https://github.com/maayanlab/geo2enrichr
A browser extension and web application for extracting gene sets from GEO and piping them to Enrichr.
https://github.com/maayanlab/geo2enrichr
Last synced: 5 months ago
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A browser extension and web application for extracting gene sets from GEO and piping them to Enrichr.
- Host: GitHub
- URL: https://github.com/maayanlab/geo2enrichr
- Owner: MaayanLab
- Created: 2015-05-20T17:51:20.000Z (almost 10 years ago)
- Default Branch: master
- Last Pushed: 2023-05-01T20:56:56.000Z (almost 2 years ago)
- Last Synced: 2023-10-20T21:24:14.220Z (over 1 year ago)
- Language: Python
- Homepage:
- Size: 176 MB
- Stars: 12
- Watchers: 15
- Forks: 6
- Open Issues: 7
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGES.md
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README
# GEO2Enrichr
#### What is GEO2Enrichr?
GEO2Enrichr 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/).
#### Where can I learn more?
[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.
## For Ma'ayan Lab developers
#### How do I setup my development environment?
```bash
# first time: setup venv
python3 -m venv venv
source venv/bin/activate
pip install -r requirements.txt
# before you start coding (when in a new terminal)
source venv/bin/activate
```
#### How do I test GEO2Enrichr?
Run `bash test.sh`
#### How do I deploy GEO2Enrichr?
See `DEPLOY.md`.
#### How do I configure GEO2Enrichr?
Create a config file at `g2e/config/config.ini`
```ini
[mode]
debug=true
[cookies]
secret_key=secret_key
[admin]
admin_key=admin_key
[db]
uri=mysql://user:pass@host:port/db?charset=utf8
```
#### How do I run GEO2Enrichr?
```bash
python run.py
# Go to http://localhost:8083/g2e/
```