{"id":17099047,"url":"https://github.com/dhimmel/stargeo","last_synced_at":"2025-03-23T18:12:56.292Z","repository":{"id":82487858,"uuid":"39271894","full_name":"dhimmel/stargeo","owner":"dhimmel","description":"Generating expression signatures for disease using STARGEO","archived":false,"fork":false,"pushed_at":"2016-03-29T03:04:04.000Z","size":88696,"stargazers_count":2,"open_issues_count":1,"forks_count":1,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-01-28T23:50:07.358Z","etag":null,"topics":["diseases","gene-expression","hetionet","meta-analysis","microarray-data","rephetio","stargeo","transcriptomics"],"latest_commit_sha":null,"homepage":"https://doi.org/10.15363/thinklab.d96","language":"Jupyter Notebook","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/dhimmel.png","metadata":{"files":{"readme":"README.md","changelog":null,"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,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2015-07-17T19:33:56.000Z","updated_at":"2022-02-27T19:17:02.000Z","dependencies_parsed_at":null,"dependency_job_id":"0aeed0af-0911-43c8-8b3b-6894acc925de","html_url":"https://github.com/dhimmel/stargeo","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dhimmel%2Fstargeo","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dhimmel%2Fstargeo/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dhimmel%2Fstargeo/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dhimmel%2Fstargeo/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/dhimmel","download_url":"https://codeload.github.com/dhimmel/stargeo/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":245144972,"owners_count":20568056,"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":["diseases","gene-expression","hetionet","meta-analysis","microarray-data","rephetio","stargeo","transcriptomics"],"created_at":"2024-10-14T15:08:52.067Z","updated_at":"2025-03-23T18:12:56.280Z","avatar_url":"https://github.com/dhimmel.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Differential expression signatures for disease using STARGEO\n\n[![DOI: 10.5281/zenodo.46866.svg](https://zenodo.org/badge/doi/10.5281/zenodo.46866.svg)](https://doi.org/10.5281/zenodo.46866) (corresponds to [`v1.0`](https://github.com/dhimmel/stargeo/releases/tag/v1.0))\n\n[STARGEO](http://stargeo.org/) is a webapp which allows users to identify differentially expressed genes between samples of their choosing. Users annotate studies in [GEO](http://www.ncbi.nlm.nih.gov/geo/ \"Gene Expression Omnibus\") to indicate which samples belong to which conditions. We've annotated many samples for their membership to specific disease or control classes. Then for a specific query (case versus control specification), STARGEO meta-analyzes across all the studies with relevant samples.\n\nHere, we perform STARGEO analyses for diseases in our drug repurposing hetnet. See the [_Thinklab_ discussion](https://doi.org/10.15363/thinklab.d96) for more information.\n\n## Execution\n\nThis repository depends on the [`starapi`](https://github.com/idrdex/star_api) package. See `environment.yml` for the other installed packages in the environment.\n\nThe notebooks are executed in the following order:\n\n1. [`retrieve-tags.ipynb`](retrieve-tags.ipynb) retrieves the current tags from the STARGEO database. The connection details are stored in `dsn.txt` (private).\n2. [`prepare_queries.ipynb`](prepare_queries.ipynb) prepares the STARGEO queries based off of manual Disease Ontology to STARGEO tag mappings ([`data/DO-tag-mapping.tsv`](data/DO-tag-mapping.tsv)). The queries specifics are stored in [`data/queries.tsv`](data/queries.tsv).\n3. [`querier.ipynb`](querier.ipynb) performs the STARGEO analyses. The output for each disease is stored in [`data/doslim`](data/doslim).\n4. [`combine.ipynb`](combine.ipynb) aggregates the differential expression results for all diseases. [`data/diffex.tsv`](data/diffex.tsv) contains the significantly differential expressions. [`data/summary.tsv`](data/summary.tsv) shows the number of up and down-regulated genes per disease.\n\n## License\n\nAll original content in this repository is released under [CC0 1.0](https://creativecommons.org/publicdomain/zero/1.0/ \"Creative Commons · Public Domain Dedication\").\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdhimmel%2Fstargeo","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdhimmel%2Fstargeo","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdhimmel%2Fstargeo/lists"}