/JACKS

Analysis package for processing counts from genome-wide CRISPR/Cas9 screens

Primary LanguagePython

In the subdirectories here you will find:

jacks:

The JACKS python package (please see jacks/README.txt for usage instructions)

2018_paper_materials:

Scripts and README files with location of results and data for the JACKS 2018 paper.

reference_grna_efficacies:

Trained values for JACKS's gRNA efficacies for the Avana, GeCKOv2, Yusa 1.0, TKOv1 and Whiteahead libraries as generated for the 2018 JACKS paper. These can be used with run_JACKS.py to evaluate screens on these libraries without re-running the full analysis.

run app locally:

create env python3 -m venv venv pip install -r ./server/requirements.txt

cd /Users/gn5/Documents/JACKS
. venv/bin/activate
export FLASK_APP=main2.py
export FLASK_ENV=development
export PYTHONPATH=/Users/gn5/Documents/JACKS:/Users/gn5/Documents/JACKS/server:/Users/gn5/Documents/JACKS/jacks
redis-server
celery -A main2.celery worker --loglevel=DEBUG -E
celery -A main2.celery flower --loglevel=DEBUG -E
python server/main2.py

flask run doesn't work with socketIO http://127.0.0.1:5000/ http://127.0.0.1:5555/