celldb

Database for functional genomics.

docker run -itd -p 6379:6379 redis
pip install celldb
jupyter notebook notebooks/getting-started.ipynb

Installation

celldb uses Redis to store functional genomics data. To begin running you'll need access to a redis instance, or can start one using docker:

docker run -itd -p 6379:6379 redis

Connecting to the server

Python client

The client contains a number of convenience functions. Check out the notebooks for examples of how it can be used.

sampleIds = celldb.list_samples(cursor)
featureIds = celldb.list_features(cursor)
matrix = celldb.matrix(cursor, sampleIds, featureIds)
# ('sampleId', Decimal(10.2), Decimal(1.5))

Development

If you'd like to contribute to celldb development there is a lot to be done!