{"id":38864,"name":"spotlight","description":"SPoTLIghT, a computational framework to extract interpretable features of the spatial distribution of multiple cell types by combining unannotated pathology images with bulk transcriptomics. ","url":"https://github.com/sysbiooncology/spotlight","last_synced_at":"2025-09-05T07:55:31.855Z","repository":{"id":260144772,"uuid":"636230746","full_name":"SysBioOncology/SPoTLIghT","owner":"SysBioOncology","description":"SPoTLIghT, a computational framework to extract interpretable features of the spatial distribution of multiple cell types by combining unannotated pathology images with bulk transcriptomics. ","archived":false,"fork":false,"pushed_at":"2025-05-21T17:44:33.000Z","size":9105,"stargazers_count":4,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-05-21T18:44:42.050Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/SysBioOncology.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"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":"2023-05-04T11:47:20.000Z","updated_at":"2025-05-21T17:44:27.000Z","dependencies_parsed_at":"2025-05-21T18:42:03.555Z","dependency_job_id":"1cbb96ce-5739-4d0f-a80d-116b4025b25d","html_url":"https://github.com/SysBioOncology/SPoTLIghT","commit_stats":null,"previous_names":["sysbiooncology/spotlight_docker","sysbiooncology/spotlight"],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/SysBioOncology/SPoTLIghT","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioOncology%2FSPoTLIghT","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioOncology%2FSPoTLIghT/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioOncology%2FSPoTLIghT/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioOncology%2FSPoTLIghT/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/SysBioOncology","download_url":"https://codeload.github.com/SysBioOncology/SPoTLIghT/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioOncology%2FSPoTLIghT/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":273728150,"owners_count":25157136,"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":"SysBioOncology","name":"SysBioOncology","uuid":"98464099","kind":"organization","description":null,"email":null,"website":null,"location":null,"twitter":null,"company":null,"icon_url":"https://avatars.githubusercontent.com/u/98464099?v=4","repositories_count":1,"last_synced_at":"2023-02-27T21:12:39.674Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/SysBioOncology","funding_links":[],"total_stars":null,"followers":null,"following":null,"created_at":"2023-02-27T21:12:39.676Z","updated_at":"2023-02-27T21:12:39.676Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/SysBioOncology","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/SysBioOncology/repositories"},"packages":[],"commits":{"message":"Repository syncing started."},"issues_stats":{"full_name":"SysBioOncology/SPoTLIghT","html_url":"https://github.com/SysBioOncology/SPoTLIghT","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":"2025-08-31T06:42:20.573Z","updated_at":"2025-08-31T06:42:49.027Z","repository_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioOncology%2FSPoTLIghT","issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioOncology%2FSPoTLIghT/issues","issue_labels_count":{},"pull_request_labels_count":{},"issue_author_associations_count":{},"pull_request_author_associations_count":{"COLLABORATOR":1},"issue_authors":{},"pull_request_authors":{"joan-yanqiong":1},"host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-05T00:00:10.444Z","repositories_count":10094553,"issues_count":31373669,"pull_requests_count":97058592,"authors_count":10699554,"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":1},"past_year_issue_authors":{},"past_year_pull_request_authors":{"joan-yanqiong":1},"maintainers":[{"login":"joan-yanqiong","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/joan-yanqiong"}],"active_maintainers":[{"login":"joan-yanqiong","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/joan-yanqiong"}]},"events":{"total":{"ReleaseEvent":1,"WatchEvent":5,"DeleteEvent":1,"PushEvent":11,"PullRequestEvent":2},"last_year":{"ReleaseEvent":1,"WatchEvent":5,"DeleteEvent":1,"PushEvent":11,"PullRequestEvent":2}},"keywords":[],"dependencies":[{"ecosystem":"cpan","filepath":"subworkflows/nf-core/utils_nextflow_pipeline/meta.yml","sha":null,"kind":"manifest","created_at":"2024-10-29T20:44:52.527Z","updated_at":"2024-10-29T20:44:52.527Z","repository_link":"https://github.com/SysBioOncology/SPoTLIghT/blob/main/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":"2025-05-21T18:42:00.125Z","updated_at":"2025-05-21T18:42:00.125Z","repository_link":"https://github.com/SysBioOncology/SPoTLIghT/blob/main/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