{"id":21274928,"url":"https://github.com/maayanlab/geo2enrichr","last_synced_at":"2025-07-11T07:30:36.123Z","repository":{"id":32387815,"uuid":"35964251","full_name":"MaayanLab/geo2enrichr","owner":"MaayanLab","description":"A browser extension and web application for extracting gene sets from GEO and piping them to Enrichr.","archived":false,"fork":false,"pushed_at":"2023-05-01T20:56:56.000Z","size":184581,"stargazers_count":12,"open_issues_count":7,"forks_count":6,"subscribers_count":15,"default_branch":"master","last_synced_at":"2023-10-20T21:24:14.220Z","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":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/MaayanLab.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGES.md","contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2015-05-20T17:51:20.000Z","updated_at":"2022-06-01T15:52:29.000Z","dependencies_parsed_at":"2022-09-12T08:51:33.820Z","dependency_job_id":"86318232-c2cf-4898-960b-caf302b0732b","html_url":"https://github.com/MaayanLab/geo2enrichr","commit_stats":null,"previous_names":[],"tags_count":0,"template":null,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MaayanLab%2Fgeo2enrichr","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MaayanLab%2Fgeo2enrichr/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MaayanLab%2Fgeo2enrichr/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MaayanLab%2Fgeo2enrichr/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/MaayanLab","download_url":"https://codeload.github.com/MaayanLab/geo2enrichr/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":225703663,"owners_count":17510946,"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","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":[],"created_at":"2024-11-21T09:26:24.017Z","updated_at":"2024-11-21T09:26:24.909Z","avatar_url":"https://github.com/MaayanLab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# GEO2Enrichr\n\n#### What is GEO2Enrichr?\n\nGEO2Enrichr is a browser extension and web application for extracting gene sets from the [Gene Expression Omnibus (GEO)](https://www.ncbi.nlm.nih.gov/geo/) and custom Simple Omnibus In Text (SOFT) files and then piping those lists to [Enrichr](https://amp.pharm.mssm.edu/Enrichr/), a gene set enrichment analysis tool. The web server and additional information can be found on the [Ma'ayan Lab's server](https://amp.pharm.mssm.edu/g2e/).\n\n#### Where can I learn more?\n\n[GEO2Enrichr: browser extension and server app to extract gene sets from GEO and analyze them for biological functions.](https://www.ncbi.nlm.nih.gov/pubmed/25971742) Gundersen GW, Jones MR, Rouillard AD, Kou Y, Monteiro CD, Feldmann AS, Hu KS, Ma'ayan A. Bioinformatics. 2015 Sep 15;31(18):3060-2. doi: 10.1093.\n\n## For Ma'ayan Lab developers\n\n#### How do I setup my development environment?\n```bash\n# first time: setup venv\npython3 -m venv venv\nsource venv/bin/activate\npip install -r requirements.txt\n\n# before you start coding (when in a new terminal)\nsource venv/bin/activate\n```\n\n#### How do I test GEO2Enrichr?\n\nRun `bash test.sh`\n\n#### How do I deploy GEO2Enrichr?\n\nSee `DEPLOY.md`.\n\n#### How do I configure GEO2Enrichr?\nCreate a config file at `g2e/config/config.ini`\n```ini\n[mode]\ndebug=true\n\n[cookies]\nsecret_key=secret_key\n\n[admin]\nadmin_key=admin_key\n\n[db]\nuri=mysql://user:pass@host:port/db?charset=utf8\n```\n\n#### How do I run GEO2Enrichr?\n```bash\npython run.py\n# Go to http://localhost:8083/g2e/\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmaayanlab%2Fgeo2enrichr","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmaayanlab%2Fgeo2enrichr","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmaayanlab%2Fgeo2enrichr/lists"}