772,"package_name":"anndata2ri","ecosystem":"conda","requirements":"1.3.1.*","direct":true,"kind":"runtime","optional":false},{"id":18588065773,"package_name":"bioconductor-celda","ecosystem":"conda","requirements":"1.18.1.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/local/scanpy/leiden/environment.yml","sha":null,"kind":"manifest","created_at":"2024-06-13T14:28:27.595Z","updated_at":"2024-06-13T14:28:27.595Z","repository_link":"https://github.com/nf-core/scdownstream/blob/dev/modules/local/scanpy/leiden/environment.yml","dependencies":[{"id":18588065880,"package_name":"leidenalg","ecosystem":"conda","requirements":"0.10.2.*","direct":true,"kind":"runtime","optional":false},{"id":18588065932,"package_name":"python-igraph","ecosystem":"conda","requirements":"0.11.4.*","direct":true,"kind":"runtime","optional":false},{"id":18588067236,"package_name":"scanpy","ecosystem":"conda","requirements":"1.10.1.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/local/scanpy/neighbors/environment.yml","sha":null,"kind":"manifest","created_at":"2024-06-13T14:28:30.144Z","updated_at":"2024-06-13T14:28:30.144Z","repository_link":"https://github.com/nf-core/scdownstream/blob/dev/modules/local/scanpy/neighbors/environment.yml","dependencies":[{"id":18588067362,"package_name":"python-igraph","ecosystem":"conda","requirements":"0.11.4.*","direct":true,"kind":"runtime","optional":false},{"id":18588067363,"package_name":"scanpy","ecosystem":"conda","requirements":"1.10.1.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/local/scanpy/plotqc/environment.yml","sha":null,"kind":"manifest","created_at":"2024-06-13T14:28:30.417Z","updated_at":"2024-06-13T14:28:30.417Z","repository_link":"https://github.com/nf-core/scdownstream/blob/dev/modules/local/scanpy/plotqc/environment.yml","dependencies":[{"id":18588067498,"package_name":"scanpy","ecosystem":"conda","requirements":"1.10.1.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/local/scanpy/umap/environment.yml","sha":null,"kind":"manifest","created_at":"2024-06-13T14:28:30.708Z","updated_at":"2024-06-13T14:28:30.708Z","repository_link":"https://github.com/nf-core/scdownstream/blob/dev/modules/local/scanpy/umap/environment.yml","dependencies":[{"id":18588067544,"package_name":"scanpy","ecosystem":"conda","requirements":"1.10.1.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/local/scvitools/scanvi/environment.yml","sha":null,"kind":"manifest","created_at":"2024-06-13T14:28:30.953Z","updated_at":"2024-06-13T14:28:30.953Z","repository_link":"https://github.com/nf-core/scdownstream/blob/dev/modules/local/scvitools/scanvi/environment.yml","dependencies":[{"id":18588067635,"package_name":"scvi-tools","ecosystem":"conda","requirements":"1.1.2.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/local/scvitools/scvi/environment.yml","sha":null,"kind":"manifest","created_at":"2024-06-13T14:28:32.259Z","updated_at":"2024-06-13T14:28:32.259Z","repository_link":"https://github.com/nf-core/scdownstream/blob/dev/modules/local/scvitools/scvi/environment.yml","dependencies":[{"id":18588069212,"package_name":"scvi-tools","ecosystem":"conda","requirements":"1.1.2.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/local/scvitools/solo/environment.yml","sha":null,"kind":"manifest","created_at":"2024-06-13T14:28:32.734Z","updated_at":"2024-06-13T14:28:32.734Z","repository_link":"https://github.com/nf-core/scdownstream/blob/dev/modules/local/scvitools/solo/environment.yml","dependencies":[{"id":18588069373,"package_name":"scvi-tools","ecosystem":"conda","requirements":"1.1.2.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/multiqc/environment.yml","sha":null,"kind":"manifest","created_at":"2024-06-13T14:28:33.599Z","updated_at":"2024-06-13T14:28:33.599Z","repository_link":"https://github.com/nf-core/scdownstream/blob/dev/modules/nf-core/multiqc/environment.yml","dependencies":[{"id":18588069526,"package_name":"multiqc","ecosystem":"conda","requirements":"1.21.*","direct":true,"kind":"runtime","optional":false}]}],"score":null,"created_at":"2025-09-04T15:51:18.871Z","updated_at":"2025-10-07T08:17:41.804Z","avatar_url":"https://github.com/nf-core.png","language":"Nextflow","category":null,"sub_category":null,"monthly_downloads":0,"funding_links":[],"readme_doi_urls":["https://doi.org/10.5281/zenodo.XXXXXXX","https://doi.org/10.5281/zenodo.XXXXXX","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/43737","html_url":"https://science.ecosyste.ms/projects/43737","bibtex_url":"https://science.ecosyste.ms/projects/43737/export.bibtex","apalike_url":"https://science.ecosyste.ms/projects/43737/export.apalike"}