"subworkflows/nf-core/utils_nfschema_plugin/meta.yml","sha":null,"kind":"manifest","created_at":"2025-05-21T18:42:00.176Z","updated_at":"2025-05-21T18:42:00.176Z","repository_link":"https://github.com/SysBioOncology/SPoTLIghT/blob/main/subworkflows/nf-core/utils_nfschema_plugin/meta.yml","dependencies":[]},{"ecosystem":"docker","filepath":"env/immunedeconvr/Dockerfile","sha":null,"kind":"manifest","created_at":"2025-05-21T18:42:00.217Z","updated_at":"2025-05-21T18:42:00.217Z","repository_link":"https://github.com/SysBioOncology/SPoTLIghT/blob/main/env/immunedeconvr/Dockerfile","dependencies":[{"id":23240368820,"package_name":"mambaorg/micromamba","ecosystem":"docker","requirements":"1-bookworm-slim","direct":true,"kind":"build","optional":false},{"id":23240368821,"package_name":"base","ecosystem":"docker","requirements":"latest","direct":true,"kind":"build","optional":false}]},{"ecosystem":"docker","filepath":"env/spotlight/Dockerfile","sha":null,"kind":"manifest","created_at":"2025-05-21T18:42:00.268Z","updated_at":"2025-05-21T18:42:00.268Z","repository_link":"https://github.com/SysBioOncology/SPoTLIghT/blob/main/env/spotlight/Dockerfile","dependencies":[{"id":23240368822,"package_name":"python","ecosystem":"docker","requirements":"3.8.10-slim","direct":true,"kind":"build","optional":false},{"id":23240368823,"package_name":"ubuntu","ecosystem":"docker","requirements":"20.04","direct":true,"kind":"build","optional":false}]},{"ecosystem":"pypi","filepath":"env/spotlight/requirements.txt","sha":null,"kind":"manifest","created_at":"2025-05-21T18:42:00.322Z","updated_at":"2025-05-21T18:42:00.322Z","repository_link":"https://github.com/SysBioOncology/SPoTLIghT/blob/main/env/spotlight/requirements.txt","dependencies":[{"id":23240368824,"package_name":"joblib","ecosystem":"pypi","requirements":"==1.2.0","direct":true,"kind":"runtime","optional":false},{"id":23240368825,"package_name":"numpy","ecosystem":"pypi","requirements":"==1.24.1","direct":true,"kind":"runtime","optional":false},{"id":23240368826,"package_name":"pandas","ecosystem":"pypi","requirements":"==1.5.2","direct":true,"kind":"runtime","optional":false},{"id":23240368827,"package_name":"pyarrow","ecosystem":"pypi","requirements":"==10.0.1","direct":true,"kind":"runtime","optional":false},{"id":23240368828,"package_name":"Pillow","ecosystem":"pypi","requirements":"==9.4.0","direct":true,"kind":"runtime","optional":false},{"id":23240368829,"package_name":"scipy","ecosystem":"pypi","requirements":"==1.10.0","direct":true,"kind":"runtime","optional":false},{"id":23240368830,"package_name":"six","ecosystem":"pypi","requirements":"==1.16.0","direct":true,"kind":"runtime","optional":false},{"id":23240368831,"package_name":"tensorflow","ecosystem":"pypi","requirements":"==2.11.0","direct":true,"kind":"runtime","optional":false},{"id":23240368832,"package_name":"tf_slim","ecosystem":"pypi","requirements":"==1.1.0","direct":true,"kind":"runtime","optional":false},{"id":23240368833,"package_name":"opencv-python","ecosystem":"pypi","requirements":"==4.6.0.66","direct":true,"kind":"runtime","optional":false},{"id":23240368834,"package_name":"tiffslide","ecosystem":"pypi","requirements":"==2.4.0","direct":true,"kind":"runtime","optional":false},{"id":23240368835,"package_name":"tornado","ecosystem":"pypi","requirements":"==6.2","direct":true,"kind":"runtime","optional":false},{"id":23240368836,"package_name":"scikit-learn","ecosystem":"pypi","requirements":"==1.2.0","direct":true,"kind":"runtime","optional":false},{"id":23240368837,"package_name":"dask","ecosystem":"pypi","requirements":"==2022.12.1","direct":true,"kind":"runtime","optional":false},{"id":23240368838,"package_name":"openpyxl","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":23240368839,"package_name":"matplotlib","ecosystem":"pypi","requirements":"==3.6.2","direct":true,"kind":"runtime","optional":false},{"id":23240368840,"package_name":"networkx","ecosystem":"pypi","requirements":"==3.0","direct":true,"kind":"runtime","optional":false},{"id":23240368841,"package_name":"seaborn","ecosystem":"pypi","requirements":"==0.12.2","direct":true,"kind":"runtime","optional":false}]}],"score":null,"created_at":"2025-09-04T15:51:12.941Z","updated_at":"2025-10-07T08:15:56.082Z","avatar_url":"https://github.com/SysBioOncology.png","language":"Python","category":null,"sub_category":null,"monthly_downloads":0,"funding_links":[],"readme_doi_urls":["https://doi.org/10.1038/s41698-024-00749-w","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/38864","html_url":"https://science.ecosyste.ms/projects/38864","bibtex_url":"https://science.ecosyste.ms/projects/38864/export.bibtex","apalike_url":"https://science.ecosyste.ms/projects/38864/export.apalike"}