novapyth / geo2enrichr

A browser extension and web application for extracting gene sets from GEO and piping them to Enrichr.

GEO2Enrichr

What is GEO2Enrichr?

GEO2Enrichr is a browser extension and web application for extracting gene sets from the Gene Expression Omnibus (GEO) and custom Simple Omnibus In Text (SOFT) files and then piping those lists to Enrichr, a gene set enrichment analysis tool. The web server and additional information can be found on the Ma'ayan Lab's server.

Where can I learn more?

GEO2Enrichr: browser extension and server app to extract gene sets from GEO and analyze them for biological functions. 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?

# 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

[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?

python run.py
# Go to http://localhost:8083/g2e/