{"id":45842296,"url":"https://github.com/sigven/oncoenrichr","last_synced_at":"2026-05-31T09:00:53.854Z","repository":{"id":37456603,"uuid":"223118510","full_name":"sigven/oncoEnrichR","owner":"sigven","description":"Explore the cancer relevance of your gene list","archived":false,"fork":false,"pushed_at":"2025-12-17T10:06:54.000Z","size":2042149,"stargazers_count":52,"open_issues_count":2,"forks_count":10,"subscribers_count":5,"default_branch":"main","last_synced_at":"2026-02-27T05:02:50.642Z","etag":null,"topics":["cancer","cancer-hallmark-evidence","cancer-survival","co-expression","crispr-target","disease-gene-association","functional-enrichment-analysis","genesets","high-throughput-screening","pathway-enrichment-analysis","prioritization","protein-complexes","protein-protein-interaction","proteins","report-generator","tcga-data","tissue-enrichment-analysis"],"latest_commit_sha":null,"homepage":"https://sigven.github.io/oncoEnrichR/","language":"R","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/sigven.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":".github/CODE_OF_CONDUCT.md","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":"2019-11-21T07:53:42.000Z","updated_at":"2025-12-17T09:46:56.000Z","dependencies_parsed_at":"2022-07-15T09:00:35.452Z","dependency_job_id":"c0a3d1d1-8499-4741-9936-57efc56dd757","html_url":"https://github.com/sigven/oncoEnrichR","commit_stats":null,"previous_names":[],"tags_count":39,"template":false,"template_full_name":null,"purl":"pkg:github/sigven/oncoEnrichR","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sigven%2FoncoEnrichR","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sigven%2FoncoEnrichR/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sigven%2FoncoEnrichR/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sigven%2FoncoEnrichR/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/sigven","download_url":"https://codeload.github.com/sigven/oncoEnrichR/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sigven%2FoncoEnrichR/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":33725060,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-26T15:22:16.424Z","status":"online","status_checked_at":"2026-05-31T02:00:06.040Z","response_time":95,"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"}},"keywords":["cancer","cancer-hallmark-evidence","cancer-survival","co-expression","crispr-target","disease-gene-association","functional-enrichment-analysis","genesets","high-throughput-screening","pathway-enrichment-analysis","prioritization","protein-complexes","protein-protein-interaction","proteins","report-generator","tcga-data","tissue-enrichment-analysis"],"created_at":"2026-02-27T00:33:31.843Z","updated_at":"2026-05-31T09:00:53.841Z","avatar_url":"https://github.com/sigven.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# oncoEnrichR \u003ca href=\"https://sigven.github.io/oncoEnrichR/\"\u003e\u003cimg src=\"man/figures/logo.png\" align=\"right\" height=\"130\" width=\"113\"/\u003e\u003c/a\u003e\n\n**oncoEnrichR** is an R package for functional interrogation of human gene lists\nin the context of cancer. The package leverages an extensive amount of prior \nmolecular knowledge that allows for biological interpretation along \nmultiple dimensions, both at the systems level and at the level of individual genes.\n\nWeb-based access to **oncoEnrichR** (through the [Galaxy platform](https://usegalaxy.org/)) is available at \n[**https://oncotools.elixir.no**](https://oncotools.elixir.no/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fsigven%2Foncoenrichr%2Foncoenrichr_wrapper%2F1.6.1). \n_The web version of oncoEnrichR is not currently operating with the latest version, \nwe are working to get the latest version in place also in Galaxy._\n\n**oncoEnrichR** is primarily intended for exploratory analysis and prioritization \nof a gene list (referred to here as **query set**) from high-throughput cancer \nbiology experiments, e.g. CRISPR screens, protein proximity labeling, or gene \nexpression profiling. In principle, oncoEnrichR can be relevant for any screen \nor analysis that produces a list of human gene _hits_ that needs functional\nannotation and/or prioritization with respect to cancer relevance. The tool \nqueries a number of high-quality data resources in order to assemble \ncancer-relevant annotations and analyses in an interactive report.\n\n\u003cbr\u003e\n\n\u003cimg src=\"man/figures/oncoenrichr_overview.png\" align=\"center\" border=\"0\"/\u003e\n\n## Getting started\n\n-   [What types of questions can be answered by oncoEnrichR?](https://sigven.github.io/oncoEnrichR/index.html#questions-addressed-by-oncoenrichr)\n-   [Output views from oncoEnrichR](https://sigven.github.io/oncoEnrichR/articles/output.html)\n-   [Installation instructions](https://sigven.github.io/oncoEnrichR/articles/installation.html)\n-   [Running instructions](https://sigven.github.io/oncoEnrichR/articles/running.html)\n-   [Annotation resources available in oncoEnrichR](https://sigven.github.io/oncoEnrichR/articles/annotation_resources.html)\n\n## News\n\n-   December 16th 2025: [**1.6.1 release**](https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html#version-1-6-1)\n-   September 19th 2025: [**1.6.0 release**](https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html#version-1-6-0)\n-   February 27th 2025: [**1.5.3 release**](https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html#version-1-5-3)\n-   September 9th 2024: [**1.5.2 release**](https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html#version-1-5-2)\n\n## Example report\n\n\u003ca href=\"https://doi.org/10.5281/zenodo.17958385\"\u003e\u003cimg src=\"https://zenodo.org/badge/DOI/10.5281/zenodo.17958385.svg\" alt=\"DOI\"\u003e\u003c/a\u003e\n\n## Citation\n\nIf you use oncoEnrichR, please cite the following publication:\n\nSigve Nakken, Sveinung Gundersen, Fabian L. M. Bernal, Dimitris Polychronopoulos, Eivind Hovig, and Jørgen Wesche. **Comprehensive interrogation of gene lists from genome-scale cancer screens with oncoEnrichR** (2023). Int J Cancer. [doi:10.1002/ijc.34666](https://doi.org/10.1002/ijc.34666)\n\n### Contact\n\nsigven AT ifi.uio.no\n\n### Funding and Collaboration\n\noncoEnrichR is supported by the [Centre for Cancer Cell Reprogramming](https://www.med.uio.no/cancell/english/) at the [University of Oslo](https://www.uio.no)/[Oslo University Hospital](https://radium.no), and [Elixir Norway (Oslo node)](https://elixir.no/organization/organisation/elixir-uio).\n\n\u003cbr\u003e \u003cbr\u003e\n\n\u003cp float=\"left\"\u003e\n  \u003ca href=\"https://www.med.uio.no/cancell/english/\"\u003e\n     \u003cimg src=\"man/figures/can-cell.png\" width=\"150\" \u003e\n  \u003c/a\u003e\n  \u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\n  \u003ca href=\"https://elixir.no/organization/organisation/elixir-uio\"\u003e\n     \u003cimg src=\"man/figures/elixir_norway.png\" width=\"200\" /\u003e\n  \u003c/a\u003e\n\u003c/p\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsigven%2Foncoenrichr","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsigven%2Foncoenrichr","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsigven%2Foncoenrichr/lists"}